Transcript of Episode 87: Elliott Margulies

Disclaimer: Transcripts are automated and may contain errors.

Grant Belgard: Welcome to the Bioinformatics CRO Podcast. Grant Belgard, joined… i’m delighted to welcome Elliot Margulies director of bioinformatics at Billion to One, a molecular diagnostics company applying quantitative approaches to prenatal screening and liquid biopsy. spent his career at the intersection of genome technology, computation, and clinical translation, including earlier work at NHGRI and Illumina. In this episode, we’ll talk about what he’s working on now, how his career developed, and what advice he has for scientists and engineers who want to build bioinformatics that matters in the real world. Elliot, welcome to the show.

Elliott Margulies: Thanks, Grant. It’s really great to be here. Great to see you again too

Grant Belgard: uh, The pleasure is mine. for listeners meeting you for the first time, what are you working on now and what problems are most alive for you day to day?

Elliott Margulies: Well, I’m like you said, at a molecular diagnostics company, and so day to day uh, my team focuses on the processing of uh, data uh, for prenatal testing. And we focus on everything from kind of the infrastructure uh, and analysis of kind of primary sequence data, making sure the instrumentation is running correctly, our QCs are, are appropriate, all the way through to building and maintaining curation and interpretation systems and building out reporting platforms.

Elliott Margulies: We’re, we’re kind of the glue across all the different parts of the organization that has to touch a sample from when it’s, uh, acquired to when it’s reported out, uh, whether that be the lab, our genetic counselors, lab directors, uh, even some software teams who are managing, uh, interfaces, uh, and portals that, uh, our physicians and patients interact with.

Grant Belgard: Would you explain the core bioinformatics challenge in your current work to a genomics audience that’s new to this particular area?

Elliott Margulies: Well, we very much focus on actionable, informative, places in the genome. Uh, This is actually, uh, a kind of a, a migration that I’ve made in my own career, uh, from, you know, figuring out algorithms and methods to interpret and analyze whole genomes, uh, bringing that to scale and thinking about how healthcare systems might adopt that, to now being at a company that focuses very much on very specific parts of the genome, uh where, um, we are able to determine with high confidence, uh, whether risk variants or other de-deleterious variants are present.

Elliott Margulies: Uh, and we, and, uh, we can do so both by looking at, um, the DNA from mom, um, but we can also look at the cell-free DNA, uh, that represents the growing fetus inside of mom, uh, and determine the probability that, uh, the baby is carrying zero, one or two, uh deleterious alleles.

Grant Belgard: Can you make technical work understandable across teams with very different vocabularies?

Elliott Margulies: Oftentimes we remind ourselves that everybody is in a silo to a certain extent with their own lingo, and we make it, uh, comfortable for people to pause and say, “Wait, I don’t understand you,” or, “What was that acronym you used?” And, uh, we really have a fun culture of kind of acknowledging that everybody is an expert in their own field, but when th-those interfaces start to talk to each other, you gotta slow down and, and not be afraid to say, “I don’t understand.”

Elliott Margulies: It’s actually a really strong part of our culture, um, at this company right now where that understanding of constant learning and explaining or, um, feeling comfortable saying, “I don’t understand,” or feeling comfortable saying, “Ah, I think I may have screwed that up,” uh, you know, “Let me fix this,” or, “Let me learn what, what happened with the process that we can improve upon.”

Elliott Margulies: But it all starts with, uh, clear communication and feeling comfortable, uh, at those interfaces and slowing, slowing the conversations down, up-leveling, using analogies

Grant Belgard: What do you wish more people understood about the bioinformatics behind clinical testing?

Elliott Margulies: We’re, incredibly rigorous, right? So when I think about the reproducibility, and the confidence we have to have that all of our pipelines are working, we’re constantly thinking about how can we cross and double and triple check that everything is working correctly, that we’re giving the, the right answers to the right people all of the time.

Elliott Margulies: And so, the– running a pipeline is easy, but running a pipeline at scale with a level of confidence that every patient is getting the right answer, as often as possible, and that we have ways of… ‘Cause oftentimes it’s the exceptions that we spend the most time on, right? So, fortunately in a prenatal testing situation, most samples are negative, and that’s g- that’s a good thing.

Elliott Margulies: or I guess another way of thinking about it is that most of the time, sequencing runs and analyses work out just fine. But, we spend the majority of our time on those, those small exceptions, whether it’s a complicated case, a sequencing run that didn’t go as well as we thought, some other issue that’s kind of coming into the pipeline.

Elliott Margulies: We spend the majority of our time, right, thinking about, you know, those small number of samples that are not within the, the norm.

Grant Belgard: When you encounter those, edge cases, are they typically treated, as, one-offs, or, do you typically make changes to the pipeline or process or something on the basis of those? Or are they just so rare and weird that they, typically don’t trigger kind of

Elliott Margulies: No, I’m actually gonna quote, a team member of mine, his name is James Hart. we were recently talking about, building new pipelines for future products. And, I s- I, we were talking, and I had said something to the effect of, you know, “We need to make sure we can handle the edge cases.” and he looks at me and he says, as he’s, has a great, mindset when it comes to building the- these types of, infrastructure.

Elliott Margulies: He says, “Elliot, there are no edge cases. There are only workflows that are run rarely.” And it was a, it was a nice epiphany, I thought, where, And it was, I was like, “Oh, we’ve got the, the, the right person thinking about this.” But it is true in the, in the sense that for some of the legacy systems that we manage, when there are edge cases or one-offs, we see them with some level of repetition.

Elliott Margulies: And particularly as things scale, it’s important for us to build systems that can more handle those types of situations in, in a more standard way.

Grant Belgard: So I guess on that note, how do you decide whether a problem needs a better assay, a better model, better data, a better process?

Elliott Margulies: the, you know, there are many types of rules and kind of prioritization, right? So you, you have, you know, a finite set of really smart people on your team, who are balancing both kind of production responsibilities as well as building new products, as well as automating and scaling kind of existing infrastructure.

Elliott Margulies: And we balance our time across these things, and oftentimes we l- we look for, you know, the proverbial low-hanging fruit or take that 80/20 rule. You know, where, where can I spend a small amount of my time and, and have that be a large impact? And oftentimes we think in that, in that way when we prioritize work, particularly over the short term.

Elliott Margulies: And so we try and balance the short term, where can we do a small amount of effort that’s gonna have a big gain? and a- another metaphor sometimes we talk about is those types of small efforts that have large gains start to get a flywheel going of, more automation, and that more a- additional automation frees up even more time to then automate even further.

Elliott Margulies: And before you know it, you’re starting to, to spend time thinking about the larger system and the longer term growth that, that is necessary.

Grant Belgard: Yeah. How do you think about uncertainty when a computational result may affect a clinical report?

Elliott Margulies: We’re very much a first principles-based company, and so a lot of the analysis that we do, uh, is rooted in statistics, uh, and probability and, and quantifying, um, you know, where we, we have the ability to essentially count molecules, um, at a– that are at a very low level. Uh, but we can do so very– in a very quantitative way.

Elliott Margulies: And so oftentimes we are, uh, we, we put probabilities around, um, all of our calls. And, uh, we are constantly looking at, um, outcomes data. Uh, so we have a fantastic outcomes team that, uh, of course it takes, you know, nine months or so to, uh, to get the, uh, the outcomes. But, uh, over time, these, these things build up, and we scrutinize our false positives, our false negatives.

Elliott Margulies: Um, they’re very, very small, and they’re, they’re rare. Um, but this is a screening test that we are looking at, and, uh, those, uh, can lead to ways in which we can think about systematically continuing and to improve the assay.

Grant Belgard: Makes a quality metric useful rather than ornamental

Elliott Margulies: if it drives at, at something that is measurable and changeable. and again, that’s, that’s very much in our kind of ethos is this concept of being guided by first principles. We often want– oftentimes want to measure something directly versus indirectly. I think as bioinformaticians, it’s easy to kind of, pull together some sort of, you know, convoluted…

Elliott Margulies: I’ll call it convoluted correlation. but if you can’t detangle, you know, what are the values and metrics going into why you’re seeing this correlation, it becomes abstract and, you don’t know what you’re missing or what you’re not seeing. And so oftentimes we try and peel away the layers of the onion so that the analyses we’re looking at are rooted in first principles.

Elliott Margulies: And we’ve seen successes, in doing that. I can think of a recent example where we were doing an analysis and, you know, we could draw, you know, a weird square around, you know, certain data points and kind of increase our sensitivity, and, you know, with a minimal, you know, increase to no-call rate.

Elliott Margulies: But, at the end of the day, we actually found that, doing a more principled Z-score approach, was much cleaner. and we, we understood what was going into that Z-score, in a, in a much better way. And so, so that’s, that’s constantly on our mind as we, as we’re doing these analyses.

Grant Belgard: Where do you see AI being genuinely useful in molecular diagnostics?

Elliott Margulies: Oh, fun question that I know is, is, p-potentially talked about all the time. But even over the last six months, we are seeing bioinformaticians turn into full stack software developers, but with this scientific level of expertise where they deeply understand the workflow and the systems.

Elliott Margulies: And so they’re in some ways hyper-enabled, to move things forward. We’ve gone from, you know, building out prototypes that involve, you know, tab-delimited files and filtering them through Excel spreadsheets to now, you know, on the first try, having a customized user interface, you know, that, is designed for the particular workflow that we’re, we’re doing.

Elliott Margulies: and, that’s all empowered because we’re historically not front-end developers, but we’re now empowered to be able to be front-end developers, with the assistance of, of AI. And so I’ve seen it– I’ve seen the, the aggressive adoption, aggressive but thoughtful adoption, both as a software development tool, and also as a data analysis tool.

Elliott Margulies: So you can quickly advance a variety of different analyses, with AI assistance. We, you know, I think, again, we’re hyper-enabled because we’re already on the command line. We’re already accessing our databases and our infrastructure and our systems. So the access to the data is not a problem.

Elliott Margulies: The envisioning of what we want to do is not a problem. And so we can very well prompt and describe to AI systems what we’re looking to do. And I’ve, I’ve watched, both on the software development side and on the data analysis side, the speed with which we can move is just incredible. You almost have to pause because a human being can’t absorb it all as fast as we’re able to generate it all, right?

Elliott Margulies: And, and that’s actually, we recently had a hackathon as a team, and one of the comments was, you know, “Yeah, I built this thing so fast, but I, I still need to like pause and like look under the hood and really fully understand w- you know, what was going on here.” And, and, and, and that, that disconnect is, to the actual line-by-line coding is what everybody is starting to get used to and try and, and, and work through.

Grant Belgard: What changes when bioinformatics moves from method development into high throughput clinical operations?

Elliott Margulies: There’s, there’s a little bit more of a rigor, uh, associated with change control, um, ensuring the quality of the output is what you expect it to be. In many ways, you know, we strive for things to be as perfect as possible, but more importantly, knowing where, where it falls over and documenting that and under– and, and having an appreciation for that is, uh, in some ways more important than getting the algorithm perfect.

Elliott Margulies: We don’t– We, we never wanna be blindsided by an error or an issue that we didn’t realize our systems weren’t performing as well as they should. And, um, so we’re on– constantly on the lookout for, for that from a clinical ca- uh, standpoint, particularly also as the scale come, comes about. Um, but we have, you know, fantastic team members who think through a problem, and anytime we’re able to, um, make an improvement, one of the exciting things is that we’re sitting on, um, a treasure trove of historical data that we’re able to understand and with, with outcomes information.

Elliott Margulies: If we make an improvement, how well does it perform? How did it– How does it, uh, compare to the way our, our, you know, previous version was with, with the system? And so we, we build automation and systems that are able to essentially do an AB comparison, right, off of, you know, tens of thousands of samples, if, if not more, um, uh, to, to be able to have that rigor whenever we push a, a new change into the system.

Grant Belgard: How do you know when a pipeline’s ready to leave R&D and enter routine use?

Elliott Margulies: I mean, the, the formal way is through a, a, an actual validation. We set up a, you know, a multi-arm trial, that kind of tests both kind of individual measurements as well, you know, and then it grows from there to reproducibility to final kind of validation outcomes.

Elliott Margulies: At, at the end of the day, we’re, we’re making a, a variant call or a, an assertion of risk, and we have to have a known truth set, and we have to, show reproducibility. and then we also try and show, you know, almost like forcibly show limits of detection. Where is there flexibility in the system where even if it doesn’t, if it’s not perfect, it’s a little bit noisier data, we’re still getting the right answer.

Elliott Margulies: Like understanding that limit of detection is, is really important. But it all happens through, you know, we, we follow very standard, processes by which we verify and validate our, our, algorithms.

Grant Belgard: Now to, shift gears and talk about your career. what, early experiences most shaped the scientist you became?

Elliott Margulies: I can point back to a lunch I had as a grad student where Francis Collins was, a professor of genetics at, University of Michigan. He was now at the NIH, but he had still come back on occasion through his relationships with the University of Michigan, at the medical school, giving lectures on occasion.

Elliott Margulies: And hearing him talk about his day moving the Human Genome Project forward, is still a core memory of mine as a kind of a young, graduate student. and that planted a seed in my head about how you can take, a doctorate degree and not just be a, an academic professor writing research grants, for the rest of your career.

Elliott Margulies: Kind of the desire to collaborate on a scale that was beyond what one person can do, it started to really kind of be a seed that was, you know, sprouting in my brain. And, and then moving to the NIH for my postdoc, with Eric Green, who I know you’ve recently had on this, this podcast as well, really opened my mind to that type of at the time it was called big science, right?

Elliott Margulies: Where you could, generate data at scale, you could collaborate at scale, and it was a ton of fun. I’ve, I’ve, I’ve constantly found myself moving in, in those directions where the learning from a diverse group of scientists, is feels much more comfortable to me than working on an individual a-assay or experiment, or project o-on my own.

Elliott Margulies: I have those little pet projects here and there, but at the end of the day, it’s watching the, the, the group of people accomplish something that was not possible as individuals. You, you know, that’s, that’s been a ton of fun for, for my career.

Grant Belgard: Can you tell us about, some of the later major inflection points in your career?

Elliott Margulies: Sure. So I, I sometimes

Elliott Margulies: think about, my career, at least right now, as, having kind of three major phases, I guess. both– So I started as a faculty member, at the National Human Genome Research Institute, where I was doing more basic science research, but in this kind of largely collaborative way, trying to make an impact on the world with, this transition t-from, kind of population scale, you know, low coverage sequencing to find variation in, in the human genome to being able to sequence individual genomes.

Elliott Margulies: And how do you build the methods that can, accurately call variants in individual genomes? I then, kind of the second phase of my career is when I moved to Illumina, working in this advanced medical research group, with David Bentley, and his team, where we really thought about both kind of balancing, what is possible, and from a clinical medical perspective at scale, and, balancing that with kind of the drive of the next generation sequencing that, Illumina at the time was, was driving forward.

Elliott Margulies: and it was a fun balance, because we were trying to provide y-you know, utility to the sequence data that was being generated, and added value and thinking about, I was able in that environment to think five to ten years out, you know, how can we build collaborations to show what’s possible about bringing, you know, high throughput, whole genome sequencing to a medical system?

Elliott Margulies: You know, at the time, you know, we had recently, started the hundred thousand genomes project in, in England as, as a kind of a f-first initiative of bringing genomes into a clinical context. and then this third phase of my career, which I’m in right now, which to me, there’s a bit of, irony in the fact that for much of my career, I had spent focusing on whole genome methods for, you know, sequencing and interpreting, genomes, to now sequencing super small parts of the genome that are incredibly actionable and meaningful and doing that at, at scale, and, being so close to patient care.

Elliott Margulies: this is something that is, is incredibly meaningful to me and my team. And I don’t think it’s often you get a bioinformatics group like we have here that when we find a high-risk result, it weighs on us, and we know that we’re now supporting genetic counselors who are gonna be giving this information to families at a very, you know, that are, the, the, at a very challenging time in their lives.

Elliott Margulies: But they’re going to be better for it because they have this information. We really believe that having that information is, is empowered, empowering to families. but we are, as a bioinformatics group, so close to those decisions, and supporting teams who are delivering this information. It really is remarkable and, in other parts of my career, even though I was building tools that were interpreting genomes or building methods that could identify variants in rare diseases, I was never this close to patient care, and it’s very rewarding, to be able to, to support an organization, like this.

Grant Belgard: How has your view of sequencing changed as the field has matured?

Elliott Margulies: Well, I think we’ve reached a point where, uh, sequencing is a, a commodity. Um, I mean, I r- I remember a time when it was very novel to be able to do massive short-read sequencing. Um, that is now a commodity, and it is just one part of a toolkit that enables clinical adoption. Um, and something that I’ve learned a lot from this most recent part of my career is how much do you have to think about holistically, a, a sound business model that is reimbursable and you’re building a system that, uh, can operate at scale, uh, within certain cost measures and where sequencing is just one part of, uh, of that cost.

Elliott Margulies: Um, but thinking about how to interact with insurance companies, with physicians, um, with patients is all part of the process now. So it’s, it’s become… It used to be a, I guess, to, to answer your question, it used to be a major part of everything that I thought of, uh, when– as a bioinformatician, and now it’s just one part of, of many that are equally, if not more important, because we’ve essentially succeeded in making DNA sequencing a commodity.

Grant Belgard: What have different work environments taught you about how science gets done?

Elliott Margulies: It’s all about the people and the relationships. I’ve been around smart people I think all throughout my career, whether I was in grad school, as a postdoc, um, at Illumina, here at Billion to One, and the times where we were successful and impactful were the times when we could get large groups of people working well together and feeling comfortable and open to uh, making decisions under difficult situations, not being afraid to call out when there are issues or concerns or timeline risks or technical risks.

Elliott Margulies: Um and I can point to the exact opposite happening, where, um, sometimes great ideas didn’t succeed because people were afraid to say, “I don’t think this is gonna work,” or, um, “I don’t know if this other person agrees with this, this plan forward,” right? And you know, everybody can be well-intended, but, um, if you don’t have that open, uh, way of communicating, uh, and being able to, um, talk about the, the more challenging things in a calm, open way, um, uh, oftentimes you can’t see these, these great wins and these great successes.

Elliott Margulies: Uh, and I found a company that truly values all of those, those parts of the, the scientific process and the development process. So I really feel supported, both w- my kind of senior colleagues, as well as the team members that, uh, I’m mentoring, um, to be– to foster this type of environment.

Grant Belgard: What’s something you’ve learned the hard way?

Elliott Margulies: I think finding an organization and a mission that is aligned with your own career goals and growth is important. I can think of a time in my career where I thought I was well-aligned with where I was trying to move things forward, but it ended up not being the same as the organization that I ended up being in.

Elliott Margulies: And for a period of time, I really struggled. Not because somebody was, was trying to set me up to fail, but because my interests, uh, and where I thought the organization wanted to go was different than where the people who were leading the organization wanted the organization to go. And, uh, it took me a while to realize that disconnect.

Elliott Margulies: And once I kind of realized that and I was fortunate enough to be able to kind of move into a different organization that was well-aligned with my goals um, my career started moving forward again. And I think that’s, um, often-oftentimes, right, nobody’s ill intent, but, uh, when you get that mismatch of, like, where you want to go, what your passions are, and if that’s not aligned with the organization that you’re in, um, that can be a rough, rough time.

Elliott Margulies: But to your point, I can also look back on that and say I learned a lot during that time that, uh, I wasn’t necessarily move-moving my career forward. Um, in hindsight, it has helped me move my career forward because there was a lot I learned during those periods of time.

Grant Belgard: Related to that, have mentors taught you that still shows up in your leadership style?

Elliott Margulies: I can point to very specific things that I do that are relics, so to speak, of things that I learned because mentors have done them to me. And some of that is fostering that deep collaboration. So Eric– I can think about Eric Green, uh, working in his lab. He just opened doors to, for me to collaborate with people that I didn’t, uh, know I could collaborate with, and I learned so much about that.

Elliott Margulies: And I enjoy when I can bring people of kind of from different parts of the company together and start to see them, their minds just go like, “Oh, wait, I’m thinking about this problem too.” And, and they’re thinking about it from a different angle, and you kind of see that, that collaboration take place. I can think about, you know, as I move my team forward, um, and I constantly am trying to think about how are they…

Elliott Margulies: Are, are they happy? Are they growing? Are they doing what they want to do? Uh, w-when we get a chance to be together, recently we had our, our teams off-site, um, we all shared a success and a challenge. And giving everybody the space and the comfort to share a challenging moment that they might be going through with the, with the entire team in a way that is very healthy and productive, and they don’t feel like they’re going to be shamed or, um, or, or disadvantaged because they shared something they’re struggling with.

Elliott Margulies: To create that environment, it becomes very empowering, and that’s something that David Bentley taught me. Uh, you know, so I can think about, you know, that, that type of interaction of leading a team that’s very thoughtful, um, and constantly trying to grow and these are things that, that, uh, definitely come from great mentors that I’ve had in the past.

Elliott Margulies: On a lighter anecdotal note, uh, music is really important to me. Francis Collins is somebody who always brings music to a lot of the science that he does and the way in which we kind of bring teams and communities together. Um, I started my off-site by singing a song to everybody and having them sing with me.

Elliott Margulies: Um, these are things that I, I often do that are fun to think back on how wonderful leaders and mentors have kind of touched my own life and, and career and how I’m trying to give it forward to the, the rest of the team that, that I now lead.

Grant Belgard: What do you look for when hiring bioinformaticians who will thrive in clinical diagnostics?

Elliott Margulies: So we hire people at different stages of their career. I’ve been very impressed with the tenacity and thoughtfulness of the right person who is kind of just coming out of an undergrad or a master’s degree. The work that we do can, be very impactful and has to be done in– with, with a lot of thought, because these are patients who may be getting a high-risk result.

Elliott Margulies: And it takes a certain kind of individual who has a level of maturity, to, understand that what they’re building has to be right as best as they can do it, where you have to own up to a mistake, in a, in a way to– that can be productive, where both you learn and we learn how to improve the system.

Elliott Margulies: so I think finding a smart individual who can code and run bioinformatics pipelines is kind of table stakes. It’s really looking at an individual, what are they passionate about? How do they wanna make an impact in the world? How do they wanna grow their career? Are those passions aligned with being in a company where, we are managing patient samples?

Elliott Margulies: being in a company where we’re doing science that is leading to new products, where we’re going to be balancing an intense period of time of scaling and b-and building new products and trying to automate more, so that multitasking ability. But at the same time, tr-tr-uh, trying to ensure that people can focus and not get overwhelmed, with everything that’s going on.

Elliott Margulies: So these are, these are kind of traits we try and, and look for. you know, these are insights that, that go beyond just coding. But, you know, can you, can you analyze a data set and, you know, describe what you’re doing while you’re coding and, you know, present the, the results to people, in a meaningful way that are, you know, getting back to one of your earlier questions, you know, that the cross-collaboration, is key.

Grant Belgard: What advice would you give to computational biologists who want their work to have clinical impact?

Elliott Margulies: Well, definitely align yourselves with, a company or a lab that has a clinical focus. I think more and more, we’re seeing the ability to translate genomics into actual clinical results. And, it’s not, you know, to something we were talking about earlier, it’s not just a matter of sequencing somebody’s DNA and doing some variant calling anymore, right?

Elliott Margulies: I mean, there’s a whole system and an organization of how do you interact with patients? How do you interact with healthcare systems? How do you interact with reimbursement? and being able to… Something that I don’t think I fully appreciated till I joined Billion to One was that this organization has that all, and this is why I think I’m feeling empowered to succeed bec- in a clinical context.

Elliott Margulies: Whereas I thought I was doing clinically impactful work, and I probably was, right? But it was more futuristic research. But what I’m doing right now is, is impacting patients today, and, that’s very, very meaningful. So looking for an organization that is thinking holistically about all the different aspects of molecular diagnostics, not just the molecular part of molecular diagnostics.

Grant Belgard: What should trainees spend more time learning than they currently do?

Elliott Margulies: I think understanding a lot of the science and engineering principles is b- is going to be incredibly important because coding as we know it today is starting to go by the wayside. it is somewhat of an identity crisis for bioinformaticians. but it means that understanding how software systems are architected, that’s not gonna go away, right?

Elliott Margulies: you still need to guide an AI to build the right tool in the right way. and making those decisions, requires knowledge of how to build scalable software systems. There’s a kind of an architectural engineering component that I think is gonna become more and more important, as well as the science, of things, right?

Elliott Margulies: B- being, you know, being able to, continuously learn and adapt to the science of what you’re doing, will be essential, in, in moving things forward. We’re, we’re no longer just people who plumb and build pipelines. that’s not what we do anymore.

Grant Belgard: If you could go back and give advice to your younger self, what would, would it be?

Elliott Margulies: don’t underestimate serendipity

Grant Belgard: And, to, to wrap things up, are you most optimistic about in genomic medicine over the next decade?

Elliott Margulies: Finding deleterious pathogenic variants and, medicines that can overcome those deleterious mutations, that is an incredible change where we, you know, first we had to develop the tech to identify mutations. Now we can identify mutations. And soon, not only can we identify these mutations, but we can proactively provide pharmacogenomic, you know, information, and, and drugs that can mitigate, those mutations.

Elliott Margulies: That’s just an incredible place to be. We’re seeing this in the prenatal space now, start– just starting to emerge with a couple of key examples. but that’s, that’s a wonderful place to be because now you can kind of complete the cycle of not just delivering challenging news, but, ways in which you can mitigate, those, those mutations.

Grant Belgard: Have any, any closing advice for, career scientists and bioinformaticians listening to the show?

Elliott Margulies: Focus on what makes you happy, uh, you know, and, and curious. Uh, stay curious. I think, um, it’s important to realize that what you learn today is not necessarily what you’ll do in five or 10 years. But maintaining that ability to constantly learn and adapt, uh, is, is a, is a fun place to be. And again, you know, lean into the serendipity part.

Elliott Margulies: You, you never know, uh, when, uh, you’re gonna work on something and the– this particular project is gonna be the extra meaningful thing. Uh, you didn’t plan for it, but it’s turns out that the next three months are, uh, uh, an, gonna be an intense moment where you might learn an extraordinary amount in that short period of time that you didn’t plan for, and you’ll make a, a disproportionate impact by investing in, in those, those periods of time.

Grant Belgard: Elliot, thank you for joining us.

Elliott Margulies: Oh, it’s been my pleasure. Thanks for having me, Grant

Transcript of Episode 86: Deniz Kavi

Disclaimer: Transcripts are automated and may contain errors.

Grant Belgard: Welcome to the Bioinformatics CRO Podcast. Today, I’m joined by Deniz Kavi, co-founder and CEO of Tamarind Bio. Tamarind is building software that helps scientists access computational biology tools at scale through a web platform and API across areas like protein design, structure prediction, and docking.

Grant Belgard: We’ll talk about what Deniz is building now, how he got there, and what advice he has for people trying to build at the intersection of biology software and AI. Welcome.

Deniz Kavi: Thanks for having me

Grant Belgard: Thanks for coming on. So tell us about Tamarind

Deniz Kavi: Yeah. Tamarind as you described, basically a aggregator of all the leading molecular design tools. So things like AlphaFold and RF diffusion and many others, we provide in a single place for all scientists to use, basically. So we try to do the work, like the boring, annoying, undifferentiated work is what we try to do our best in.

Deniz Kavi: So yeah, scaling up these tools, applying them to real problems, connecting them into multiple stage pipelines, so on. I got into this problem basically doing this as a human for my colleagues at Stanford. So in my undergrad lab, my job was to get an email, run AlphaFold 10,000 times, email it back to one of my colleagues, and at some point I felt there does not need to be a person doing this.

Deniz Kavi: You can just have a software solution from there. So basically trying to lower the accessibility gap, but also handling the infrastructure, the, software aspect of how you deploy computational tools like molecular design models

Grant Belgard: What are you most excited to build or learn about right now?

Deniz Kavi: Yeah, I think today we spending a lot of time on developer tooling to some extent. I think we have found that sort of– we work mostly with large pharma and biotech companies, and we found that these organizations have a lot of interest in how they do– how their R&D teams deploy AI to their use cases. And, ultimately these have served that demographic and like we are building a lot of tooling for that. So I think most exciting– most of what’s most exciting to me right now is a organization-wide, whatever, one to ten thousand person deployment of molecular AI tools for, serious drug discovery applications, things that will go to clinical trials or become tool proteins, what have you. Yeah, I think serving data scientists and AI folks to then deploy that to the whole organization is something I’m very excited about today.

Grant Belgard: What problem do you most want to solve for scientists?

Deniz Kavi: I think the general genesis of the company has this theme of accessibility. Historically, if you look at how software has worked in our industry, do a– you do a computational chemistry PhD, you’d take a four-month course on this one software product, and you become an expert on it, and then you are the person tasked with running all these workflows for your colleagues. I think we think there’s a spectacular amount of inefficiency in sort of the handoff in information or in convincing your computational colleague to do this work for you, like all the lobbying internal work. I think our general case is that of the increased capabilities of AI recently, it’ll be available for every scientist and not just specialists in, 20, 30-person data science teams, but the entire org will be the consumer answer of people applying the AI tools in our day-to-day.

Deniz Kavi: So I think very much the, having every scientist be empowered by computational tools as opposed to a realm of specialists doing it for them

Grant Belgard: What’s the backstory on the name?

Deniz Kavi: Yeah, unfortunately not a very exciting story, but we basically wanted it to be named after a living thing. We went through a list of trees, found tamarind as a, memorable fruit and a notable name, and then went from there

Grant Belgard: Where do you think the real bottleneck sits today? Is it model capabilities, infrastructure, workflow design, adoption, something else?

Deniz Kavi: Yeah, I guess I would be biased to say infrastructure. I think model capability is a credible thing to look at as well. I think the better the individual tools are, the more– the less certain-uncertainty you have, the more reliability you have on the individual models, the sort of more valuable the infrastructure becomes.

Deniz Kavi: Because if you have to tweak a bunch of knobs and find all the errors and evaluate against them, the model itself may not be very useful if you don’t know those exact details. But in our case, we’re seeing the molecular design tools especially become good enough in the space that, you can just point at a problem and apply it there and go from there, basically. Our general view would be having it be available to a scientist. I’m repeating myself over and over. So generally, very much the sort of focus of the company is how do you get somebody with an interesting idea for a target or a, drug program or a way to optimize a lead protein or lead sequence and how do you get them to convert that idea into, a molecule on the computer, basically.

Deniz Kavi: I think broadly the issue is not so much the hypothesis generation or having targets to go after. It’s more so like how do you– Once you have a problem to solve, how do you apply tooling to solve that problem? It’s like how we think about the, one of the gnarly-est problems in the space.

Grant Belgard: What does great software for life scientists look like for you?

Deniz Kavi: Yeah, I think we, from the start, focused on having an opinionated way to apply these tools in the first place. You– if you take a look at the papers of these there are a lot of focus on, like, how the model is trained, how their– how the inputs should look. Our view has always been basically, we built a sort of opinionated, structured way to consume those tools in a serious, drug discovery use case. So for structure prediction, complexes and docking is a big use case. For protein design a lot of papers come out and say just, we are creating a way to create new structures, and these are arbitrary, not really– these are not becoming drugs, these are not becoming antibodies or vaccines or what have you. And we build templates and recipes to make that work more effectively. That’s one avenue, is like you need to codify and build the best practices into your product.

Deniz Kavi: The other side is, I think, integration. So we have been very like the entire product from day one has been usable programmatically.

Deniz Kavi: So our API or MCP or agent offering is basically a way for any arbitrary code to call our product. So I think in a way, we can just go away in the background, just be done as infrastructure, and that just gives you flexibility to consume the tooling in wherever you want it. So it might be in your ELN, your LIMS system in your internal custom applications or your AI agents within Claude, what have you.

Deniz Kavi: I think those two are the main points of you want to build a opinionated, codified way, like a very practical-focused applications of the AI tools. And the other side is the how do you get it to– how do you get a scientist to use you where they want you to use them? That’s the two pillars, I would say.

Grant Belgard: What part of the scientist experience do people outside the field most often miss?

Deniz Kavi: I think amount of, uncertainty in everything you do, basically. Like I think some people think about the process as, I have an idea, I will do an experiment to fail or not fail that idea, and then that’ll be the end of it. And if it works, it’s gonna be a drug and it’s going into clinical trials.

Deniz Kavi: If it doesn’t work, I like toss it. But oftentimes, there’s uncertainty in the actual experiments you do and the computational tools you use. ‘Cause anything you do has some error bars associated with, and you have to believe and persist every time something is like going wrong where it might be a sign of it being interesting. Very rarely something in science is, immediately a useful result or like you, you even get data that like proves it in either direction. So I think that’s a very much something people not think about is you’re not really sure where you’re going when you’re in the middle of a process or like hypothesis in general.

Grant Belgard: What have conversations with users taught you that theory never would have?

Deniz Kavi: I think we don’t talk much about– People talk a lot about like where AI is interesting, where the applications are, but applications like are pretty broadly on what people think about as things that computers can do. I think if you think about the grand idea of a virtual cell, the sort of like a philosophical leaning of a research work there would be you want to create a thing that simulates the entire behavior of a cell in the computer. But realistically, that is like too big of a problem to be applied immediately today. So in some ways, I don’t have– I have a computer science background. I have a sort of, basic science background in, in relevance to that as well, but I’d never worked in a sort of specific R&D org before in a drug discovery context.

Deniz Kavi: And I have learned a lot about what the day-to-day problems are in a specific, in the context of a research program for a drug program what the use cases there are. So that’s things around what assays are most interesting, what sort of you can trust on, what you can trust what the sort of clinical or risks are before going into the later stages.

Deniz Kavi: I think that type of day-to-day experience is very hard to see. Certainly in academia, even if you’re a very strong scientist, you might not know the sort of how the applications go. And there is a meaningful difference in academic science and, commercial drug discovery-focused science, I would say. And, having not worked in that space, talking to– the privilege of talking to like pretty senior folks who manage these R&D programs and learning how they think about those use cases is very valuable for me.

Grant Belgard: How do you decide what to hide behind the interface and what scientists should still control directly?

Deniz Kavi: That’s always a changing structure for us for the most part. I would say people tell us that this point is a big value add for the platform, like maybe whatever tens of thousands of scientists, people will email us when they want a model added. I think we’ve always had a question of complexity versus abstraction, where, we have, say a few hundred person org in a company using us and also like some 30, 50 person data science team using us. And the interests of those groups are not necessarily the same. The scientist wants it to be easy to use. They can come in, use it, and then forget about it, but the data scientist might be, I want to check every single possible option. Generally, we’ve built our product in two distinct sort of ways.

Deniz Kavi: So the API, for example, is you can– you do anything you want programmatically, can write code to build on top of our product. And then nowadays, the API actually serves as a way to like abstract even further. So we found AI agents as a good way to guide the user to, you know… Most of our value from AI agents, like not even necessarily the reasoning, but just the hiding the complexity of how you consume a tool.

Deniz Kavi: That’s the one avenue. And the web interface is also there for the most complex way to Basically, anything you need for a given tool, you can use with another web interface. So we bifurcated our products in that way for different cases. And then generally just being close to the customer, and people tell us when they’re unhappy and, it’s a boring answer, but just people– you be very close to, your check-ins and regular meetings, what have you, where people will tell you what the, what problems they have and how– whether or not we’re able to solve them.

Deniz Kavi: Or if we can solve them, are they able to access that problem or access that solution to that problem are the main ways.

Grant Belgard: What does a trustworthy AI-assisted workflow look like to you?

Deniz Kavi: Yeah, I think generally the– I guess these are two different answers for, what we live in, the molecular domain, and also the sort of general knowledge work reasoning LLM tasks. Would say the molecular side, you just want wet lab data. I think we’ve seen a big explosion of the recent models doing very well in the sort of classical, one binder design or structure prediction problems, and much of that was launched by you can do experiment to see that this model works and like you can see the hit rates, what have you. I think that both added a lot of trust, but also despite not substantial changes in architecture, showed just that the models can be good and you can demonstrate that they’re good in that way. I think there’s still some questions there, like how much you can see from experiments. There’s– obviously, you can’t run a clinical trial to show that your model works every time.

Deniz Kavi: The molecular design side, I would say it’s the, just want to run experiment that can be as close to the use case as possible. Then surprisingly enough, like in some, most of the best performing models, they don’t really tend to correlate with a direct experiment. Like most of them are not simulations of an assay you would do.

Deniz Kavi: Many of them are, but not probably the most successful aren’t. That’s one. For LLMs, I think the

Deniz Kavi: main

Deniz Kavi: question is around, You know, to some extent, the tools LLMs have access to are not particularly strong. I think if you give the tools a bioinformatician uses to an LLM, there’s still some uncertainty and problems around that because of the sort of inaccuracy of the specific tools you’re using or the value of the, the reliability and the accuracy of the tools it’s using in the first place. If you give an LLM a protein design model, you now have two things to worry about, which is a faulty tool using another faulty tool, and you have to make sure that you have to find out which one’s the wrong part there. View for there– for that has been basically being very transparent and clear about what the tools it’s using are looking like and evaluating those results.

Deniz Kavi: Our LLM agents basically call our same– Like, whatever humans would use, the LLM uses that tool, and you can interpret it in the same way. So all the sort of inter– the abstractions we built help there. other questions are how good is the LLM in scientific parsing and understanding what’s going on. at this moment in time, the, Claude Op– Claude 4.6 and as of recording is 5.4, Thinking for GPT are reasonably good at not hallucinating anymore. I think questions tend to be where do you take the result of a paper at face– like what the result you’re citing at face value versus is it applicable?

Deniz Kavi: So let’s say if a model setting use a tool, the only tool it has access to for, let’s say protein solubility prediction, it just says protein solubility predictor, and it does not have any error bars or caveats or any details there. The model has no choice but to just, “I have this. This is the one thing I have.

Deniz Kavi: Let me just call this and give it to my user.” But in fact, maybe refusing to do something or showing its limits is probably a most more valuable thing there. Somewhat long-winded answer, but I should say, and showing uncertainty and then maybe even rejecting tasks when it’s on not confident in its ability to do them are two major points, I would say. And so I think the RLHF efforts on the LLMs are doing this well for other– medical advice or what have you. I think these will apply for science because we’re not really– we’re not trying to adversarially convince the model to do something that’s bad because there’s no benefit to having it do a ineffective in silico experiment, I should say.

Grant Belgard: How do you think about simplicity without flattening the science?

Deniz Kavi: Yeah, definitely a difficult problem. I would say the honest answer is like education and support is the honest or best way to go about this. I think we, we try not to limit capabilities of the tools we serve. To some extent we do, honestly, like for the, again, the, say small molecule design tools, for example. Like so many custom options you could be doing that it becomes untenable to use them for anything in the first place. So we try to build recipes of best, best– most commonly used use cases. I think the, again, the sort of open-ended AI models, like things like, protein design or small molecule discovery or even the LLMs themselves, they have a lot of use cases that can be disc– discretized into buckets of, this is my one use case.

Deniz Kavi: I want to do, docking prediction for small molecules, and I have a big world model that does it for me. I think narrowing those down to different tasks is the current approach people take. I think this is like unfortunate because if you can have a single model do everything, it’s quite, quite a more interesting experience and more interesting results most likely. But for the most part, it’s carving out chunks of the capabilities and giving them as recipes you can use is one, one approach. So you don’t really use– lose the capability there. You just become a bit more constrained into a way of doing things, which can be good if the model is not that good, is the– not that performant is the other detail there.

Deniz Kavi: For the most part, I think focusing on the where the models are good and like you can know that by being close to your customers, but also being close to the results in the first place with a sure review and then carving out those places to be individual tasks you’re looking at are the things we try to do.

Grant Belgard: What things are easiest to overbuild in this space?

Deniz Kavi: I think you can make a lot of analogies to like horizontal software players. So I think in some ways we resemble something like a Databricks or Snowflake quite a bit. We do model inference, training onboarding our custom tools, app builders most of those hold, but those products are also used a lot in the life science industry, and they can’t quite apply to them directly. the over-index on verticalized solutions for the industry. You think of yourself as a very bespoke product. There’s lawyers who do life sciences, there’s, procurement teams who do life sciences. And in fact, some of that might just be if you just take the horizontal version, like up and modify and optimize, that might be a decent way to approach it in the first place. You don’t need to reinvent everything.

Deniz Kavi: You can probably use the, the workflow builder, the pipeline builder for generalized use cases probably works well for the bioinformatics use cases as well. I think we don’t need to overindulge in our specialness and difference from the software industry or whatever the AI applications are.

Deniz Kavi: I think that’s the one thing I see a lot of is, you want to reinvent the tool hosting and say the bio– bioinformatics is basically, computer science, and then you don’t– a lot of the tools there, you can apply to the general use cases. So I think we– both from a people who gets into the industry perspective, like we hire a lot of non-biotech folks on the software side and then also what tools you use to build products are the– they don’t all need to be from scratch.

Deniz Kavi: They can be building on the horizontal solutions.

Grant Belgard: When new tools or models appear, what makes you pay attention?

Deniz Kavi: Yeah, I think the– surprisingly enough, I think the, to some extent, like the social media hive mind is like a decent predictor of like how much interest there is in something. That doesn’t necessarily mean it’s like the most accurate or the most interesting. Like some of our models are probably very, like very well known.

Deniz Kavi: People outside the industry know them, what have you, but they’re like basically not used. I think some level of interest tends to be a sign of in- of value. I think if something just goes out to bioRxiv and nobody talks about it, like it doesn’t tend to be the most valuable. I think that like in that case, like the most obvious thing is immediately valuable. The other side is these days, a lot of validation you can discretize and show for, especially in our use cases, in random molecular design use cases. I think if you show clear objective results there I think we’re doing a decent job of putting out benchmarks. There’s more to be done there for sure as well, like for other use cases. In my mind, it’s basically two, two avenues. One is, it can do something that was never doable before. I can make a fully– a protein completely from scratch and put it out and express in the real world.

Deniz Kavi: That’s meaningful scientific results. The other is it does something that was s- theoretically doable, but it was so much better than that, say 100 times better than that, that it can reliably get there.

Deniz Kavi: So again, going back to the protein design example, we’ve had a renaissance of binder design tools recently, and those are mostly because they’ve had, 100 times the hit rate of the previous generation of tools, and now people can actually use them and, instead of, they don’t need to have a huge V display set up where they spend a million bucks on the assay.

Deniz Kavi: They can just spend, whatever, $10,000 and show the results there. So I think it’s either increased accuracy and then the other side is just a net new use cases like in-invented by this protocol.

Grant Belgard: What trade-offs do you face between frontier capability and everyday reliability?

Deniz Kavi: I think you don’t want to be overambitious in applying tools to a given use case. Theoretically, there’s a model that claims to do everything you need to be doing for a drug discovery program. If you read the Wikipedia or you said the GitHub repo the definitions, and you just did them, you say you gave them to an LLM agent and then told them, “Don’t question these.

Deniz Kavi: These can do exactly what they claim to be doing.” And then probably like it will fail in the first step, but it’ll fail in the second step and the third step and fourth, con– successively. I think there’s a– incentive is always to publish like a decent result, and you just claim a… Maybe the most humble people say towards this task or towards, towards even a Jesse prediction on the computer. You do need to build the muscle of identifying what is there to publish a paper or what is there to show an actually or what shows an interesting result. I think that’s one question we have. Something that might be at the frontier might not be good enough for it to be actually practically useful.

Deniz Kavi: GPT-2 was on the frontier for a while, and it was basically useless for a lot of tasks. And similar things apply for our world, which is basically the incentive is to provide the most audacious result you can. But even– That might be true in relative terms. It might just be, it might be 100 times better than the previous stage, but that might not be enough from– If it never worked and it’s zero is zero.

Deniz Kavi: So just making sure that the individual applications are– I think restraints are, I should say in that note, restraints are a big thing we think a lot about where can a model be applied, what the actual sort of error bars around the results are, how can we codify that into a product where you can understand what the limitations might be. I think it’s just that there’s a lot of things that claim to be the best, and then the best is not good enough for a lot of use cases too.

Grant Belgard: What do outsiders misunderstand about making advanced computational biology tools genuinely usable?

Deniz Kavi: I think the view or the understanding is basically that everybody’s aware of what the protocols they want to use are and like what the best, what the hit rates are, what the– People think about, computational modeling tools as the same as they would think about like assays, where there’s some clearly defined set of worlds.

Deniz Kavi: You can buy a recipe or have a recipe built internally and just apply that, and like it’s, 90% of the time it’s gonna be the same thing, except some modifications you have to make, what have you. I think the– both the world is changing so quickly that like very few scientists are actually on top of what’s the frontier.

Deniz Kavi: I think like we do that role informally by just giving guidance on that and providing educational materials there. For the most part, yeah, the limitations are just, people don’t really know what works as a community, basically. So like I think it’s very much in flux, and that might maybe be stabilized like every couple of weeks and then we go off the rails again. The question basically is: scientists know what they want to do? Do scientists know what works well? And, the criticism of the science community is a sort of general observation that the world is moving too quickly and the incentives are, or incentives are such that everybody claims state-of-the-art for everything, and it’s hard to be on top of what the direct applications are.

Grant Belgard: What first pulled you toward the overlap of software and biology?

Deniz Kavi: Yeah, I actually– so coming into Stanford, I had done some work for doing natural language processing work. I very wrongly predicted that sort of transformers would not be a good application for life sciences. And so I was doing some older text translation and summarization, sentiment analysis type work, and I just assumed, “Oh, these are not gonna be useful tasks,” and, I’m gonna look at another application. And I got into biology from trying to find cool applications of AI tools as I was going into a pre-science degree. And in reaction to that, I got a job in a drug discovery context at a lab at Stanford. Yeah, I think it was very much I was trying to find an interesting application for computer science, which sort of led me to biology.

Deniz Kavi: I’ve heard this from a lot of mathematicians as well, where the modeling of a complex system tends to be an interesting problem as a mathematician. You become a bio-focused mathematician or what have you.

Grant Belgard: Was there an early moment when you saw a gap between what scientists needed and what the tooling actually allowed?

Deniz Kavi: Yeah, I think the most obvious for me personally, the earliest sign was basically that I was hired for a full-time or full-time job doing this for my lab mates. Somebody– I think to this day we see a lot of this as well, where even large pharma– A director of data science at a big pharma company who has 15 years of experience, half their job is just somebody sends them an email and says, “Can you run this in silico workflow for me?”

Deniz Kavi: And then they do it for them, but it like takes a few weeks, what have you. I was basically doing that for my job. So we had a protocol for finding targets for peptide candidates in a, in silico way, and that was interesting for applications of my lab, and that sort of led to some other separate work that was a cell systems publication. And that was out there in the world for people to use, and then nobody in the world could use it, basically. They would have to have me do it for them. And that was the genesis of the company in general, was just solving that problem of, I have an idea to apply this, but I have no idea how to actually, use the tool to apply them to a real use case. And that’s how the company came to be too.

Grant Belgard: What did being close to research environments teach you about how science really gets done?

Deniz Kavi: I think that there’s just, the most part, being close to scientists makes you appreciate both how valuable their work is, like how much how hard they’re working for these use cases. But the other side is, I guess I’ll– going back to my previous point, like a lot of uncertainty around how well do you think your idea will work. The experiment you do might fail, the computational tool you use might fail. There, there might be some, side effect you’ve never known about and, that sort of– you have to embrace that as a researcher. And I think researchers also think about the world in this way. I think it’s more, more importantly than typical day-to-day experience is a very strong skepticism of everything that comes their way.

Deniz Kavi: Like anything that could be interesting or useful, people are, just by training of the job, I think very much skeptical and often negative on these things, which I think is an interesting habit to have, and I think it has its pros and cons. I think the temperamental approach is like what the temperament of a scientist is, or life sciences, I should say, is for what the future holds, quite interesting, where they simultaneously have a job that is much, I’m in the frontier.

Deniz Kavi: I’m trying to invent the next thing, but also I am also very skeptical and generally negative on everything that might be interesting. And you have to fuse these ways to do the process of science basically which is– I thought was quite interesting.

Grant Belgard: What made the founder path feel right for you?

Deniz Kavi: Yeah, I think in our case, we built the first version of Tamarind for my lab as like a side project with my co-founder basically, and gave it to my colleagues. And then I posted on some random forum about, we have this use case, these alpha fold on the web, and web, and that led to several hundred users.

Deniz Kavi: So there was a lot of demand for academic users to– who like felt this in– problem of how they do computational tooling. that sort of felt strong enough as a pool of interest from users that we felt we, we should do this full-time and not spend our times doing this as a side project in school. And I think that was the primary reason. Like for the most part, in my mind, always not really thought about being– Like I always wanted to be a scientist or a researcher, and the approach in my mind was: What is most valuable to the world right now of the things I could be doing? What is the fastest path I could get there? And I also was very much pulled towards this idea of, I can move faster in a quick, quicker way than typical timelines you would take.

Deniz Kavi: Instead of doing a– four-year undergrad and a PhD and another, postdoc and many years of working at a biotech company, I now get to basically do the job of a executive at a relatively serious, bio-software company and just just by having the virtue of having built this thing as opposed to getting approval from everybody else on top of me is the sort of primary motivation.

Deniz Kavi: So combination. We had a thing that was working that we wanted to make it more serious. Just the waiting and the having to play the games of getting, accredited and approved and going better and better over time by some other institution was not very appealing to me. And the other side was basically for us to realize this idea of how we get this to– these tools to be used by scientists more effectively and at more practical use cases. It do- it has to be a company as opposed to a nonprofit or academic research project because the incentives are not strong enough for those use cases or for those methods of applying this problem that we had to make it a company, basically.

Grant Belgard: How did you learn to tell the difference between an interesting technical problem and an important user problem?

Deniz Kavi: Yeah, I think I was somewhat commercially minded which I didn’t realize at the time, but I’m basically a salesperson now, so I’m more aware of it today. I think many interesting technical problems can be commercial or user problems as well. The question is, we’ve been asking for people to pay us from day one, basically, as the one side. I think if you keep it as a free tool that everybody can use, it’s a– have too many nice-to-have type problems. I think you want a investment from the user of their time or their money or their feedback, what have you, where the problem has to be severe enough in their day that they would take some risk, basically, is how we think about that. I think I have a decent way to emulate that in my head today. I can understand what the workflow looks like from just talking to somebody about their day-to-day.

Deniz Kavi: But for the most part, do inference scaling for AI models. The condition for that to be useful for users is that the AI models are useful for them, and we had to validate that for that use case. my finding was, if you are willing to put something of yourself on the table, like risk something of yourself or time or money, what have you, is the main beneficiary of user solutions. And then technical products are often, you know– I think engineers are very much drawn to this case of “I think this is interesting. It’s a thing to solve,” but there’s no real thought about what it means to solve a problem as opposed to research curiosity. Yeah, that’s my general approach is getting commitment from the user is the main thing to look at.

Grant Belgard: What surprised you most about turning research-driven insight into a company?

Deniz Kavi: I think I was broadly surprised by how disconnected academia is to some extent from industry. Like theoretically, all the IP from these companies, all the biotechs comes from industry. It gets spun out of labs, it’s the professor’s research, what have you. But in many ways also, there are dedicated industry research conferences.

Deniz Kavi: The problems you tackle are quite different. Yeah, I think a lot of the basic science is sort of– you know, obviously, there’s some actual practical R&D work also happening in, in academic settings. I think very much the context was, biotech and pharma think about the world in a, series of drug programs or like potential assets you can acquire versus, research will be more platform style.

Deniz Kavi: You want to get a– I want to make the machine that makes drugs as opposed to I just want to make a drug and get– create a company around that or, provide a way to create that drug in the first place. Generally, I would say industry is much more open to investing resources to make things more convenient and efficient versus, academia or research in general can be, I will have an undergrad do this for five, 10 years and just keep going through and churning through them.

Deniz Kavi: I think there’s a lot of benefits to some problems that can just be like thoughtfully thought of and then ground through for many years or many long amounts of time. But it also means the timeline for everything you do in academia is very much shortened by what you can do. Like academia or research in general can be a source of commercialization. But if you approach the world from a perspective like I am doing something that’s very hard, it’s impossible to do, and I’m just like seeing how close to impossible I can get, that sort of somewhat grounds you in your ability to do interesting sort of groundbreaking work in some way versus if you think the thing you’re doing is very hard, but it’s like possible and like you have a timeline for that.

Deniz Kavi: I think, projects that are set up in a way where it’s gonna be I’m gonna do this in the next two years versus I’m gonna do this however long it takes tends to be an interesting dichotomy there.

Grant Belgard: Where did you underestimate the human side of the job?

Deniz Kavi: I think for the most part for us it was adoption. So there’s, one– even once you like c-close a contract or a customer signs up, like you use it within their organization there needs to be a deployment process. You need to be able– can you do basically lobby and convince functional heads, get their teams to use us? More than I… And think we have a more rational sales process than we most other industries do. Like we don’t do these steak dinners or whatever. Like it’s mostly a case of proving product value and then scientific interest and value there, and getting people to trust you and be the source of expertise, I think pays a lot of dividends.

Deniz Kavi: And that is to some extent bounded by knowledge, but also the cases, you want to be writing a lot, talking to people a lot, and that sort of tends to be the way you become a brand or a known entity in both attracting talent or customers or what have you, is very much driven by these human social problems. And then I would say in the deployment side, it’s very much driven by like political problems, like how you get a team to adopt you and how do you get a larger team to adopt you and how do you get them to use more or pay more and what have you are… ideally, you’re convincing that they’re– you’re spending more on Tamarind is a sign of getting better science, but also more adoption means more people have access to these tools that are more practically useful for their day-to-day. I think I’d never really done any of these tasks.

Deniz Kavi: I think I’ve become a salesperson, as I mentioned, and learning that on the job was very exciting.

Grant Belgard: Looking back, what moments feel like the real turning points?

Deniz Kavi: I think we– So the company’s about two and a half years old today, or two years and a few months. And the first year, we basically didn’t really know what we wanted to build. We had this idea of a, web interface for all the models, and you can use them easily. But the models weren’t good enough yet.

Deniz Kavi: We weren’t sure about what the applications would look like. What the– is the use case, production agents? Is it experimentation? Is it like proteins or small molecules or, how much of the scale part matter? And we had to invent that with our customers, and that was a pretty meaningful thing for us to go through over time. In that sense to invent a category basically. It was the most surprising experience for us was to figure that out. And unlike, if you’re starting a CRM company or like a pretty typical software company, you can just check what’s happening in the world and you do it– you could do it again, but better. In our case, it was very much a case of how does this product happen ever and how does it become actually applied? I think for the most part, there’s been a lot of efforts in this direction, but none of them have gotten that much actual usage.

Deniz Kavi: So we had to invent what the of that product would be.

Grant Belgard: What skills compound fastest at the biology software interface?

Deniz Kavi: I think I would put just like being an information sponge as a very valuable skill to have. I think people underappreciate how much– if you just know a lot about the use case you’re interested in, if you know a lot about the customer you get to or just what the product you’re building is. Oftentimes, again, the world is changing very quickly. You want to be on top of everything. My view has always been I’m gonna spend all the time I have in the world passively learning what I can and being as close, curious, and interested in people as much as I can be. This can be, whatever, social media posts, YouTube lectures, or, it could just be a scientist you want to talk to. think a benefit of being in the world is that you get to talk to experts all the time.

Deniz Kavi: And I think if you’re doing a computational science PhD, and all you do is like you re- you write papers and you just publish them and nothing happens afterwards. Talking– like having a person that uses and is depending on you is a very strong incentive to learn in general. And the ability to learn is a very powerful thing to have. And putting yourself in a structural position where you can learn a lot is just quite valuable. The PhD obviously like you’ll learn a lot there, but the things you learn are very much how do I invest– advance my general PhD research theme versus, people are relying on me that are quite important in their organizations.

Deniz Kavi: What can I do to just solve their problems or go another avenue on the learning side?

Grant Belgard: What’s worth learning deeply even though the tools keep changing?

Deniz Kavi: I think honestly, the– one of the strongest– one of the biggest gaps we have is like very strong core AI folks. I think you can see the incentives here, like if you’re a really good AI person, why would you want to work in biology? Basically, like you can do the core foundation model research, you can do some interesting robotics work or do computer vision, what have you.

Deniz Kavi: You’ll probably be paid more. There’s a couple of companies I think like bucking this trend. There’s a few like good research organizations, but I think the core foundational computational skills are quite important to learn right now. And there’s a lot of these getting replaced by the old LLM coding agents, but I think having that technical fluency is quite valuable in that, I think many bioinformaticians have become basically people in the interface of software and techno– software and biotech, is they become masters of none. And that is not a great place to be for most.

Deniz Kavi: You’re being bought– you’re being hired for a specific skill, or you’re starting a company for a specific skill, and if you’re okay at everything you might be a decent cog in a machine, and you might just be helpful in an organization, but you’re probably not gonna move the frontier of that field forward very much beyond that. I think founders become a lot of generalists. I think you do need to be a generalist. I fundraise and sell, and also you write papers about like our benchmarking results, what have you. And to some extent, being an expert in something that is to computer science and then applying that to life science problems can be a very valuable way to approach this.

Grant Belgard: How should early career people think about breadth versus specialization?

Deniz Kavi: I think my general concern about breadth, especially in our field, is that you are putting together a lot of things where I’ve taken some classes at Stanford that were basically surveys of the field because you like want to simultaneously appeal to computer science folks. You want to learn about bioinformatics.

Deniz Kavi: to apply t- to apply the computational scientists, learn about more computer science. And those courses are like useful, but they also become basically surveys or like very high-level walkthroughs of the field. And then those don’t tend to create a thoughtful scientist in and of themselves. I think my view in the world in general, like not even beyond this field, is if you want to be an expert in something, and then if you are an expert in one thing, you can then become an expert in another thing and go from there, as opposed to trying to do those things simultaneously. To some extent, I have some concerns about the… I have skepticism of inter-interdisciplinary degrees, for example, in that direction where like classes or majors that prefer to be doing these two, two things simultaneously.

Deniz Kavi: Because if you’re trying to learn two things at a time and then combine them together, the degree program like makes a theme or makes up a way to connect those together, but not necessarily a way to actually be a good credentialed expert for that use case. My view would basically be, become the smartest person you can be for one field. I would probably start with computer science, honestly, and then see where you can apply the science from there, is my general view.

Grant Belgard: How can people get close to real scientific pain points instead of building in the abstract?

Deniz Kavi: I think honestly, talk to people or put yourself in a place where you have to do it. I think in some ways one of the best ways to learn about the economics of a therapeutics company might be to start a therapeutics company. I don’t know that I would recommend doing that for everybody just to learn about that stuff. But I think I really believe in the power of being forced by your environment to do something hard and learning those things on the fly. I think if you’re reading papers about how the drug discovery, this process is done, like it’s just hard to be in that mindset. Like it’s even hard to motivate yourself to read those things, right?

Deniz Kavi: ‘Cause like it’s not gonna be immediately useful to you. So I think put yourself in an uncomfortable situation. I guess in the like general case, I have friends who have applied for jobs in places that they’re, they were definitely not qualified to do, and they offered geo service for free for them, and if somebody responded, they would, they have to make that work in the next one or two weeks, and they respond in that way. I think putting yourself in an uncomfortable spot like forces you to learn something, and like that might be a bit embarrassing also if you fail. this is how I think about those things.

Grant Belgard: How should scientists decide among various career paths?

Deniz Kavi: I think it’s just, it’s a question of, in my mind, I optimize on what I think is gonna be most impactful. The most people or has the most meaningful scientific sort of core that grows into something else, is how I think about that. Part of the reason I became a founder was very much in this context of if I did a research route, might be a good scientist like five or 10 years from now, but if I’m the median scientist, I’m not gonna be very important to the whole of science. And I’ll have a lot of papers with have 20, 20 citations, don’t really go that far was what I was concerned about personally. You can be a great scientist. I think academic research or, re- general research focus is very important, and some people will do very powerful, impactful jobs there work, work there, I should say. My view has always been what are you optimizing life? In my mind, that was impact.

Deniz Kavi: So however many people I can impact, I would like to optimize for that, was how I thought about that. So if your belief is that, the s-science in– of the next generation of, say virtual cells will be in academia, you should go all into that and then become a PhD and a professor and doing virtual cell work. If you think it’s gonna be applying some AI tools to therapeutics work, you can start a biotech company or start your own company to some extent. Or the other side might be, I think the most important bottleneck is clinical trials, even though I have this life science background, let me go try to find out what the clinical trials can be solved with. Yeah, I think so find the thing to optimize that you think is most valuable and go for that.

Grant Belgard: What mistakes do smart, ambitious people make when they enter this space?

Deniz Kavi: I think the… I think the mistakes smart people make are always almost the same in independent of the field. I think oftentimes the questions are you try to learn from somebody else, become a clone of what you think is a good thing to be doing. I think it’s a– for the most part, it’s like a decent way to live your life is to copy someone who is better than you and pretty close proximity to you. I think that’s reasonable, but to some extent, you do want to take a leap at some point. You do want to take a risk as much as possible, and that doesn’t necessarily have to be like, dropping out of school and starting a company, but it can also be something like, going beyond replicating somebody else’s work, I should say.

Deniz Kavi: I think we set ourselves like heroes and people to admire and work to replicate and to be similar to, but that is– that gets you only so far in what you can accomplish. It’s helpful to have knowledge of history and what things happened before, but you probably don’t want to be living in the shadow of somebody else or someone else’s work as much as you would in an empirical context.

Grant Belgard: What habits help you stay grounded when the hype cycle gets loud?

Deniz Kavi: I think I just might say talking to customers again. I think sometimes I’ll– people will tell me their negative results, so I think it’s quite go– There’s a lot of ex accounts who just talk about how biology will be solved next week. And like I am quite like– I think I’m very much exposed to that technology world when I’m quite excited by the technology in the first place. But once you know what’s happening in a field, it becomes much less exciting for the most part. I think, I suspect, people who do the core AI research for LLMs are probably much more conservative than the people making products on top of them. They’re probably both very excited and ambitious right now. I think we’re actually yeah, I think ke-keeping yourself in a place where, you know, people whose job it is not to sell AI for their company, but people whose job it is to apply it to their use case.

Deniz Kavi: This is very AI-specific, but also can go through most everything else is, when you open news-newspaper, you see the headlines about science, and you think they’re all bad, and you read all the, headlines about politics, and you think they’re all credible.

Deniz Kavi: I think it’s one of these things where you just want to be close to the source as much as possible if you care about the results from a given category.

Grant Belgard: What question do you wish more people asked you?

Deniz Kavi: I think a lot about why there have not been great software companies in the life sciences over the, say past 50, 20, 30 years. I guess to answer that, I think the value of software was somewhat limited. most of R&D spend in biopharma goes to development, like it’s, assays, experiments, headcount and then like a bunch more of that money goes to clinical trials and all the commercialization efforts for like obvious reasons, because it’s much more expensive. And I think a lot about like why we are different in this world where, basically our belief would be AI is sufficiently new that– or powerful that compute will be a more meaningful spend on the biotech side, and this company can be a whatever billion dollar revenue company in the next five, 10 years. And, I get asked this from like VCs a lot, but not so much by products and practicioners a lot.

Deniz Kavi: And I am curious how folks think about the tools they use, like how viable and sustainable the companies themselves will be. Like in many ways, a lot of these companies get bought by private equity, they get merged into some other thing, like the product does not improve over five, 10 years. And, if you’re scientists who use these tools, don’t think too much about what happens. It feels like whatever happens to the company happens to them also, and like they don’t really get to control what happens. And I’d be curious about how scientists think about what software tools they use exist as sustainable, long-living companies versus, a thing they bought for a year that might disappear next year.

Grant Belgard: What belief do you hold more strongly now than you did a few years ago?

Deniz Kavi: I think I’m a believer that AI will be valuable drug discovery. I think like this is a– I don’t see the starting company as a more open-ended question, because of the bottlenecks in clinical trials. Again is AI the right place or the– is drug discovery the right problem to apply this even in the life sciences world where– and what if you’re optimizing clinical trials, you’re like shaving one year off a clinical trial? I’ve become very convinced that at the current rate of getting better, the models improving, will have, net new assets added to every biopharma company’s portfolio of assets that will be, driving revenue for them. I think like we think a lot about, science outcomes like approvals and clinical trials, but I think, AI will make more money for pharma companies is on the drug discovery side by making more drugs for you to get to clinical trials and then approvals eventually.

Deniz Kavi: And I think this will almost inevitably will happen in the next of years or very soon, basically. I think, the adoption is there, there’s interest, but also I think the results will be speaking for themselves very soon.

Grant Belgard: What about the inverse? What have you changed your mind about in the last few years?

Deniz Kavi: Yeah, I think the– I am generally actually averse to science for like, goodness sake. I think you do want to think more about what the outcomes will be. Yeah, I think revenue is a core metric when you’re trying to make medicine, think about the commercial results. But to some extent you are serving tooling for an organization, and I have not thought about, I think about science as an interesting, valuable way to impact humanity and be good for the world, what have you, and I believe that still. But what you do day-to-day on– at your job is basically the same, whatever job you do. Like some– or between the roles I can do anyway are very much the same. And you want to pick your battles more carefully what you apply yourself to. I think I used to think that, you want in a field that is good for the world necessarily has to be strictly a very clear value add.

Deniz Kavi: if I went back to my, yeah, to three years ago and I start– just starting a company, I might just tell him, think more clearly about do you want to work in science forever?

Deniz Kavi: Do you want to make a bioinformatics software company? To some extent, you don’t necessarily want to be making a plan for yourself without knowing the requirements for that plan. So in this case, it would be, let me rephrase what I was trying to say, which is basically is the sort of aligning core thing you’re motivating your acts by?

Deniz Kavi: I mentioned previously you want to pick a job or a thing– or one singular thing that you’re optimizing for, but be more thoughtful about what that thing is and not just which fields are is good or perceived to be good by from a fuzzy, open-ended sense. And I think there’s a lot of value to be added for clinical trials, like a lot more boring even like payroll or like better health insurance, what have you.

Deniz Kavi: That type of thing is still quite valuable, and I would not– I would have looked down on those companies beforehand, where I’m now much more agnostic to humanity. This is a singular sort of effort to make the species better, and whatever you dare can be quite valuable.

Grant Belgard: What boring looking skill turns out to matter far more than people think?

Deniz Kavi: I think generally remembering things is quite important. I think like making structures for yourself to remember people’s names and where they work and what their, use cases are. I think it pays a lot of dividends in getting to know people effectively. If you keep seeing the same person over and over again, you can talk to them more effectively.

Deniz Kavi: Yeah, I think taking a lot of time to remember other people and also the specifics of their work or like what they might be related to you is quite valuable. We’ve seen this a lot in hiring, where like keeping track of somebody for many months, like just eventually converting them to a part of the team or a customer in our case.

Deniz Kavi: Or it might just be scientific collaboration or working with a partner on a specific program. I think just being very– taking interest in people and being thoughtful about keeping that interest in your– like in a structured way. Maybe you should remember from the top of your head, maybe you should write it down for yourself. I think paying attention, is the general theme here, is like purposely and spending a lot of time paying attention is quite valuable.

Grant Belgard: What are you still trying to get better at?

Deniz Kavi: Yeah, I think I spent a lot of time living and breathing with scientists, and I still do most of the time. I think we are as a company looking a lot more like how we can get this enterprise level adoption question of, a mature company in our space should look like, nine-figure revenue per customer. And that means basically everybody at this company uses you and like for a wide variety of core tasks. I want to become a better– I run a what, 15, 20 person company today. I’m not like a huge organizational figure. They’re all in the same room, basically. My– I want to learn about how our customers think about systems, how they think about the organizations of their large organiz- companies, like making those func- machines function well.

Deniz Kavi: Having managed a small number of people so far is a very complex problem, and both from understanding of what product we build next, I would like to be understanding of how the organization behaves and reacts to those things, but also running my own team more effectively. I think so I have basically over the course of the company, I’ve picked up skills I’ve never had and I was quite bad at the start, and I’ve become pretty good at.

Deniz Kavi: I think the next thing I want to be best at is understanding the behaviors and intents of a large organization and building products first and foremost for those organizations, but also apply those learnings to my own

Grant Belgard: What would be exciting for you to see happen in this space over the next few years?

Deniz Kavi: I think if we got 50% of the way to what the models claim they’re able to do, honestly, it would be very exciting. I think that would be a pretty meaningful proliferation of these models for different use cases. The approaching design is reasonably good, but if we got to I guess whoever those sort of hype people say on Twitter about these models, if they become real, which I think is like within the bounds of the we get today, would be very exciting. I think ultimately Tamarind is a index on the belief that, models will be getting better for molecular design applications, and it’s obviously good for me that the models get better, but also for the value of how we can produce more medicines more quickly, more effectively, and then even before that, just producing new medicines, period, so you can have another list item in the list.

Deniz Kavi: So I guess beyond the more boring and the models get better, but if they got as good as what people, some people think it, they are at right now would be the main thing I’m looking forward to.

Grant Belgard: Last but not least what would you like our listeners to take away from this conversation?

Deniz Kavi: Yeah, I think the general thing is you don’t really need permission to do things. You can start a company, you can work on a research project. That doesn’t mean that it’ll be easy. People will be rejecting you very frequently. But being in an environment where you are constantly rejected, being very– in an environment where you you’re punching above your weight is a very valuable place to be. I think people go and follow existing tracks a lot in life, which is very comfortable. It’s not pleasant, but what you need, what you’re supposed to be doing. I think you can go above your station and if you can hold yourself long enough there, you probably will ascend to a larger point. I am a not very long career– I did this out of school, and I started a pretty meaningful company still, and, much more to be done for sure. It’s a pretty, pretty small company still.

Deniz Kavi: And I think that the way– The limited success I have had came from being– putting myself in a place where I did not feel welcome or I felt like I was not supposed to be in this place.

Deniz Kavi: And oftentimes I was not supposed to be. Like, I was clearly not qualified for some of the things I began doing. And then just being in that situation makes You rise to the occasion when you’re put in an occasion where you have to be responding to something very hard, and putting yourself purposely in a place where you have to do something quite hard or at the time not possible for you to be doing is quite valuable.

Grant Belgard: Dennis, this has been fun. Thank you for joining us.

Deniz Kavi: Yeah, thank you for having me.

Transcript of Episode 86: Zahra Jawad

Disclaimer: Transcripts are automated and may contain errors.

Grant Belgard: Welcome back to The Bioinformatics CRO Podcast. Today I’m joined by Dr. Zahra Jawad, founder and CEO of Creasallis, a biotech developing antibody engineering technology aimed at helping antibody-based drugs penetrate solid tumors. Zahra’s career has spanned antibody engineering and innovation roles across biotech and pharma, and today we’re talking about what she’s building now, how she got there, and what advice she’d offer to others building their own path in science and biotech. Zahra, welcome.

Zahra Jawad: Thanks for having me. It’s a pleasure.

Grant Belgard: So what are you building at Creasallis right now?

Zahra Jawad: At Creasallis we are really trying to improve how antibodies therapeutics penetrate solid tumors with our antibody engineering solution. It’s something that I came up with, during my sort of 20 year research in antibody engineering that I thought is really needed in the field.

Grant Belgard: What problem are you most determined to make meaningfully better?

Zahra Jawad: Antibodies are, have been amazing therapeutics and it’s really changed a lot of patients’ lives, but in reality, they’re so large in, in their molecular size that they don’t penetrate solid tumors very well at all. If you look at what a tumor is it’s got like very tightly packed cells with a very abnormal vasculature around it. And the antibodies, once they leave the blood vessel, really don’t diffuse very much into the solid tumor. And there’s been very few solutions in trying to improve that. One of them is just making the antibody a lot smaller, but when you make it a lot smaller, you have another problem is that it diffuse, it just filters out of the kidney very rapidly, and so you lose this half life and there’s always this dichotomy between half life and versus tumor penetration that no one’s really solved. So what we’ve done. Is really taking inspiration from the space industry.

Zahra Jawad: And like a rocket takes off, like we saw recently into outer space. It’s got all this fuselage attached to it, but when it actually reaches the atmosphere, drops a lot of the fuselage that’s needed. We do the same thing. We re-engineer antibodies so that they break into small fragments and only the really critical parts get into the tumor cells rapidly. And so that’s. We get that sort of size change in the tumor that we’ve engineered in.

Grant Belgard: What are the biggest buckets of work on your plate at the moment?

Zahra Jawad: The biggest problem always in therapeutics is translating what we see in the lab and what we see in animals into real clinical, meaningful data for patients. That’s really what keeps me up at night more than anything. How can I make sure what we are doing in the lab will really benefit patients at the end of the day. And how can we capture that diversity in patients, in terms of their medical diversity, their ethnic diversity, gender diversity, genetic diversity, and still be able to give them a meaningful therapeutic that isn’t gonna be so personalized that it’s gonna cost phenomenally. So the economics versus the patient benefit.

Grant Belgard: Can you tell us about your journey as a founder?

Zahra Jawad: So yeah, I probably have a bit of an unusual journey because I was working in biotech and pharma since about 2006. After I finished PhD in some postdocs, all in protein engineering, I was really happy and content in my, my role. I was learning so much from the people around me and how to make therapeutics. And was very satisfied. And I just moved naturally up the, career ladder from sort of scientist to senior scientist to investigator to team leader and then a director level in charge of innovation. And I was really content in my job. I think the turning point for me was when somebody in my group developed a stage four lymphoma. This is when I was a director. I was in charge of innovation, antibody innovation, and I think, and she was young. She was 32 and she made a full recovery.

Zahra Jawad: She was a superstar, but she said I think she was on her fourth cycle that her mother wasn’t able to come with her to the hospital for that chemotherapy and it was actually antibody therapy that she was getting. I thought I’d just be a good boss and take the day off and go with her to the hospital. I guess that was really the turning point for me ’cause that was the first time I’ve ever really been in contact the real patient experience of people, patients taking antibody therapies real life, in an outpatient department where there were several, maybe half a dozen people there all in the same situation. And when I realized we had a problem with antibody therapeutics, that they’re actually really toxic for the patients. And I was and that really affected me, impacted me quite significantly.

Zahra Jawad: And that’s really where my thinking changed to how can we improve antibody therapeutics to make it safer and less toxic for patients? And that’s where sort of this idea of changing the size of the antibody within the tumor came about. It’s not easy for someone in industry to have a startup because I don’t have the tech transfer support from a university. I don’t have- any I, any IP actually I own is owned by, or my, entirely by my employer. So I couldn’t generate any data. I actually never spoke at all about the idea and I sat on it for about three years. It was then that I joined a startup called Bit.Bio where, at the time the CEO convinced me to come and join them to help them get projects through the door. And I’m like I’m a scientist. I’m not a project manager. It was like yeah but that’s why we really want you, ’cause you understand the science and you understand scientists.

Zahra Jawad: But I did say at the time I’m a scientist and I like developing therapeutics. And the CEO was like, that’s fine, we have ambitions for that and we’ll give you a scientific role within the company. So I decided to join them, not thinking at all about my idea of penetrating antibodies and really threw myself into that role, found myself after a year being actually, a little part of me died that I really wanted to be close to the science again. But when I wanted to get back into the science, the company really needed me in project management more. And so I was quite happy to do that, but I still missed the science immensely.

Zahra Jawad: And it was really with the support of that CEO, where him and many others who encouraged me to think about like my original idea of penetrating antibodies, very generous in letting me explore that while I was in employment and eventually got to a point where I generated enough interest to be able to raise a very small pre-seed round that enabled me to leave my job and do my first ever experiment around the idea. So I was a little bit unusual where I managed to raise a little bit of VC funding, really just on an idea and, with no IP and no team. But it was really the great support network I had around me that enabled me to do that.

Grant Belgard: How has the time you’ve spent at the bench changed since then?

Zahra Jawad: What in that year that I was in Bit Bio a couple of years?

Grant Belgard: Starting from then to now.

Zahra Jawad: Not much actually. I think like when the process that we drive for therapeutics has been similar in the last, I’d say 20 years of my career. people who develop therapeutics don’t like to change their process very much. And. I just think there’s so much opportunity to go faster, to streamline a lot of things with a lot of automation coming online, AI enabling. I think it’s wonderful. So I think like I would say the only thing that changes, I moved a lot faster than I’ve traditionally moved. Taking all the experience I have, knowing where I can take a shortcut and where I couldn’t. So it was really focused. I, as soon as I quit my job I went into the bench and I filed a prophetic patent and my lawyers warned me I have 12 months to get everything in there. And I’m like, to what point? They’re like to in vivo proof of concept you’ve gotta show in a mouth. That it works.

Zahra Jawad: And I’m like, okay, I’ve got 12 months ready, steady go. using a lot of the knowledge I knew of where, what really moved the needle to get data through. I just got that all in, in just over 11 months and was able to comfortably file that patent, with all the data needed.

Grant Belgard: Can you tell us how Creasallis is using AI?

Zahra Jawad: Oh, I have like several chat bots going at the same time. So we don’t, AI isn’t integral to our engineering. But it’s integral to what, so there’s several bots that I have not only to run the company, I really do believe we are very small with, we’re really four people, I do really believe in using bots to streamline and automate a lot of operational work processes that I don’t need to get involved in. So definitely a big fan of that. But I also have a research twin or a buddy of which I use to scan the literature, interrogate X and interrogate discussions on social media to challenge my thoughts, to come up with new ideas, new targets use it for recruitment to try and find the right people. Everything. So it is quite integrated, I would say within our, the way we work every day. AI is used every single day in our organization.

Grant Belgard: How would you estimate that’s increased your productivity? Pre AI, how large would your team have to be compared to how large it is now to achieve the same level of productivity?

Zahra Jawad: Yeah. So really the only roles we haven’t replaced with AI are the people at the bench Although a lot of what we can do in terms of analysis can be streamlined with AI even with just off just with chatGPT and Claude is probably more than enough for us to do all the analysis we need to. so I think. Typically in a biotech company, I would say we used to run antibody therapeutics programs with, I’d say a minimum of four to five FTEs at the bench. It’s not operations and we are doing two programs with three FTEs at the bench. So we are definitely able to get a lot more done with a far, maybe half even, maybe. A quarter of the number of people? Operations is completely AI. All the sort of mundane tasks of emails, financing projections, report financing reports, putting things into board decks social media. It is all automated really.

Zahra Jawad: I don’t really want to I want to be, think, I want to be using AI to converse, most important strategic decisions rather than spending my time filling in Excel tables.

Grant Belgard: Makes sense. So what, what would meaningful progress look like for Creasallis over the next few years?

Zahra Jawad: Oh, racing to get to the clinic as quickly and smartly as possible on a very lean team. Definitely our plans are to probably, we are probably going to be filing an IND or some sort of regulatory submission end of next year. So that’s the next 18 months. And in that, then after that, I would really wanna be able to see some sort of safety phase one data around our concept with some early efficacy readouts. Um, there. So we do have, we have several options. We have options of. Taking all these products all the way, like improving, making the next generation of antibody therapeutics that are better than the first generation and getting all the way to market, what really my vision is that every single antibody is going to need our technology. The fastest way of doing that is partnering as much as possible with pharma companies and. Uh, to do that.

Zahra Jawad: So that’s my vision is that Creasallis’s technology will have to be in every single antibody moving forward. And the fastest way to achieve that, in my view is partnerships. So that’s really what I’m trying to focus on more, is to make that, that next generation of antibodies through as many partnerships, not just with pharma, biotech, startup, research institute, CROs, everything, like exploring that all.

Grant Belgard: What makes a partnership worth pursuing?

Zahra Jawad: I think it’s really when it comes down to it, partnerships are all down to people working with people more than anything else. And to me, that’s so important. Do I trust this partner? Do I trust that we’ve got the same vision and the same enthusiasm, the same research ethics, maybe the same drive and do we think that we can work together in being able to achieve? My big vision is that every antibody is gonna need a Creasallis technology in it in the field of oncology. And I think if we share those values, then that makes a great partnership more than any monetary or name or anything else that comes. Comes with that.

Grant Belgard: How do you decide which scientific problems are worth turning into company strategy?

Zahra Jawad: I think for me like that, that it was that firsthand patient experience. It’s whatever you, whatever scientific problem turns into a company, I think it needs to hit personally for that founder. Something that you’ve seen done, been affected by close member have been affected by, because. You need something to get you through those very dark days of when times are tough. Definitely that employee that was in my team then gets me through those very dark days when I think, why am I doing this? And there’s no point, that there’s actually people who, if firsthand I’ve seen that desperate for some improvement in the solutions. So I think there needs to be some sort of personal connection to the problem. It’s not just a scientific problem. because you need that resilience to continue all the way to the end.

Grant Belgard: Can you give an example of a low in, in building Creasallis and how you overcame that?

Zahra Jawad: Oh definitely like closing financing rounds is stressful. Very low mark points. Financing, generally, raising money in general is very demotivating. You’ve got maybe 200 nos and maybe five yeses, so it’s a lot of nos that you’re listening to a lot of people criticizing you what you’re doing. Can’t see the value in what you’re doing. You haven’t managed to convince them. Then that sort of fear of are you able to finance the company moving forward? Especially when you’ve got employees, there’s a sense of responsibility to them. Okay, I took the gamble, I’m the founder. I’m the crazy one with a crazy idea, but I convinced people to join me. And those people, I have an obligation to sure they still have a salary going. And so that’s quite a low point I think in a startup generally, very small lows are hugely exaggerated and very small highs are hugely exaggerated.

Zahra Jawad: So just seeing a band on a gel and you’re like doing cartwheels down the corridor to the lab you can’t believe your luck. In hindsight, for most researchers, that’s nothing. But it’s those little wins and even things getting you down of like. Oh our tax returns wrong. We’re gonna do that again. That can make you feel really low and it’s really insignificant ’cause you haven’t been fined and you haven’t been told off. But it can really make you feel low.

Grant Belgard: How do you think about balancing building a platform and advancing specific programs?

Zahra Jawad: So we were a platform, ’cause we’ve got a general technology of how to improve antibodies and I thought initially everyone is gonna want that. It’s gonna be a platform that every pharma company is gonna want in there. Best assets quickly. And then the and it was probably like that maybe about five years ago. And then the environment changed. And what changed is that, a lot of big blockbuster drugs for a lot of these pharma companies are coming off patents and they need to fill that gap. They are looking, then they start, they’ve shifted from looking at early stage platform things to, we actually need to plug in those, we need to get assets to plug it in. And so you have to react to that. If you can keep building a platform and you can hope that will come back, or you can, you have to, keep your pulse on the market and see what your customer really wants and they want assets.

Zahra Jawad: So we pivoted about just over a year ago we decided to go for assets as well as the platform. We still do about 20% of our work platform development, about 80% on the assets itself. because I still feel that even if we wanted to pursue the platform, we’ve got to show an end-to-end process and what best to show it than on an asset that could also be partnered or developed ourselves. Um. Tangible. So we still, any partner is gonna wanna see how you go from idea to a first injection into a human being. so it’s not wasted to work on an asset when you’re a platform company, but you do have to react to your market and what your customer really is looking for as well.

Grant Belgard: What makes an idea look exciting early, but weak in the real world?

Zahra Jawad: When you haven’t done your customer discovery well at all, every founder thinks their idea is amazing. We are delusional, we are, we can’t, we’re very blinkered in our views, and I’m definitely guilty of that. And there’s nothing more grounding than talking to your potential customers and listening, not pitching listening to what their pain points are and what they really need. And if that doesn’t align with the product you’re developing, That is gonna be a weak idea. You’ve got to pressure test your idea very as early as possible, and actually not just once. You’ve gotta continuously, and it’s really on the founder to do that because you are delusional until you actually are humbled by what your, by what your customer tells you. And if your customer is not interested in your product, then.

Zahra Jawad: You’ve got, you either continue building something that has no market value, which is then a weak idea, or you have to pivot quite rapidly to be able to meet that customer’s needs. and that’s what makes a great company from one that fails eventually, in my view.

Grant Belgard: What kinds of evidence give you the most confidence that something is really moving in the right direction?

Zahra Jawad: Definitely like customer interest. I’m gonna put the customer first. ’cause I think that’s what it is. Whoever your customer is, if they’re willing to pay for you what you’re doing or partner with you or buy what you’re doing, that’s really great evidence early on that you are on the right path and you’re building something that somebody wants and values. Yeah.

Grant Belgard: What do people outside drug development tend to underestimate about getting from a good idea to a real therapy?

Zahra Jawad: Drug discovery, drug development is a very structured process and it’s really well mapped out in my view. Once you’ve, there are nuances, of course. Every project has slightly different needs depending on who you’re trying to treat and what your competition is and how you’re gonna stand out from your competitors. I think that’s one thing that people don’t understand is that you start, you have to start a project with thinking about what does your final drug look like for it to be competitive. And of course you’ve done your customer discovery and you know that this is what my customer needs, whether it’s the patient, the hospital, the oncologist, or the pharma company. This is what they need. And so you start with that sort of. Guideline firmly at the beginning of every meet, every project meeting of this is what we are looking for. It needs to bind this, but not this.

Zahra Jawad: It needs to have this kind of affinity, not that it needs to be formulated like this so that we can give it in a syringe versus giving it in an IV bag. Like all the things that would make you competitive, you need to have there in every meeting you’ve got to. Prove it or disprove that you’ve met those criteria. And what would you do if things, and of course you’re not gonna meet everything ’cause it’s a wishlist. And then it’s what are you willing to compromise on? And every drug is a compromise. There’s no perfect drug out there. everything binds something that is not meant to. Everything is slightly toxic more than we want it to be. it’s that, and that’s where the experience comes in of people going, I think we can compromise on this, but we can never compromise on that. And, And making that judgment call to take that drug all the way to market.

Grant Belgard: When you look back, what were the biggest turning points that shaped your own path?

Zahra Jawad: I guess the first my, to being a founder or a scientist?

Grant Belgard: Both. One leads to the other, right?

Zahra Jawad: Okay. So definitely scientist, I’d say people had the most amazing from my science teacher at school from when I was 12 onwards. People who encouraged me and, um got me to actually where I am, even when I didn’t believe in myself. I never thought I was gonna ever be a scientist at 12 if it wasn’t for my science teacher who encouraged me. I never thought I would ever start a company if it wasn’t for a line manager. I had, a Janice, who told me that I could go all the way. Um, and it’s always these like key mentors in my life who have pushed me and have seen something in me that I’ve often not seen in myself. And then opportunities, right? Everyone gets to turning points in their life of which you feel doom and despair. You’ve taken the wrong job. Your job isn’t working out and you are really not enjoying it.

Zahra Jawad: your contract, your postdoc contract’s coming to an end and you need another postdoc, but no one’s giving you a job. How do you react to that? those are the, usually the biggest turning points is where I’ve gone. Oh my God, I can’t get a job. I’m just gonna have to apply for everything. And sometimes life takes you to places that you didn’t quite expect and what, the market sees you is not quite how you see yourself. those are quite big turning points where was pretty sure after I finished a PhD I was gonna be an academic then until I couldn’t get a fellowship and, but industry offered me a job. I was like, oh, that’s interesting. I never thought of industry and things like that. And, it was people, opportunities that come your way when you’re at your lowest point. So I think that’s my big advice is when time, when times are tough, look for the opportunity that’s available at that time.

Grant Belgard: What drew you into antibody engineering in the first place?

Zahra Jawad: So I’ve always been fascinated by protein engineering. I think it was the one lecture at university where I would just sit there with a pen down, just like listening intently. It was so fascinating that changes in amino, one amino acid could have such a big impact on a function. So definitely wanted to do a PhD in protein engineering. Um, again, I was actually adamant I was gonna stay in protein engineering and have an academic career I know I was on my second postdoc and struggled to find a job, really to find a third postdoc or a third fellowship, or someone who would take me on. it was an antibody engineering company that they offered me a job and that was the one industry job I applied for amongst about 20 to 30 postdocs that I applied for at that time. So life, the world had something to tell me, so I fell into it.

Zahra Jawad: Still interested in engineering proteins, but antibodies I’d never thought of before. And it was there at my first sort of industry job. I was just surrounded by some of the best people in the field, um, that I was just so hungry to learn from them. That got me really into antibody engineering.

Grant Belgard: What have different kinds of organizations taught you about how science gets done?

Zahra Jawad: So there’s of course, the startup world, the mid-size, and the pharma, I’ve seen it all and I’ve worked in it all, and science gets done really differently in all of them. I’m telling you it’s drastic and I think you are. Either you sit in one of those buckets, but I don’t think you can find yourself enjoying all three environments. In big pharma, science is compartmentalized. You play one very small role that you do every day very well. And part of a bigger field. Nobody wants to know your opinion unless it’s asked for. And if you want something to change, you have to wait for governance, you have to take it to a meeting. It needs to be approved by someone senior, and then you’re allowed to change. So there’s very little freedom, but that works really well for people who love the process and the pre predictability of their job every day.

Zahra Jawad: And there are people that love working in pharma in. You can see in that kind of way, the science is done. It stifles innovation because everyone wants to do it. The process is more important than the thought process, let’s put it that way. Startup is completely different. Science is done very differently, a little bit chaotically especially, and also in universities a lot more. In a university you would do everything from start to finish to get that project completed. In a startup, it’s a bit more compartmentalized where you are not maybe as tightly compartmentalize as in a pharma company and you have a little bit of creativity, but there is some order still. You can’t just take the project where you want to. You really have to follow and get to that big next big inflection point for the company. And that’s really important there.

Zahra Jawad: Depending on where you sit and mid-size pharma is something in between where there is a lot of structure, some governance, a little bit of freedom. But, startup is because you can follow the science, there’s a lot more innovation. Pharma are not brilliant on innovation, but really good at getting everything out on time, and cost effectively as well because they are following the process. So it’s really different how science is done in different kinds of organizations.

Grant Belgard: What have you learned from roles that stretched you in unexpected ways?

Zahra Jawad: I think it’s really important to just listen. You are not gonna hear things you like and that you may be a bit hard to take. Those are the most challenging jobs where you’ve been told that you are not doing a great job, people don’t like what you’re doing. You’ve really, advice is not to react, it’s just to listen. It’s your choice. If you want to take that feedback on whether you believe it, we think there’s some truth in it, or it’s completely not true, but someone said it, there’s some truth in it, and so you need to listen. and Those are, those difficult moments. I really, the, that pain is, I really believe that is growth. That’s you growing and maturing and adapting. And, still doing that every day. I’m not, I’m nowhere near ready have nailed it all.

Zahra Jawad: There’s challenging moments all the time, whether you’re cha challenging employees, challenging investors, challenging board, challenging partnerships. Eventually you’re gonna have to learn to deal with people and the quicker you figure that out and the you stick it through and the resilience, those are the real turning points in your personality that’s worth having.

Grant Belgard: What skills have you found transfer to leadership more naturally than you expected? And what have you found doesn’t transfer well?

Zahra Jawad: Yeah, I think like I’ve always been a good storyteller and I think being a leader, you need to tell a good story or at least explain things very well and set a vision. Those, that ability from early in my career of defending a Viva, doing a presentation, being able to like even talk about the problems you’re having in your experiment and getting that sort of constructive feedback back quite similar to being a leader. You’ve still got to set that, be able to have that clear communication with the team. Unexpected things. Are different to you and I think that’s the most unexpected thing. What motivates me, what gets me up is not what gets everyone else in the team up and that’s difficult to figure out that individual, what motivates them and how can I get the best out of them because it’s definitely not what gets you outta bed in the morning.

Zahra Jawad: And that, that took me a while to figure out that people are just not motivated in the same way that I’m motivated.

Grant Belgard: What skills have you had to learn the hard way?

Zahra Jawad: Diplomacy, like when somebody is having a bad day, any, anyone, whether it’s a supplier a partner, an investor, a team member. They’re, and they’re just going at you, you’re just tempted to go back at them. So I’ve learnt that the hard way, it’s better to just be diplomatic and step back and wait for a moment where everyone’s calmed down to. Let’s talk about that again in a calm and grounded way. And, you have to practice that. ‘Cause you can feel your blood pressure rising when someone’s going at you. I do have to like practice. Internally, counting, breathing, feeling the hem of my shirt to ground myself. It all comes like I’ve had to actively, ground myself to be able to, yeah, to be able to not react when someone’s going. You, especially as a leader, you can’t react.

Grant Belgard: How has your relationship with risk changed over time?

Zahra Jawad: I, I always see myself as the most risk averse person that ever existed. So I think it’s, it was a surprise to a lot of people when I decided I was gonna go and do the riskiest thing you could do is start your own company. Not only that, start it without a shred of data to support the idea at all. So I guess. Like I said, sometimes I just don’t know myself and how much I see myself in a particular way. And I see myself as a very risk averse person. I like the structure, I like being part of a team. And then to go and do something silly start your own startup and take all that risk. And I didn’t see it as a risk. I just tell myself a different story of this is an important problem that needs to be solved.

Zahra Jawad: I need a safe space to solve it, it’s not a failure if it doesn’t work, on me, but I’m glad I gave it a shot and that kind of was the attitude I had when going into the company that I didn’t wanna be on my deathbed with the regrets that I didn’t even try.

Grant Belgard: What advice would you give someone choosing between going deeper scientifically and going broader operationally? If they’re coming from a background as a scientist.

Zahra Jawad: First figure out yourself, what you’ll really like. If you are a scientist who likes to tinker and doesn’t like the ops operational structure, stick to the scientific route. I think do what comes naturally to you. And if you are operational and you can’t stand like the tinkering around in this lab that really bothers you, then stick to operational. I’m an unusual blend of both. and I think I could give advice to those who think they are also both. I remember being told very early on in my career that Zahra, you’ve got to choose whether you’re going down the scientific or managerial career path. And I just used to say, look, I really strongly believe in leading my team from within the laboratory, so I’m not leaving the lab. And if you think that’s a scientific role, then be it. And if you think that’s an operational, a managerial role, then so be it. But.

Zahra Jawad: I’m Zahra and I’m a square peg in a round hole. And you just have to deal with that. And I remember saying that to my manager and so they left me alone. They let me have a team. They let me still stay in the lab, and I do strongly believe in leading from within the laboratory. I think the lab is a fabulous space. There’s so much. Banter, there’s so much discussion that happens over a centrifuge that you’re turning off or a gel that you’re running. There’s just so much downtime in a lab creates real opportunities for leaders to influence or have discussion and show, show positive traits from within their, to me, more than sitting from behind a desk. So I do have that unusual skill of being able to get things done scientifically, and I enjoy, I really enjoy the science and being in the lab and I am still in the lab also being able to motivate people. But I do it from within the lab.

Grant Belgard: How should someone judge whether a role is helping them grow or quietly boxing them in?

Zahra Jawad: Listen, ask for the feedback. A lot of people are really scared of asking for feedback, in our, in Creasallis, we don’t call it feedback. We call it an encouragement and and an appreciation, because I think when you say it’s an appreciation and an encouragement, it comes from a very different place than feedback. You cannot– listen to what people say about you. You’ll always have a feeling of whether this, this position is constricting you or letting you go freely. But if you’ve got really good mentors, bosses, line managers, other people in the organization, other people that are outside of the organization, anyone you’ve met who you think, I really click with you, I’ve got respect for you, network, find those people and ask them.

Honestly: is that what you think? I think a lot of young people think that every job is boxing them in it’s not allowing them to, why? Why am I not promoted? I’ve been here a year or six months already and. I hear that a lot. Be curious about the people around you and be honest with yourself. Are you really, like promotion isn’t just about how good you are. Yeah. You’re brilliant. I know that. But promotion’s also about is there an opportunity in the company for that promotion? So be curious it’s not a failure if you’re not promoted every year. So be curious and get that feedback and and be patient. You’ve got 40 year, in some cases gonna be 50 year career ahead of you because our retirement ages are rising. You don’t have to have it all in the first five or 10 years of your career. You can pace yourself and really um, be curious about the role that you are in.

Honestly: And actually you have to find your own opportunities at the end of the day. Call yourself boxed in. But there are tons of opportunities in organizations to volunteer, to do things, to put yourself forward for things that gives you that sort of variety in the role that you really need.

Grant Belgard: What makes a manager or a mentor genuinely life changing?

Zahra Jawad: Someone who can give you really honest feedback. I can’t stress that more. Some of the most life changing managers I’ve had have been the ones who’ve made me cry the most. So yeah, cry, go to the toilets and let it all out. And then listen again and to those words because it might not be what you want to hear, but it’s definitely how people are perceiving you. people only, or people would give you real feedback if they care about you. If I didn’t care about you as a manager, I wouldn’t tell, give you any feedback. And that’s not good for you. So if you are seeing someone who likes to give you feedback, don’t shun them, I think get closer to them because they obviously, want to see you improve, change, grow. All of that is positive. Hang on to those people for dear life and don’t ever lose touch with them.

Grant Belgard: What do you wish more scientists understood about leadership?

Zahra Jawad: I think a lot of the times it’s not just about the data and the facts, it’s that you’ve gotta bring people on the journey with you. I still sometimes struggle with that, with my own team, getting people to see beyond the the logic. And a lot of scientists are like, it’s logical, therefore we should do this. And it’s more about the influencing this, coming hard at somebody with a lot of logic is not gonna turn them over. You probably have the opposite effect. They’ll probably be like you’ve just dissed all my data and I am not on your journey with you. So there’s, I think what scientists underestimate is the power of influencing. Important, that we need to learn that quickly so that we can get people on board if we think that we’re doing the right thing.

Grant Belgard: And what’s something you’ve changed your mind about in the last few years?

Zahra Jawad: I change my mind all the time as new things definitely about AI. I’ve changed my mind about that. It needs to be embraced and needs to be integrated. I’ve changed my mind. Maybe investors were quite scary when the first, before I started the company, someone I didn’t wanna talk to. I think I’ve changed my mind about that. I think they can be real. Um, pillars of support for you when you’re building your company, they’ve got the same incentive as you have. They wanna see it succeed and you can really embrace them as partners. And there’s all always little things that you change your mind about continuously. And I think it’s really good to have that open mind and and admit sometimes that you are wrong.

Grant Belgard: What advice would you give to someone who thinks they may want to found a company one day, but they don’t feel ready yet?

Zahra Jawad: Don’t do it until you’re ready. I completely agree. You’ve gotta be ready. It’s it’s it’s con, it’s so life consuming. And it’s fun For the first six months, you’re like, yeah, look at me working all hours. I’m only getting four hours sleep. All I think about is the company. But you remember, it’s not a six month stint. This is could be a 10 year stint for you. So you’ve gotta be really ready that you want to do this. Being a founder and selling a company is not for everyone. It’s. Your relationships will suffer with people personally. Children, if you’ve got that families you’ll have to sacrifice. Forget taking a holiday. You will have to take a call at some point on vacation. Or you’ll have to pay a bill or you’ll have something urgent to sort out. So it’s not for everyone. ’cause some people just want to spend time. With their families and they want to get away from it all.

Zahra Jawad: And a founder is not gonna, you’re not gonna have that. So you’ve gotta be sure that you’re really ready for it before you go. So it’s fine and you don’t have to do it. Now if you’ve got a great idea and you think maybe this isn’t the right time of my life, I’ve got. A young family, I’m about to buy a house. My parents are unwell. I have to look after them. That’s totally fine too, to wait until the time is right for you because when it does start, it is o over consuming.

Grant Belgard: Where do data computation or bioinformatics create the most leverage in therapeutic discovery today?

Zahra Jawad: I think it hasn’t happened yet, but I really think it’s that problem of going from the lab into going into mice, which I think we are okay with, but it’s then going into human, going from mice to human. I really think that is where computational biology is going to help solve that, that problem for us. All that genetic information that we are collecting. Sample information. RNASeq data from patients from tumors. We need that computational power to make sense of whether my drug is going to react in that patient or not. And then to like really simplify that down to a profile of where your drug is gonna work, rather than what we’re doing now is just, give it to everyone and then we are like, wonder why we’ve only got a 20% response rate on it. So that’s where I’ve got high hopes for the computational world that they’re gonna solve that problem of data from a mouse into data into a human.

Grant Belgard: What’s one belief you hold more strongly now than you did five years ago?

Zahra Jawad: That’s a very difficult question. I think like [plugging] through in resilience is something that I hold now much stronger than before. Like not giving up, keep going. Yeah, when things are tough sometimes you just wanna go. Okay. I can see that definitely with jobs I’ve had in the past. It’s tough, bad boss, bad colleagues, I’m not able to do the research I want to, you’ve just canned my project. It was such a good project, why? I’m leaving. And you could just throw the towel in and go to another job because you’re just annoyed. And I don’t think that anymore. I think like sticking it through has got a lot of value right to the end.

Grant Belgard: And what advice do you return to personally when things get difficult?

Zahra Jawad: So I’ve got a toolbox. When things are difficult, first of all I can, I know it’s happening because I can see physical changes in me. That I know this is Zahra’s not in a good place right now. And I know when Zahra’s not in a good place right now ’cause times are tough, I need to go for a run is one of them. So the team all knows, when Zahra’s in a bad mood tell her to go on a run because it’ll make me feel better. And I know that make always makes me feel better. There’s a lot of. Like I said, the deep breathing and the grounding myself exercises that I’ve actually trained myself as a, so that doesn’t come naturally. I have to train myself to ground myself and get myself out of that. Practice just calming myself down and getting myself out of that situation. But I’ve been really highly trained in trying to recognize. When I feel stressed, I feel it in my chest.

Zahra Jawad: I feel it difficult to breathe, and I know when those signals come on. I need to open my toolbox and go for a run, make a di–, make dinner is a big one. I do enjoy cooking and I forget just going and being creative in the kitchen and just throwing things together makes me happy and eating it makes me really happy. Seeing friends, seeing my family. Going on holiday, getting some sunshine. Okay. Sunshine is a big one. Makes me a lot happier if I’m just sat in the sun for half an hour. So I just have to open that toolbox and see what’s available. If it’s a cloudy day, then it’s definitely a run or making dinner. Yeah.

Grant Belgard: That’s nice. So what do you hope listeners remember from this conversation?

Zahra Jawad: I hope, okay, number one, if you’re gonna start a company, do your customer discovery. I cannot express that enough. Do your research and make sure your customer really likes your, wants and will pay for your idea. This is a business, not a charity. Number two. There will be lots of times when lots of times when things are very tough, you just have to plow through, find a toolbox of things that make you happy. Write them down, put them in a poster in front of like your bed so that you see them every day. remem– remind yourself of when things are tough, I’ve gotta dig into the things that make me happy to get myself as quickly as possible. Out of that, you’ve gotta get yourself out of that as quickly as possible, are the two things I would say to anyone.

Grant Belgard: Well Zahra, thank you so much for joining us. It’s been great.

Zahra Jawad: You’re very welcome. Thanks for having me, Grant.

Transcript of Episode 85: Jason Mellad

Disclaimer: Transcripts are automated and may contain errors.

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Grant Belgard: Welcome back to The Bioinformatics CRO Podcast. Today I’m joined by Dr. Jason Mellad, co-founder and CEO of OtoImmune, as the company steps into public view. Jason’s path spans Cambridge trained scientist, biotech operator, and venture builder, and now he’s channeling that experience into a precision immunology company that publicly describes itself as founded by and for autoimmune sufferers. In this conversation, we’re going to unpack what OtoImmune is, why this problem matters, how Jason’s career led him here, and what it takes to build something genuinely useful at the intersection of biology data and patient need. Jason, welcome to the show.

Jason Mellad: Thanks, Grant. Great to be here.

Grant Belgard: So for listeners meeting OtoImmune for the first time today, what is the company?

Jason Mellad: So OtoImmune is a precision immunology company. We recognize that oncology is decades ahead of the immunology field today, in most places, in least, in Western geographies. If you have a tumor, it’s sequenced and that information is used to inform care. So the genetic mutational landscape is mapped out. You can start to stratify the patients in terms of progression of disease, what they may or may not respond to in terms of drugs, and also understanding the severity and grading, and even the origin in many cases of the tumor. In immunology, you’re lucky if you get anything more than basic testing, and that is trial by error. Try this front line of care. If that doesn’t work, we’ll try something else. We’ll try something else. It can take years for people to get diagnosed because the symptoms are quite vague and there’s just not that precision that so many sufferers need.

Jason Mellad: So OtoImmune, my co-founder, Dan and I set it up last year so that we could fix that problem, bring precision by leveraging multiomics and advanced informatics to really help drive the field forward.

Grant Belgard: Beyond the general problem. Is there a particular experience that made you feel this company needed to exist?

Jason Mellad: Yes, so I can speak personally for myself. My mother-in-law has rheumatoid arthritis and has been battling it for several years, decades. And my husband and I, we had our kids during COVID and we’re so grateful that we were able to bring them to Greece finally, when the pandemic ended. So they could meet their grandparents. And because she was on methotrexate, a really harsh chemotherapeutic drug that’s frontline for a lot of rheumatoid arthritis patients, her immune system was completely knackered. And so when she met her grandkids for the first time and gave them a big hug, she caught a nursery cold like so many of us do. But in her case, because she didn’t have the immune system, it had been suppressed by the meds. She was knocked out for weeks and it was awful.

Jason Mellad: And I will never forget the moment when she came into the living room and she was in tears and she told me either I can take this medicine to use my hands, or I can be with my grandchildren, but I can’t have both. And that was a light bulb moment for me because until that moment, autoimmunity is something I’d heard of. I hadn’t studied it, but I didn’t know anybody in my family who had, it. Turns out that a lot of people, women in particular, are suffering in silence and that is very common, over 10% of the global population and increasing. And people like my mother-in-law have to go from doctor to doctor, bouncing around from treatment to treatment, trying to get care, and it’s just not good enough. That was a turning point for me.

Grant Belgard: And why is this the right moment to talk publicly about OtoImmune?

Jason Mellad: I think it’s the right moment. Not only because we’re launching and we’ve pulled everything together with my amazing team, but it’s because we know that the pace of medicine. Precision, the ability and access to things like whole genome sequencing, AI, and all of these different tools. We’re now at the intersection where people are more aware of autoimmune conditions and how important they are, that there’s more attention from pharma, developing a pipeline of drugs to treat these chronic conditions, and we have the informatic tools available to really understand the diagnosis and stratification for care. So it’s now the perfect moment where all of these elements are intersecting.

Grant Belgard: When you use the phrase precision immunology, what does that mean in practice?

Jason Mellad: In practice, it means taking the right information longitudinally to not only diagnose and in some cases prevent, but in reality, characterize the unique immune system that each of us has. Our company name Oto comes from a Yoruba word, which means unique. And we chose that with intention because we believe each of us has a unique immune system. It’s informed by our genetics and it changes over time. And so that means that generic treatment pathways, generic bits of advice you might read online is not going to be suitable for most people. So precision is by definition required for immunology because it is something that’s so unique to us as individuals and evolves over time. You need to also have that longitudinal view as well, and we want to provide both not only snapshots of analysis, but also longitudinal joined depth analysis.

Grant Belgard: And what patients do you want to focus on first and why start there?

Jason Mellad: So we’ve mapped out a wide number of personas, and it’s something that we spend a lot of time working on. Early days, we interviewed over 5,000 patients and clinicians. We’ve all have lived experience in the team, my co-founder Dan, has diagnosed inflammatory arthritis is an autoimmune condition, and most of our team members have autoimmune or autoinflammatory conditions. But we wanted to make sure that as we are building out the platform, it was very clear that different personas had to be supported. So whether or not you have a family history and we call you a vigilant person, or if you’ve got unexplained symptoms that seem quite vague, but it could be your immune system all the way through to somebody who’s just newly received a diagnosis. Certain people who are unfortunately experiencing multiple flares, and then finally when someone is in stable remission.

Jason Mellad: So the platform we’re building, we believe, will support people at all stages of those journeys from just proactively looking after their health all the way through diagnosis and through to remission, and hopefully make each one of those transitions easier. To start off with, we’re very keen to find individuals who have undiagnosed symptoms and have been floating around in the system for some time, and for those who’ve just been recently diagnosed and are dealing with the magnitude. Of that diagnosis, which is now a lifetime change for them.

Grant Belgard: What are the core ingredients of your approach?

Jason Mellad: So at the very basic level, we have a digital health platform. So we take in information from symptom tracking, medications our individuals are using, their family history, their personal health history, metadata, height, weight, you name it, and bring all of that together to build out a solid foundation. The next level up is we like to bring in whole genome sequencing. Not everybody is able to access their genome today. We want to make that as democratized as possible. Because we feel that everyone in the future will have their whole genome sequence and they’ll be very informative for care. So that’s the solid foundation and your germline genome in particular, which doesn’t change that much over time except for somatic mutations that can occur. Your germline mutation is important as that foundation.

Jason Mellad: Then we start to layer in other omics on top, so blood biomarkers, inflammatory markers, lipid profiles, and just keep stacking and stacking, gut health profiling, and build up that case of. Real world evidence coming from wearables that are integrated. So your exercise, how much sleep you’re getting, the quality of your sleep, your metadata, genetics, blood tests, gut health, and bring it all together for what we call integrated insights.

Grant Belgard: In a noisy world of AI diagnostics and precision medicine, what do you want OtoImmune to be known for?

Jason Mellad: We want to be known for impact. I think a lot of people think on AI as a big disruptor which it as it is, and there’s a bit of a land grab where. Everyone’s saying, I’ve got AI, you’ve got AI, everyone’s got AI. We are less focused on the how and more about the what was achieved. So we are very clear on why we’re doing it. We are clear on all the tools that we’re using for how we’re going to make it happen. But what I want OtoImmune to be remembered for and known for is we actually had a positive impact in patients’ lives. We were able to get people diagnosed sooner with more accurate diagnoses and on the right treatments. We were able to help people avoid getting ill in the first place. For certain conditions, it looks like that might be possible.

Jason Mellad: We’ve helped pharma unlock their pipeline of drugs and make sure that they actually get more shots on goal that actually pass through all the way into clinic because those life-saving therapies are needed. It’s impact. Not just another biotech, not just another fundraising startup, but we really made a positive impact in patients’ lives, their families’ lives, and society.

Grant Belgard: What evidence will you need to generate to earn real trust?

Jason Mellad: I think it starts with the authenticity of the team. Because we’ve used the platform, it’s benefiting us, and so we can show to people that we understand we have lived experience, whether we’re caregivers or diagnosed. Then our focus now is to really go out and solve very key issues that affect the different personas that I outlined earlier. So are you having trouble getting your GP to pay attention to you? Let’s help with that. Are you trying to navigate which of the many. Immunosuppressant drugs, you might have to use the [DMARDs] with your clinician. How can we help support that? Are you trying to understand your risk profile given that your mother and your father both have autoimmune conditions and you want to be able to catch something early so that you can intervene early? We can help with that as well.

Jason Mellad: Are you looking to understand once you’ve had your genome sequenced, if there are any variants that could influence how you would respond to different medication or your risk profile? We also would help there. So having very clear value propositions that we deliver on, and getting that positive testimonial and feedback that we’ve had that impact is essential. That’s far more important to us than going out to millions of people in day one. We’re saying every person that we help in those first days, we absolutely have to demonstrate our value.

Grant Belgard: Which career pivots best explain how you got to this point?

Jason Mellad: Oh yes, where to begin. So I originally wanted to be a. An academic, like my father, I’m a mixture, mixture of my parents and my mother is a social worker by training and was very entrepreneurial, had multiple successful jobs. And some companies she set up were successful and others weren’t. But we learnt from that. And my father was at the same university for over 40 years and was a professor of animal genetics and the Vice Chancellor of Agricultural Research. So I, I have both in me and I wanted to be an academic like my father and I quickly learned that wasn’t the path for me. Then I went into technology transfer, working at the University of Cambridge, learned about intellectual property rights, spinning out companies, getting them funded, and the importance of translation, and that really hooked me and I thought, this is what I want to do with my life.

Jason Mellad: I transitioned from that into biotech and ended up at Cambridge Epigenetics as one of the first employees, and Cambridge Epigenetics has now become Biomodal, but that opened my eyes to multiomix. The idea that your genome is there, but epigenetics is dynamic and it gives you so much more information. That kind of qualifier. The dimmer switch on the genome opened my mind to the power of omics and the importance. And then from there, set up Start Codon, my fund with my co-founder Dan, and we learned how to grow and scale across multiple companies that we helped build and support those founders from scratch. But it really showed me that I wanted to be an operator.

Jason Mellad: That I understood how the venture raising, how bringing products to market, how biomarker discovery worked, and I wanted to bring all of that together into something I was truly passionate about, and that’s how we set up OtoImmune.

Grant Belgard: How has helping other founders shaped how you’re building this company?

Jason Mellad: We have seen that there’s a lot of advice we could give from our previous experience, but also we know what it’s like for founders today. It is more challenging to raise. The regulatory landscape has changed. AI has been the latest massive disruption to the field. We understand what it takes to secure financing, to secure partnerships with pharma and biotechs to get products to market, what it means to really demonstrate value, how to grow a team, how to manage a team. These are all things that we honed because doing it for one company is one thing, but doing it across a portfolio of 28 and helping founders with multiple different platform types was another. So it really supercharged our learning, like the 10,000 hours that Malcolm Gladwell talks about. I feel like we definitely put in our 10,000 hours.

Grant Belgard: What advice would you give people building in data rich but biologically messy spaces?

Jason Mellad: I’d say, number one is be very intentional about the type and quality of data that you’re building. I think now that AI’s becoming increasingly commoditized, everyone is saying, let’s look at legacy datasets and we’ll derive insights. I think you can to a point, but those datasets and biobanks weren’t collected necessarily with AI and the scale that we have in mind. So as you’re building these data lakes, think about rubbish in, rubbish out. You’ve gotta be really clear what are the controls? How are samples taken? How was the data developed? What was the QC and QA that was involved with doing it? And then also be clear on how much you can interpret from that data. Don’t overfit, don’t over interpret. Be very focused. I think a lot of people over promise and under deliver. That’s absolutely the wrong thing to do, and also consent is so important.

Jason Mellad: It’s hard to see everything that will happen in the future, but transparent, informed, and understood consent is essential.

Grant Belgard: If autoimmune succeeds, what will be different for the people you most want to serve three to five years from now?

Jason Mellad: I think that we can shorten dramatically the time it takes for somebody to be diagnosed and to get a proper diagnosis. I think that we can really curtail the long trial by error process. That goes for a lot of the medications that people are subjected to. I think that we might even be able to help people avoid getting ill in the first place with the right lifestyle changes and preventative measures so that they don’t progress into autoimmunity. And I think that earlier detection and earlier intervention, several trials have shown that you get much better outcomes for across the board of multiple different autoimmune conditions. Also, I think that it will be hopefully. Much more visible. There are multiple patient advocacy groups that we admire and other companies in the space that we’re trying to stand on their shoulders and support them as well.

Jason Mellad: I want everybody to be aware of autoimmunity. I don’t want anyone to suffer in silence, and I’m hoping that even within the next three years we’ll have a significant impact.

Grant Belgard: So that’s very comprehensive, very end to end. Where in that autoimmune journey are you most focused right now?

Jason Mellad: So right now it is on the detection to drive for diagnosis and to help guide people through the early stages of treatment. That’s our wedge. So if you’re stuck in that four to seven year loop of trying to get a diagnosis, we want to help unstick that. And once you get through to the next phase, we don’t want to leave you hanging. We want to say, now that you’re in a therapeutic pathway, whatever that treatment pathway may be, we still are holding your hand. And we’re gonna help you navigate both understanding what your body is doing, understanding how the meds are impacting you, and then to better work with your clinician. To get the care that you deserve. We’re not here to diagnose. We are not here to treat ourselves. We are here to increase the connection between the patient and the clinician.

Jason Mellad: Make sure that they get the best out of that relationship, and really to help streamline the shortened timelines.

Grant Belgard: What kinds of signals or data do you think matter most? If you want better answers in autoimmune disease?

Jason Mellad: I think genomics is going to be so essential. There are some isolated things that we do, like HLA typing. Pharmacogenomics is becoming increasingly adopted, but there’s so much to be understood from the whole genome coding and non-coding variants and structural variants that impact our immune system in terms of the B-cell and T-cell repertoire that we develop. And the various receptors that we have in our different innate immune cells. A wide range of things are impacted by us genetically, and I feel that we can’t really interpret the standard blood tests that we have in the clinic without having that genetic layer to the full extent that we should. Of course, complete blood counts and CRP and all these other standard biomarkers are very important and very actionable today, but there’s a limit when you don’t have the genetic underpinnings. So I think the genome piece is really missing.

Jason Mellad: Also, the longitudinality of what we do. Episodic care is necessary, but not sufficient. The immune system is being impacted by diet, sleep, stress, exposure to pathogens, and you can get dramatic shifts in a person’s immune system that go far and above. You had a test six months ago and they made you, they’ll put you on a course of treatment. So we have to find a better way for people to self-report so we can monitor that change over time, and also make it more affordable and accessible to have the right biomarkers tested, the right biomarkers, inflammatory biomarkers tested at the right time as well.

Grant Belgard: What’s so hard about building in a space like this where symptom subtypes and trajectories are so variable?

Jason Mellad: I think there’s always a cost factor and an implementation factor. We need to make sure that we empower patients to be central to the journey. We need to make sure that the logistics makes sense because it’s very rare, especially for those who are adults. With autoimmune diseases that their lives are not carrying on. At the same time they’re dealing with the condition. So we have to work around families, work schedules. People forget to get their bloods drawn so they miss their appointments so they can’t get their prescription renewed. Then they end up flaring up the, all these things about just the basics of life not coming together. We’re hoping to streamline that as well too.

Jason Mellad: Make it easier for people to record their symptoms, make it easier for them to get through their appointments, make the baseline strong and robust so then we can then go to the things that are more advanced, like the multiomic testing. But even getting the basics right is important.

Grant Belgard: What role can computation play in this and where do you think it gets overhyped?

Jason Mellad: I am very much in the vein of. Computation and AI in particular is a tool that we can leverage to make things more efficient, but it does not fully replace the human in the loop when it comes to medical care. So I think that there are a lot of organizations and companies that are trying to say. We’re a doctor in your pocket, we will replace the clinician. AI can do it better. We say the opposite. We are more about how can we leverage AI to ease the burden on patients, to help them provide the information that they need to doctors to get the best care possible, to gather the evidence they need to drive diagnosis and further testing. How can we help doctors manage their caseload? They will have a number of patients under their care, how can they better organize and address their needs? That’s where AI is powerful.

Jason Mellad: It’s a facilitator that can operate at scale and really remove a lot of the hurdles that are blocking the field, but it’s not a replacement for humans, at least in this case.

Grant Belgard: What have you deliberately chosen not to tackle yet?

Jason Mellad: We’ve deliberately chosen not to tackle diagnosis because we know that people can have multiple immune conditions, and quite frankly, the old school designations aren’t fit for purpose. I’ve met so many people who’ve said they’ve had lupus or rheumatoid arthritis with totally different disease progressions. You think. Is Lupus one disease? Is it two? Is it 15? There must be so many subclasses. So for us to get into that realm, we first want to really understand the underlying driving mechanisms behind these disorders and then start to classify people based on that. That’s very much informed by precision oncology. We’re now seeing, we’re moving away from saying breast cancer and liver cancer only. But more into what is the molecular profile of the cancer? How is it responding? What are the drivers? Because there can be breast cancers that look like liver cancer.

Jason Mellad: There could be liver cancers that look like colorectal cancer, even if they weren’t derived from that tissue to begin with, because of the molecular patterns we see in the genome and other omics. So I’d like to get to a point where immunology is in that same space where we are looking at our unique immune system, we take a detailed molecular review as well as the phenotype of the individual. And we say, okay, based upon what we can see, this is what we think is driving your phenotype, and here’s the direction of travel. As opposed to, I’m diagnosing you with lupus, or I’m diagnosing you with IBD, or I’m diagnosing you with rheumatoid arthritis. There’s still a place for that. But before we step into the diagnostic realm, we want to focus on drivers and understanding how we can cluster all the different subtypes of conditions.

Grant Belgard: Where do you think the first real foothold is for the company: research, clinical workflow, decision support, partnerships, something else.

Jason Mellad: I think the care journey and clinical decision support is going to be a real big wedge into the market for us. I think when we first started, and as you, I’m very big on informatics. That’s my background. I’m big on big data. I naively thought, oh, the multiomics and big data will just solve everything. And then after speaking to patients and clinicians and payer providers and also pharma, you started to realize, wow, there’s just a lot of logistical things that we need to sort out first before we even get there. I have always cautioned founders that we invested in at Start Codon that it’s very easy to get enamored with your hammer, and you go around telling everybody they’ve got a nail. And you’re just going around, bashing around look at my beautiful hammer. It’s like Thor’s hammer shoots lightning bolts and it’s made from platinum.

Jason Mellad: And trust me I got my multi omic hammer and they go, actually, you know what? I just need to make it easier to make an appointment. Or I just need a way to put my symptoms together so when I go to my doctor, I can have a coherent conversation in the 10 minutes I have to get their attention. Those basics. If you don’t fix that, no one’s talking about the whole genome. So we said fix that first, and then we can make sure that we unlock the bottleneck towards the multiomic future.

Grant Belgard: That makes a lot of sense. What partnerships or collaborators matter most early on for you?

Jason Mellad: I think obviously we are reaching a lot to patient advocacy groups because they have their finger on the pulse of what the communities need. We are really keen on working with clinicians and hospital care systems to get the best understanding possible of what their pain points are, and hopefully leverage them to get more patients and customers using moi. Also biotech and pharma. We understand that there are existing data sets and biobanks available. There are also CROs that do things like clinical trial recruitment and a lot of NextGen platforms with AI. But we want to be a go-to partner because we’re focused on immunology. We are building from the ground up with that end goal in mind partnerships and that we ’cause of our backgrounds working with pharma and building biotechs. We understand some of the needs.

Jason Mellad: For example, something as simple as knowing that the data you generate, also having a biobank sample so a partner can generate their own data set with their own assay is also important. I think a lot of people don’t fully appreciate that. Knowing that the metadata that comes with the sample is so important as well. How is it processed? How is it stored? Who did it come- All these things are like the details that when you, a partner comes knocking, they say, wait a minute. You didn’t have these regulations in place, you didn’t have your LIMS set up. Your QMS is a, all these are things that we’ve lived through, and so we’re building now with that partnership goal in mind.

Grant Belgard: What milestone over the next 12 to 18 months will matter most for you?

Jason Mellad: I would say market traction, but not in the sense of volume of users, but more in the testimonials that we’ve had, the impact. That is our full focus. Now. We’d much rather have a few hundred really dedicated, very intense users who we can show we are categorically changing their lives in a positive way than thinking, oh, let’s go for thousands and thousands of early adopters who aren’t engaged at all, and we’re not able to show any impact because they, inevitably there’ll be an attrition and they will drop off. Any investor worth their salt, any business person worth their salt knows that’s a false, kind of comfort to say, oh wow, look at the adoption we had early on. You need people who are truly engaged and are really feeling that you’re solving a pain point for them. So those are the milestones for us.

Jason Mellad: Get our first cohort of, a few hundred really devoted testimonial customers who can go out and say, this works.

Grant Belgard: What would a thoughtful skeptic need to see before believing the company can make a meaningful difference?

Jason Mellad: I think first and foremost, they need to talk to somebody who’s used our platform and said, okay, this isn’t a nice to have, it’s essential. I think also they’d need to know that we have the ability to scale, because starting off with a hundred people is one thing, but going from a hundred to a hundred thousand to a million plus is another. So I would say that if I were outside looking in, is this scalable or is it just a niche thing that you can only do at a very small level? So we need to demonstrate as well, scalability.

Grant Belgard: What part of your scientific training still shows up in how you operate?

Jason Mellad: Wow. I recently went back into the lab to start tinkering around with some new workflows because I have an assay development background, particularly for my days at Cambridge Epigenetics/biomodal, and that’s been a lot of fun. Took me two weeks to get a PCR working, but that’s fine. I had support. And a shout out to the wonderful people at O2H Labs in Cambridge. But that is, I think, really important for us too, that we are not just relying on off the shelf assays. We now identified the type of data sets that we want to build and the scalability and making sure you get robust data. And so we’re developing our own proprietary assays. And so since that’s my background, it’s been a lot of fun to really think through, not just a me too assay for the sake of it, but one that will generate the data sets at the level that we need affordably to drive our insights engine.

Grant Belgard: What part of company building did you only learn by doing?

Jason Mellad: How everything goes wrong, crisis management. I would say that’s it, because you know,

Grant Belgard: That’s That’s fair.

Jason Mellad: Everything you put on paper, everything that ChatGPT tells you and all that wonderful stuff, great. Okay. That’s business 101. What you learn by doing is when things go pear shaped. When you’ve got an HR issue or the market shifts, or the experiment didn’t work, or a whole host of things, a new competitor pops up, whatever it may be, you learn by doing.

Grant Belgard: How different does it feel to be in operator mode?

Jason Mellad: Oh, I love it. It’s interesting. It’s like when you are doing something that you are happy doing. Like when I was an investor I was very happy ’cause I love supporting other people. So that, that did feel really good. But now it’s wow, I’m back into what just, it just felt like getting back on a bike. It feels so good to be in operator mode again. And although I do continue to support the founders that we backed and I still continue to do a lot of community work trying to support anybody who’s going on this journey themselves. I know this is exactly where I’m meant to be.

Grant Belgard: What have you had to unlearn from earlier chapters of your career?

Jason Mellad: I’d say that I’ve had to unlearn that hard work is the name of the game. When I was growing up, I always had this message, rightly so from my parents, about work harder. You’ve gotta be a hard worker. You’ve gotta be a hard worker. I learned over the years that you have to be a smart worker. So I always say work smarter, not harder. How can you leverage your team members? How can you use different platforms to do things more efficiently? What are some things that actually, at midnight, there’s no point sending that email. In fact, you probably shouldn’t, go get some sleep. These are all things I had to learn over time that I’m far much more efficient by working smarter than thinking it’s just working harder and potentially burning out.

Grant Belgard: What kind of team are you trying to assemble around this problem at OtoImmune?

Jason Mellad: I am so happy that everybody on the team has lived experience and is really, truly passionate. That may not always be the case, but it’s something that we’re emphasizing even for the website. We don’t want to use stock photos. We want to use images of people who actually have lived conditions, whether it be a caregiver or a diagnosed immune condition. This is something that’s core to the ethos of the company for how we present ourselves and the team that we grow. People who have lived it are super passionate and will stop at nothing to fix it for others. I love that. The other thing is I want to have diversity at the heart of it. I’m a, I call myself a Jedi, so justice, equity, diversity and inclusion warriors, it’s more fun to say that. So I love being a Jedi, but it’s because diversity is the answer. It’s not a problem.

Jason Mellad: Too many people think, oh, diversity, is this a thing, and it’s all a fad and it’s all being woke and it’s, no, categorically we know more inclusive teams that are more diverse, win. Every study has shown that. So I want diversity of thought, gender, background, neurodiversity, educational path, you name it, geographical. And we’re already very diverse, and I want to maintain that because I love that creative friction where people come at it from different perspectives and different fields.

Grant Belgard: What do first time founders underestimate when they build around diagnostics, health data, or precision medicine?

Jason Mellad: Just how challenging it is to get funded. That sometimes diagnosis-

Grant Belgard: Especially right now.

Jason Mellad: Especially right now. Sometimes diagnosis is the ugly stepchild of therapeutics. And a lot of investors will say, so you’ve got this platform and you can do analytics, could you use that for drug discovery? And you go, yeah, I could, but this is my, they’re like, oh, that’s interesting. Have you thought about maybe developing an asset pipeline and going to therapeutics? And they tell this to this team of people who are wholly unsuited to go into therapeutics. It’s not their background at all. And then they try to pivot and the next thing you know, they fail. And it’s oh, too bad. I’d say a lot of founders, speak to the right investors, speak to the right partners, and build a team for what it is you want to accomplish.

Jason Mellad: Know that it’s hard and challenging, but also understand the health economics of what you’re, the problem you’re trying to address, and know that although it’s difficult doesn’t mean it’s not possible. I think that’s the thing people, they mistake things being challenging or difficult with, is it worth doing? So just because it’s harder to get funding or it’s not as sexy an indication or whatever it may be, if the health economics makes sense, you’ve got a clear care pathway and a path to market, and it’s what you’re passionate about, you will find a way, be creative. Don’t think, oh I’m just not going to do it at all. There’s always a way. You just have to rethink about your path and find the right partners and speak to the right people.

Grant Belgard: What should people validate before they get attached to a solution?

Jason Mellad: That the problem exists and also that a solution is worth building. I think the third thing is there’s a difference, and I learned this in when I was working as a consultant in early days. There’s a big difference between want state and need state. So for anybody out there who has children like I do. They may need to eat their vegetables, for example, but do they want to eat their vegetables for dinner tonight? They need to brush their teeth, but do they want to brush their teeth? Do not assume that just because you have something that people need and you spent so much time characterizing that unmet need, and you’re so clear and you’ve validated it, and you’ve reinforced yourself and you’re running off, do they want it? Will they pay for it?

Grant Belgard: Very good point. How should a scientist decide if they should found a company, join a, maybe a startup or stay in research at a, a more established organization?

Jason Mellad: Well, it’s a personal decision, but it always starts with introspection. So I tell people you have to be self-aware. It starts with them. If you don’t understand your personal motivations, if you don’t understand what it’s you’re trying to accomplish. What’s your rationale for doing this? You should be running towards something not away. It can’t be, oh, I, my PI’s crazy and I’m, I don’t wanna be a postdoc for life, so I’ll go set up a company or it also can’t be, I want to be in control. There’s a great article called The Founder’s Dilemma, where they talk about do you want to be rich or do you want to be king? King being it’s all about control. Those companies typically fail or rich, meaning everybody wants to be successful, not rich in the monetary sense. That’s part of it. But the whole team wants to be successful.

Jason Mellad: So if you’re the kind of person who wants everyone to succeed, you have a burning desire to have an impact in the world. Pick your lane. It may be a startup, it may be joining somebody else’s. It could be in academia, but you’ve gotta decide what it is that you personally want and then know that you can’t do it all. How are you going to build a team around you to pull it off? And where do you best fit? Just because it’s your idea doesn’t mean that you should be in charge of the company. Just because you’ve got an idea doesn’t mean it’s a good one worth pursuing and be open to the idea or the fact that most people pivot multiple times. So be prepared to actively, objectively pressure test your idea. Seek critical, constructive feedback early and often. I’m always second triple, quadruple guessing what I’m doing and trying to get people to tell me, no, you’re bonking mad.

Jason Mellad: Like I, that’s, I don’t look for people to convince me if I got a good idea. I look for people to convince me that I don’t. I think that’s some of the most valuable conversations ever. ’cause if you came with the idea chances are you already think you’re, oh, look at me, I’m clever. I wanna go out to people. I’m like, please explain to me why my idea makes no sense. Give me all the reasons why this won’t work. Let’s talk her through. That’s invaluable. Actively seek that feedback.

Grant Belgard: What question do you wish more people asked about autoimmune disease?

Jason Mellad: Why is it so prevalent in women? We know that for certain autoimmune conditions, it’s roughly 50/50. In some cases, it can skew a bit more towards men in a couple of them, but overall, for the almost a hundred different autoimmune conditions that have been diagnosed, 80% of women or 80% of sufferers rather are women. Some in the past thought perhaps it was due to women going to the doctor and getting diagnosed, but I don’t think that’s quite it. Maybe that a little bit might be contributing of just who’s going and getting diagnosed. I think there’s something fundamental about the biology of XX chromosomes and women that is driving this massive disparity between the numbers. And we don’t ask enough because women historically have been underserved in the medical community and the research community.

Jason Mellad: Couple of papers have come out with hypotheses, but they haven’t really been robustly proven. We need to figure it out instead of just accepting it as is.

Grant Belgard: What belief are you betting on that more people will agree with in five years?

Jason Mellad: That diagnostics do matter, that they’re important, and that early detection and prevention is the future for medicine. Prevention better than cure, early detection, early intervention. Timely detection. These are all things, I think we’re moving in that direction already, but I feel firmly we’re going to wake up one day and realize that’s the truth. And also that we as individuals are fully responsible for our health. We cannot assume that somebody else is out there is going to catch us when we fall through the cracks. So to the extent that we can control our diet, our lifestyle, educate ourselves. I think it’s so important that we’re not kept in the dark and that we have the information we need to make informed decisions with our clinicians advising us.

Grant Belgard: What would delight you most to hear from a patient, clinician or a partner someday?

Jason Mellad: What would delight me the most would be for them to say, I don’t know. And I mean that because I think often as a patient, you’re going to a doctor and you’re expecting a definitive answer. And as a doctor, you’re hoping that there’s gonna be some clear diagnosis, some clear treatment pathway, maybe follow the guidelines, maybe go a little off rails. But there’s something very definitive and patients want definitive answers. And then when it’s a misdiagnosis or a missed diagnosis, people get really upset, rightly and get really frustrated. I would love for us to be able to have open and honest conversations where people say, I don’t know what’s causing this, but we’re going to figure it out together. That would make me joyful.

Jason Mellad: It, I think it would mean that there’s a cultural shift in the way that we do medicine from learned doctor, ignorant patient going and getting told what’s what to hey, we’re a care team working together and together we’re going to figure out what’s going on, and we need this data input from you. So you’re playing your part and we’ve got our capabilities. So we’re playing our part and together we’re going to sort it out.

Grant Belgard: If we have you back in three years, what do you hope we’re talking about?

Jason Mellad: Oh, I hope we’re talking in three years about the number of precision medicine opportunities that are now mainstream thanks to AI and the markets opening up and really backing companies like OtoImmune and others. We obviously are focused on what we’re doing, but there are so many great ideas and amazing teams out there who need support as well. And I would love to come back and talk about all the really cool things that I, we see in the market and all the amazing advances that are happening. So not just OtoImmune doing well, but everybody, ’cause I believe a rising tide lifts all ships.

Grant Belgard: Jason, thanks so much for taking us inside OtoImmune. It’s such an important moment. I like that this conversation gave us both the company story and the founder story, what you’re building, why you’re building it, and how you’re thinking about doing it. Thanks for joining us on the podcast.

Jason Mellad: Thanks for having me.

Outro: To learn more about mOI and immune health, visit moihealth.com.

Transcript of Episode 84: Eric Green 

Disclaimer: Transcripts are automated and may contain errors.

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Grant Belgard: Today on the Bioinformatics CRO Podcast, I’m joined by Dr. Eric Green, chief Medical Officer at Illumina. Eric has spent decades at the center of Modern Genomics with a career that spans the Human Genome Project more than three decades at NHGRI and 15 years leading that institute. As director at Illumina, he now helps guide global efforts around clinical genomics, access to precision medicine, and the diversity of genomic data.

Grant Belgard: We’re going to talk about what he’s doing in this chapter, how his path unfolded, and what advice he has for people building at the intersection of biology, computation, and medicine. Eric, welcome.

Eric Green: Thanks. It’s great to be here and it’s wonderful to talk to you again.

Grant Belgard: We’re very excited to have you. So how would you describe what you’re doing now, both day to day and at a high level?

Eric Green: Let’s start at a high level. To say that I’m only completing my third month here as not only as Illumina’s Chief Medical Officer, but it’s only my third month working in the private sector. I have a long career. First started in academia and then, nearly 32 years in the government. Now only three months in, in not only the private sector, but then at, specifically at Illumina. At a high level Illumina is absolutely at the forefront of efforts to try to see genomics have maximal positive impact on the practice of medicine. Something fundamental to how I got in genomics in the first place and certainly a centerpiece of my efforts while at the National Human Genome Research Institute, in particular when I was the director for 15 years.

Eric Green: And so when they approached me, which really wasn’t that many months ago, after I retired from federal service a year ago listening to their ideas about how they wanna morph themselves from being a very technology oriented company to being a solutions application oriented company, and particularly in the arena of genomic medicine implementation, was like music to my ears. And and so at a very high level I now get to the honor of serving as a chief medical officer of what I think is the premier genomics company that really offers the greatest promise. To really push the envelope by bringing their technology, their expertise into an arena that is primed and ripe and ready to see genomics truly make an impact on patient’s life and improve human health. that’s, that is a very high level statement.

Eric Green: I will also tell you, which is what, the day-to-day part is more difficult, is the other really wonderful part of this job is um, I’m gonna craft it. Illumina has had Chief Medical Officers in the past, but they were at different times. It was, you know, you know, a while ago was their first, and then the last one that was here, hasn’t been here for three years.

Eric Green: And it’s just a different moment in time for so many reasons. And so one of the other great things about this opportunity is really being given a big block of wet, clay, that I’ve now started to mold it to see what the things are that I think we should immediately be working on.

Eric Green: But I am quite certain. Even six months from now when maybe I have a better day to day understanding of what I do, I bet you two years from now, it’ll even be different than that. Because I, I think there’s a very fast dy, fast changing, very dynamic area and to, to, to some extent. I may have ideas, but the more I learn about Illumina, I might even change my approach to what I suggest that they do or how I help them formulate their strategic priorities in terms of genomic medicine implementation.

Grant Belgard: What does the field look like from your seat right now that most people don’t see from theirs?

Eric Green: If I can tell you that 16 years ago, which is I think about the time that I became the director of NHGRI, and the big push I made as becoming the new director was that I thought, and this was around 2010, that I thought the time was right to get serious about investing in research to guide the way on how genomics is gonna be used in the practice of medicine. And we did this in a fashion where we weren’t being overly scripted and saying, all right, first we’re gonna integrate it here and then we’re gonna integrate it there, but rather we, you know, let a bunch of flowers bloom. And invest where you can in terms of research dollars from the NIH and see what happens.

Eric Green: But there was a lot of skepticism. If you go back 16 years, I can tell you that not everybody thought the time was right. The big difference now versus then is that, we proved that absolutely the time was right and starting, eight years ago, five years, depending what area you’re talking about, nobody questions the fact now that cancer genomics is real. That the use of genomics as part of cancer diagnostics, as part of cancer, therapeutic development, et cetera it’s just, it’s absolutely gonna be more and more mainstream. It’s still early days, but nobody questions. It’s gonna be real.

Eric Green: Nobody questions anymore. The idea that genomics is now a frontline diagnostic tool in helping patients who have rare genetic diseases. It’s just routine and in fact, it’s finding more and more, niche uses in that area, including in acutely ill settings such as intensive care units where especially in the neonatal period and even the pediatric period, there’s even some evidence that might be relevant in the adult ICU setting.

Eric Green: Where, patients have come in with undiagnosed rare diseases. If you could rapidly sequence their genome, you can change their medical management. This, nobody’s, nobody would’ve been convinced that was gonna be the case 15 years ago. That’s absolutely mainstream now. Or take an area like prenatal genetic testing. Where now non-invasive methods are used millions and millions of times for pregnant individuals around the world. And these tests are not very expensive. They’re increasingly being covered by insurance and it’s now mainstream that you offer to pregnant individuals non-invasive genetic testing using very powerful new technologies, some developed and refined by Illumina and others that have built on those same kind of technologies and adapted them in other ways. So these are just the early examples. But there’s more coming and there’s a lot of excitement around pharmacogenomics.

Eric Green: There’s a lot of excitement. Even around prevention and thinking about more and more that we can learn things and maybe we learn it earlier and earlier in life, that may help how patients are medically managed, which is why what I’ve gotten very excited about over the last two to three years is the seriousness that many countries are taking in studying the idea of sequencing the genomes of all newborns. To expand upon the well established genetic screening that goes on in most countries for some modest number of rare genetic diseases. And building on that to say, wow, why are we limiting ourselves to just, a handful of diseases? Why don’t we just get comprehensive genomic blueprint information that we could learn a, we can action around and even more than what we’re currently doing.

Eric Green: And yet we know that in the coming decades we’ll even figure out more and more ways to make these things actionable. And so there’s lots of studies multiple ones in the US and dozens around the world.

Grant Belgard: So you gave several examples of incredible applications of genomics that are being rolled out at scale now. What are some areas of genomics that have stayed stubbornly hard. Where maybe they, they didn’t meet people’s expectations from some years ago.

Eric Green: The most obvious area to go to stubbornly well, there’s two kinds of stubbornly hard actually. I mean, maybe that’s the first thing we should do is if you say, what are the stubbornly hard barriers to genomic medicine implementation? I would immediately bifurcate and tell you two different bins.

Eric Green: One is biological and medical complexity, and two is society and the complexities of healthcare. I think we always should be separating those. Not that one is easy and one is hard. It is just that we should recognize some of this is because biology is really complicated and physiology and pathophysiology is really complicated and unraveling that, yes, technically we can generate immense amounts of data and about things that hopefully will one day give us biological insights about it.

Eric Green: But getting those insights is still hard and then we need to separate that from health, healthcare is just so complicated in every country in the world. And we are now in a circumstance where we are trying to bring a significant change to healthcare by, in the use of genomic information.

Eric Green: And we’re running into all of the usual challenges that come with any change in healthcare. So let’s, we, if you want, we can talk about both separately, but let me focus on the biological complexities. The fact is if I, if we go back 23 years when the Human Genome project ended. We, we knew we had a challenge ahead of us in terms of actually interpreting the 3 billion letters roughly, that we had ordered. And we knew it was gonna take probably multiple generations to fully interpret it. But I think a lot of the thought at the, at that time was, all right, we’ll get this inventory of the many tens of thousands of genes we have.

Eric Green: And then when we sequence this and lots of people we’ll find lots of mutations in the genes that’ll tell us a lot about human disease. And, what’s transpired in the last 23 years? First of all, we learned that we only have 20,000 genes. Not that many more than worms and flies. So human complexity does not come in our gene count. And then we learn that holy cow, there’s all this non-coding DNA. which ha is many cases, in many areas, incredibly conserved through evolution, which was immediately signaling to us. That means it’s biologically important. ’cause otherwise evolution would’ve gotten rid of it. And it’s in, in a, the part of the genome that we don’t have the knowledge of the language.

Eric Green: We, we don’t really know how to read out, like the way we can read out the code on table to understand the coding parts of the genome. And then the more we keep studying these things, we also realize, wait a second, there’s an awful lot of reasons to believe that genomic variants are living out in these non-coding regions. That, and that these are the genomic variants that when we do these fancy human genetic studies are the ones that seem to be statistically associated with some of the most common diseases that we need to completely tackle and understand and eventually be able to make predictions about, make better treatments for, diabetes and hypertension and cardiovascular disease and so forth. And one, the, one of the big challenges that remain is learning. About the biology and the medical consequences of variation that exists outside of coding regions.

Eric Green: And there’s every reason to believe that there’s an immense amount of medically important, hopefully medically actionable variation out there.

Eric Green: But we’ve gotta define it. We’ve gotta understand it. We’ve gotta mechanistically characterize it, and that’s really hard. And we’re getting better at it. There’s lots of exciting things that are being done. And yeah, at some point you may wanna ask me about AI ’cause it seems that everybody will always ask the questions about no matter what the topic and in the world is these days, you always say, how is AI gonna influence it?

Eric Green: And of course, I do think AI is gonna have a considerable influence on helping our human brains understand all the intricacies of genome function and, and once again, I wanna stress that over the last 23 years since the genome project ended , as we realize that our complexity, a lot of it lies outside of our coding regions. Thank goodness we’ve had brilliant scientists discover all the different ways that RNA is biologically important and all the different subtypes of RNA and all the craziness of, we’re learning more and more about RNA modification we already knew about RNA splicing and alternate splice forms, et cetera, et cetera. Oh, and of course then there’s epigenomics and thank goodness that the technologies for sequencing DNA have become increasingly adaptable to study epigenomic modifications and. There we go. There we are.

Eric Green: So, you know, all these technologies are just lining up really nice. Oh, and the other variable, of course if we’re sort of saying what are the big barriers, is our, I know know what I learned in medical school. I, I learned about the kidney and I, yeah, I learned about sub parts of the kidney. But the fact of the matter is, even the sub components of the kidney, we label ’em with one name, but of course they have multiple cells within it, and not every one of those cells is behaving the same. And so there’s just a lot of biology at the single cell level. And fortunately we’re getting technologies to be able to study, all these complicated things about omics as we would often say, and doing it at a single cell level. There’s a lot of great science to be done and I and I will say, and maybe this is an important point to, to really make, is.

Eric Green: I do think sometimes when people talk about precision medicine and genomic medicine and multi omics of human health I think sometimes people think because, and they hear it from people like me and others who are very excited about it and we love to point out the home runs ’cause we love to demonstrate that, wow, this really can change clinical management. But I think occasionally people might, and especially younger people, trainees might get the impression that everything proximal to that has been solved. You know that, oh, now all the emphasis is on patient care and patient implementation. And I, every once in a while, just like to fully admit that everything we are doing that has gotten us there is cream skimming. We are, we’re just skimming the cream to be able to show how we can impact patient care.

Eric Green: But left behind in the wake is still the vast majority of fundamental biological knowledge that we need the next generation to pick up the mantle. Some that are gonna be doing overwhelmingly basic research that you know will be a bazillion miles away from clinical care.

Eric Green: And that’s okay. We need them because there’s every little step along the way that we have left unanswered questions. And one, one of the messages I would always like to give and I even think it applies to people doing bioinformatics data science, AI, is, you could say that’s what I’m doing, but you could apply that at the most fundamental level of how a genome works or how genomic variation influences genome function. Or you could use a, [?] to really help implement genomic medicine. But that full spectrum of activities will continue, I’m sure, for decades to come. And anybody who wants to get into that should feel very comfortable to know that there will be opportunities across that entire spectrum that doors are not getting shut.

Eric Green: We are just simply, just trying to open as many as we can and there’s so much more knowledge to be captured.

Grant Belgard: Where do you see the biggest gap between what genomics can do today and what the healthcare system’s able to absorb?

Eric Green: Yeah, so that’s a, it is a, it’s a great question. And you, the answer is there’s just lists and lists of reasons. What I’m learning and maybe even learning a little bit more in the most recent three months at a company that is global compared to my previous 31 years in a federal government that mostly focused on the US.

Eric Green: We, there’s a lot of interest in NIH about how healthcare is delivered worldwide, just getting my head around US healthcare was complicated enough. I, but whereas Illumina thinks more globally, there, there’s just, every possible complexity that you bump up against. And it’s different at every country, but one of the things I would like to point out, ’cause sometimes people say, ah, genomics, just, it’s so disappointing is you’re just not getting that clinical uptake. There is all this promise. I think, again, part of the problem is. Is you’ve gotta take a step back and just fully appreciate how new and how young all of this is.

Eric Green: And one of the points I always like to make is the word genomics didn’t even exist until 1987, which is the year I graduated medical school, and I say that because most of my medical school classmates are still practicing medicine and I got news for you. They never heard the word genomics once in medical school, ’cause the word didn’t exist. Okay? So you gotta feel a little– now, now I’ve gone off and become a genomics expert; they’ve been busy, treating patients and taking– and all of a sudden we thrust onto them all this new abilities in genomics. And, practicing medicine is really hard and they’ve got a lot of stresses and strains. They’re constantly fighting with insurance companies. They’re constantly dealing with a lot of regulatory issues and constantly dealing with a lot of hard problems. Then all of a sudden you throw this genomics thing.

Eric Green: I mean, we haven’t quite gotten to a point where this can be push button for them, and I’m very sympathetic, but why are we there? We’re, there, we’re victims of our own success. If genomics would just slow down for a while, then we’d have time to train the next generation.

Eric Green: But we’ve been so successful that we’ve now thrust upon the current medical system, a whole new set of things where they’ve never had any formal training. And oh, and meanwhile I would also, they’re also encountering, patients who either don’t understand anything about genomics; they, you have patients who actually know quite a bit because they’ve had time to to chat GPT it or to Google it. So sometimes, and I hear this from some of my medical classmates who I talk to they walk into a patient’s room. The patient’s already had their genome sequenced, they’ve already had all these entire, they’ve had time to do it. And the, my poor classmate never had any training on how to deal with the data, the patient’s way ahead of them. So we’re, we have a little bit of catch up to do.

Eric Green: It’s, some of the things I’m gonna be thinking about as Chief Medical Officer here is what do we do to think about genomic literacy enhancement for patients, for healthcare professionals? It’s, and it’s not just physicians. We gotta think about pharmacists and think about pharmacogenomics becoming so important. I think pharmacists can really be helpful here. Nurses, physician’s assistants, genetic counselors, so on and so forth. I think there’s that. I, then, the other example I would give is and this is where I think it’s both, it’s both a challenge now, but it’s also gonna be part of the solution is you don’t have to go– well, well, let’s just go back to the genome project completion 23 years ago.

Eric Green: 23 years ago, there were not really electronic medical records, at least not in the United States. Okay. And now everything is going to an electronic medical record. Now all of this, a lot the way medicine is practiced is interfacing with electronic health record systems but we have not been able to yet have seamless integration between genomic testing, genomic analysis and then get it all fed into an elect, electronic medical records and have it then be with immediate recommendations and all these things called clinical support tools and so on and so forth. Now, the, so the challenge is that we haven’t gotten us all together ’cause it’s all happening so fast.

Eric Green: But the good news is, is actually, these are all sort of made for one another. Genomic information is digital information. More and more medical information is digital information. More and more physicians rely on clinical decision support with popups and assist and blah, blah, blah. And so when we get to the point where we can get all this design correctly and if only we had time to build the airplane and then fly it, but we don’t because we gotta build it while we’re still practicing medicine. We’ll eventually get to that point. But what it does require is oftentimes health systems investing. The infrastructure to get the genomic information, to get it integrated in the health records, et cetera, et cetera.

Eric Green: And it’s not necessarily gonna generate money, generate revenue. It’s gonna be, you gotta make the investment in the short term to get the long term return. And some health systems are surging ahead and they believe it and some are not. And there, there’s just a lot of challenges associated with that.

Eric Green: And then, meanwhile you gotta deal the whole issue about reimbursement, who’s paying for this, et cetera, et cetera. So again, what is more complicated in society than healthcare. And yet what we’re trying to do is really change healthcare. We are, it’s not surprising that we’re seeing a lot of challenges come up.

Grant Belgard: What does good judgment look like in a field that’s moving this fast?

Eric Green: It depends who you ask. And and it depends where you sit, right? And it is it is interesting. And it even speaks to issues about, how when you have, nothing’s unlimited and certainly not, healthcare dollars are not unlimited. There’s lots of decisions that get made all the time of how do you distribute resources across an area and I, and the thing about genomics is that that there’s a lot of immediate utility, but there’s a lot more long-term promise. That, those of us like me really believe in this, but we know it’s gonna be a lot of work and we don’t know exactly the time. And so then what does good judgment look like?

Eric Green: People who are running health systems, people who are making these decisions are gonna have to make actuarial decisions about what problems they’re trying to solve that are here and now problems versus. As the famous Gretzky quote, skating to where the puck is gonna be, making the investment because you truly believe that you’re gonna be in a different place, that if a little bit of financial pain now will put you in a better position down the road and different, I can tell you different countries are tackling this differently for the same reason.

Eric Green: The different countries have different approaches to how they feel the government’s responsibility is with respect to providing healthcare to their citizens. Um, United States is not leading in genomic medicine implementation. That’s just a clear fact. And a few other countries are the, the UK in particular. When I was at the National Institutes of Health, I really, we were watching and interacting and really admiring what some other countries were doing, in part because they were experiments, right? All of us are a heart of, I’m a physician scientist. I’m an experimentalist. it was interesting to watch what other countries are doing. Now at Illumina I have a slightly different set of responsibilities.

Eric Green: And because we’re global, I mean we’re partnering with some of these other countries and their health systems and trying to figure out how we could be helpful and how can we collaborate and how can we facilitate the work they wanna do.

Eric Green: Because long-term goal is to facilitate genomic medicine and precision medicine implementation worldwide.

Grant Belgard: What first pulled you into this field?

Eric Green: That’s a great question.

Eric Green: So, So my story in the field of genomics, my story is a little bit of luck, a little bit of nascent insight and, I grew up in a science family, so it wasn’t totally shocking. My father was a scientist. It wasn’t shocking that I gravitated towards a science undergraduate degree. I watched my older brother decide to get an MD and a PhD to become a physician scientist, and that seemed like a good decision. And I, it felt right to me. I really liked the idea. I knew I always wanted to do science and research. I like the idea of combining it with becoming a physician. But up until the point that I graduated with a MD PhD, I was always– I got a PhD in cell biology. I could barely spell DNA when I graduated medical school and graduate school. ’cause I had done my PhD in studying sugar molecules attached to proteins, these things, glycoproteins.

Eric Green: I was very interested how cells try to sort their proteins within to go to different places within the cell to, to kick them out of the cell. And I really hadn’t thought much about molecular biology or DNA science, et cetera, et cetera. then I decided to train in clinical pathology ’cause it was a very light clinical training. ’cause I wanted to get back to the lab as soon as possible. And at the time there was some in my first, my internship year before I then became a postdoc and back in a research lab. There were some early things that were called Molecular Diagnostic Labs where they were just starting to look at DNA rearrangements in cancer by, by, by technologies that we almost laugh at now. But I thought that seemed interesting. And then again, remember when I graduated, the word genomics was coined.

Eric Green: There was a lot of discussion about this thing called the Human Genome Project. And my circumstance, that I stayed at Washington University where I’d gotten my MD/PhD for residency ’cause my wife was a medical student. And just so happened that Washington University had some of the leading founding folks in the field of genomics who were just leaders immediately and really helped catapult the field forward. And so I got to pick a postdoc mentor and I looked around, I said, I haven’t done anything in molecular biology or DNA science at all. And there’s talk about genomics and there’s these great people here. And I went to talk to one of them. And the rest is history. ’cause I just said, wow, this just seems incredible. They were talking about maybe a human genome project starting and they would be really poised to maybe participate. And so I said I should just build up my tool belt.

Eric Green: I knew biochemistry, I knew you know a lot about glyco biology, I knew about cell biology.

Eric Green: I said, oh, I should probably learn a little bit cutting edge work in DNA science or this thing called genomics. So that was, it was a naive idea. And then when I got into the lab, they started a year later talking about applying for becoming a center for the Human Genome project.

Eric Green: It just felt right. My project was right in line with what they needed to do in the Human Genome project. I just said I got all in, I just got completely mesmerized by this. I found myself suddenly working on the Human Genome Project on day one. I was a postdoc. I’m hiring technicians. Washington University was wonderful to me.

Eric Green: They said “You should just run this ’cause you’re, this is great. This is what, you could build your career in it.” And off I went. I had a vague idea if you took me back in time to 1988, when I made the decision what I was gonna do as a postdoc. I had a vague idea that you could connect the idea of having, if we really sequence the human genome, maybe the way we practice diagnostic medicine or clinical pathology, which was my, my clinical specialty, I could imagine some generation, two, three generations from now. Maybe you would have genomics become part of standard diagnostic medicine, but I couldn’t possibly have defined the timeline or the specific steps to get there. And maybe that’s the most gratifying thing of all is that, then I got involved in the Genome project, got recruited to join the NIH at the National Human Genome Research Institute.

Eric Green: Still never, you know, even when you go back 23 years ago, when we finished sequencing the first human genome by the Human Genome Project, it cost a billion dollars. This was still not in the realm of a clinical test that I, as a trained clinical pathologist, knew. But, but you know, we called for the need at that time for reducing the cost of sequencing DNA as a key thing to follow the Human Genome Project. Um, I was the one that helped craft a sentence in a strategic vision that NHGRI out that talked about how we needed to get it down below a thousand dollars. ’cause I knew a thousand dollars was a good cutoff for a clinical test. that sounded great at the time, 23 years ago, I said, wow, I can’t wait till my grandchildren realize that.

Eric Green: I never thought it would happen on my lifetime, my professional lifetime, let alone on my watch as NHGRI director. But all those things happen. So, And even now, I’m just continually surprised, which is how fast things move. Such that, the fact that I am now existing at a, as a CMO at a company that truly is going to help make genomic medicine a reality worldwide is pretty, pretty remarkable.

Eric Green: And I could I can’t take full credit for having the vision, back in 1988 or whenever that, what this was gonna lead to. But I could see the general direction, but I just feel incredibly lucky that it’s all happening in, in my professional lifetime.

Grant Belgard: What other choices changed your trajectory the most?

Eric Green: I think what other choices, if, when you think about it some choices were, mine and some choices weren’t always mine. One of the, the things I always like to tell young people is. By the way, you don’t ever look at more senior people and think they had a life plan where everything was laid out and don’t even think that they even were in control of all their decisions because a lot of things develop and things. Some of it’s just luck and some of it’s personal, right? It could be, what you have to do as part of your family in terms of when you can move, when you could not move. But I never saw myself, I never saw myself going into the government. I just it wasn’t something that occurred to me. And then one set of circumstance, you know, I thought I was gonna be an academician. I thought I’d be at a university forever.

Eric Green: And I I was an assistant professor at Washington University in 1990, starting in 1992. But nobody ever saw it coming that, that Jim Watson, who was the first director of the Genome Institute and launched the Human Genome Project, that he would end up departing NIH unexpectedly, leaving the Human Genome Project without a leader. All of a sudden, Francis Collins gets recruited to take over the Genome Institute and he says, I’m only gonna do it if we can create a government based genomics program called the, it’s called the intramural program. All of a sudden they say, yeah, you should do that. And Francis immediately tried to recruit a bunch of top flight genomics researchers and genetics research.

Eric Green: He called me up and all of a sudden in one phone call, I completely changed the trajectory of my life. I went from academia and jumped into the government having no idea what I was getting into, but it was, it turned out to be a wonderful opportunity. And within two years I was taking on leadership roles.

Eric Green: I took several, I was able to start a sequencing center and then I was even able to become the director of the institute and then things changed for me. A year ago I retired and and I was I retired from federal service ’cause I was retirement eligible after 31 years. even then, I didn’t know exactly what I was gonna do and I, but I was given a new chapter to explore it.

Eric Green: I, my immediate gut said, go back to academia. And I tried to do some of that. I explored some options. I did some consulting. I also started talking to some other organizations for consulting and and I, all of a sudden was approached by Illumina and it’s it really was almost like instantly, oh my God, this just makes complete sense. And and part of it is, I, it wouldn’t have been just that way for any company. I think it was I’m immensely proud of my time of at NHGRI, and I always say it’s like the icon of genomic funders. It is. It is the top flight one. And I feel the same way about, I’ve always felt the same way about Illumina. They are the icon of genomics companies. It’s, to me, the top one. So all of a sudden when they called me and said, chief Medical Officer and the way it was gonna be formulated was just perfect for me and my family. It was a really easy decision.

Eric Green: I just never saw, yeah, I never saw it coming. And if actually, if. And I had been out looking at jobs and really thinking through what do I wanna do? Where do I wanna, how do I wanna do it? And it just, it hadn’t occurred to me. And although I, to, to some extent it, I was very involved in talking to lots of people and it started through a set of conversations I had, including with the person that eventually became my boss here and the CEO.

Eric Green: So I was open to lots of conversations. I just didn’t see it all falling together until all of a sudden it just did.

Grant Belgard: It’s I’m guessing you’ll have to reach far back for this, but when in your career did you first start to think well beyond individual projects, towards bigger systems?

Eric Green: Yeah, I think implicit in your question is just taking a very big picture view. Of and of scientific challenges. And in some ways it, that was part of what I found very appealing about the Genome project. And if I think about my my graduate work, that was very traditional. Although even then most people have one PhD mentor. I had two. I know. I just immediately saw the opportunity to cobble together that and I also would say that even then, I really enjoyed collaborating with people, some graduate students, some PIs.

Eric Green: I just like working themselves, do my project. I was always very collaborative. Then there was, the Genome project was all about being collaborative and all about being selfless and not worrying about, you really were part of this massive enterprise of thousands of scientists around the world. And really wanna point out for, especially people don’t realize that now we just take that for granted that you know now, you look across biomedical research around the world and there’s still some individual labs, lots of them and individual projects, but consortium science is very accepted. Papers with hundreds of authors, very conventional, you know, now we see that all the time, but back then it was almost frowned upon. Or certainly some people just were uncomfortable with it.

Eric Green: I can certainly tell you that even when I went out looking for jobs in 1991, when I became, you know, not all universities were so, you know, they, I literally applied and got interviewed by some universities in 1991 and they were really interested in having somebody who had some genomics expertise.

Eric Green: It was still a very young discipline. And you’d go there and they’d say what are you gonna work on? And I’d say, oh, I’m gonna keep working on the Human Genome Project. And they said, oh, that’s like really cute that you’re working on the Genome project, you’re not gonna build a career on that.

Eric Green: What are you really gonna do when you grow up? And it’s like, no, no, I’m really gonna do this. And it quickly became apparent that was not a university I wanted to go to. I will say over the years, universities have had to decide whether or not they’re comfortable having their investigators be part of these big consortium, because the genome project was the first of many just in genomics.

Eric Green: But now we’ve seen it in neuroscience, we’ve seen it in microbiology. We see it all over. For some science consortium based work is the way to go. And especially as science gets more complicated and more technical, you need a dream team of interdisciplinary experts and you gotta, you, it’s like a Noah’s ark kind of a thing.

Eric Green: You need to have two people that really know genome sequencing. Two people that really know AI, two people that really know biochemistry, two people that really know physiology. This is how you move big things forward. My thinking about what I what, and it’s not for everybody, but it’s, it meets my personality extremely well. I had, I’ve been thrilled and fortunate to be able to be part of consortium as the Genome Project and things like Encode and some other programs like that. But then in 15 years as NHGRI, director and NHGRI is the poster child of running a consortium. We ran a bunch and we even did some that were NIH wide, even beyond our own institute because NHGRI showed tremendous leadership for NIH Common Front efforts like. Human Microbiome Project, like the human heredity in health in Africa, H three Africa program.

Eric Green: that’s, that’s, this is our expertise for many years and still is. NHGRI really is the leader in how to run consortium based science.

Grant Belgard: What did you underestimate about leadership earlier in your career?

Eric Green: What did I under I think I would say what I underestimated about leadership early in my career, which I always chuckle about, is that, you just had no formal training in what you were being asked to do. You know, and whether that leadership is just running your lab or running a small, like a branch or a department or running a center or running, an entire institute is, all of that.

Eric Green: When you really think about even just running your own lab, it’s like running a small business, right? You have to deal with bringing money in. You gotta balance your budget. You gotta, you have personnel issues. You have, those can get complicated. You gotta hire, you gotta fire, you gotta discipline, you gotta encourage, you gotta mentor, as you’re not really taught much of that.

Eric Green: And sometimes you and then as you take on more and more leadership roles, the res roles and responsibilities get bigger and harder. I will tell you, when you’re at the top of an organization like the yuckier the problem, it’s gonna go to the top. So all of a sudden you’re dealing with things you just can’t even imagine you ever had to deal with. You just don’t realize it until you’re there and you real. But on the other hand, what makes great leaders is I think, and I could talk a lot about leadership. But, two things I think that are absolutely essential is one you’ve gotta just be completely ready to be a lifelong learner of skills.

Eric Green: You just can’t assume that you’re going in and you’re gonna just know what you’re doing. You’re gonna learn it because you have not been taught. But the other key aspect of it is you have to learn how to surround yourself by outstanding people. You have to have the ability to just be very comfortable delegating to them, trusting them, and you have to develop incredibly strong relationships with your immediate folks around you.

Eric Green: ’cause it is a team sport. You run something like an NIH Institute, it is a team sport. And when you’ve got a great team, you’ve got a great institute. And when you, and it’s, you gotta cultivate that team. You gotta pick ’em carefully. You gotta nurture ’em, you gotta mentor ’em. And you gotta let ’em tell you when you’re being wrong and you gotta be humble and be ready to learn and adapt. But it’s it’s critically important. You’re only as good as your, as the team that you surround yourself with.

Grant Belgard: Now for the question you know is coming. What about AI? What are your expectations for the impacts AI will have in the coming years and the new and new challenges it may pose as well.

Eric Green: Yeah it it’s just it’s the same question you could almost ask anybody on the street about society. It’s, you’re just seeing it everywhere and it’s remarkable. Here’s what I, here’s what I would say is it’s almost impossible to even claim your an, for me to claim I’m an expert in this other than I, I can just watch what is happening and it is like everything else it’s just changing in a breathtaking way. Practically measured week by week. You can just see this what I would point out is that not that AI is an incredibly important in all the other ways of everyday life that it’s now finding itself. I, you know, I’ve been saying even before this incredible uptick, so I probably was saying this 5, 6, 7 years ago. Is it’s this humbling nature of, of the genome that I spoke about earlier, that it is just so incredibly complicated.

Eric Green: And the more we dig, the more we realize it’s even more complicated than that. And it’s so humbling. It’s only 3 billion letters and it’s just amazing how much it does to create and operate a human being. And then you realize how incredibly complicated non-coding DNA is, for example, and it’s all a language issue that our, the human brain is just struggling getting our heads around that. It just, this is just seems like the perfect marriage. It just seems like the perfect application is to bring this in to be able to see, generate these massive data sets.

Eric Green: So we’re good at generating the data. We’re just not good at extracting the knowledge from it. It just seems like you know that it’s a match made in heaven. But the other aspect of it is, it’s what I’ve seen in particular in the last 10, 15 years, is that it does attract the best minds. And that’s, that gives me a lot of optimism.

Eric Green: So some of the best computational biology, best AI experts really see this opportunity in biology. And then, and that’s just in the genome. And then of course, if you start to pivot us into sort of the genomic medicine, precision medicine realm, you start layering into that other omic data and other data about ourselves that we capture environmental data, physiology data.

Eric Green: And then you marry that with electronic health records. You know, It’s this big bouillabaise of data that, sounds really great. You wanna integrate. Holy cow. The complexity of that data integration process is we’re we actually, it’s not that we’re gonna benefit from AI. We absolutely, desperately need it.

Eric Green: We’re never gonna get through it without it. It’s like, to remind people that 23 years ago when the genome project ended, I remember we tried, at NHGRI, we tried to convene a workshop. we said, Hey, look at us. We’re really cool. We got 3 billion letters of the human genome finally elucidated. We’ve got a big data issue and I remember we tried to convene a workshop and we invited a whole lot of the, some of the best computational biologists from Harvard, Stanford, yeah princeton all, and we were a little disappointed. A lot of people just weren’t interested. They didn’t wanna come to this workshop.

Eric Green: And normally they would come to NIH workshops and when you would talk to them, they’d say, we’re really big data people, this is climate data, financial data, you, 3 billion, you don’t really have that much data. And it was very humbling ’cause we were drowning in these 3 billion letters. That’s completely changed now. And I think you’ve seen it ’cause the technology uptick, lots of genomic data, a lot of other omic data and obviously electronic health. So now the one thing, unlike 23 years ago now, the best and the brightest come and they wanna work in this area because, ’cause we finally got to the big data stage, even though we thought we were there before.

Eric Green: We weren’t until now or until recently.

Grant Belgard: What advice would you give someone early in a genomics or bioinformatics career?

Eric Green: I would probably have a lot of advice to give them the fir, The first thing I would advise them and ’cause I’m, and is: don’t worry. What I first find about young folks these days, they just worry a lot. And I, and I see this in my own kids just, it’s a generational thing. They just worry.

Eric Green: And yet all I see is opportunities. All I see is in incredible, a spectrum of things to be done that, that are really meaningful, important problems that I am quite hopeful there’ll be great employment opportunities, and I know we hit speed bumps and some years are better than others.

Eric Green: And I know we’re in a rough period now but I really do see this incredible set of opportunities and I hope people don’t get so worried. They say, Ugh, I don’t want to go into life science. I don’t want to go into medicine. I don’t wanna go into biology, so forth. So first thing, and then, but the other thing I would say is and part of what they’re worrying about and it gave, was related to the story I told you earlier is worry that you can’t map this out for the next 20 years. Just what I constantly tell people is pick something that really gets you excited, almost to the point where you can’t sleep in the morning. ’cause you just wanna get back to doing what you were doing. And if you’re not that excited about what you’re doing, find something else to do.

Eric Green: And if you’re, if you wanted to be in the, and I think as much data science and AI and all, those are great tools to pick up, but they’re so applicable in so many different areas. Make sure you’re excited about what you’re working on and if it’s, and if you don’t, and also realize the opportunities are gonna change over time and doors are gonna open that you never could have anticipated. And and just be enthusiastic and excited. And if you’re not enthusiastic, excited, find something else. ’cause at the end of the day, there’s plenty of opportunities and chances are if you have enough curiosity that you wanted to get trained in computational biology or data science, AI and so forth, I’m sure you’re gonna find something you’re gonna get excited about.

Grant Belgard: What skills are rising in importance faster than people realize?

Eric Green: You know, well, one of the I think I’d say is I, one thing I get a little worried about is that the, you know, especially around my younger people is the pandemic was very isolating. now there’s a lot of a lot of abilities to do remote work and to be very isolating professionally. And I think one of the skills, a little and I’m allowed to worry a little. I don’t worry a lot, but I, one of the things worry a little bit about, And maybe if in the terms of advice is, don’t get too comfortable just being isolated and feeling like I’m just, I actually think one of the really important things that are underappreciated interacting in person with people. Maybe not every day, maybe not but just recognizing that human interaction, especially in in, in the pursuit of advances in science or in medicine, that human interactions are really important.

Eric Green: Some of them could be fine virtually, but they can’t all be fine virtually. I just wanna make sure that the mixing bowl of strategizing, discussing, debating, interacting, And and developing a relationship I think is so important. All this, one Of the things, and I, again, I say this all the time, I think a lot of people a lot of people who are not scientists think that, um, science is a very asocial profession. They think, oh, they think of the scientist at the bench just pipetting and thinking great thoughts and writing great papers. science is one of the most social things I know.

Eric Green: And I’ve, and my career throughout has been overwhelmingly benefited by interactions and then at the extreme interactions at the consortium level where, you’re interacting with people all around the world and you’re, and I’m just worried about the recent trend of, the pandemic and isolating and the ability to exist and work virtually and interact virtually may take a little of the momentum away from what I think is one of, beneficial parts of science, which is being a highly social endeavor. I just would caution people about thinking the perfect job is one where they never have to interact with people. ’cause I think that the interaction is really important, including in-person interaction,

Grant Belgard: So on, on that note. What do you find makes a mentor relationship most useful.

Eric Green: The mentor mentee relationship. Most useful. I think it’s, I think it’s one Having the mentee’s interest mind and not let anything be cookie cutter. you know what? I always tell people, I and I mentor lots of people in lots of ways. Even today, I’m still mentoring lots of people. I can tell you on my calendar this week, there’s like two or three meetings I’m having mentoring folks the, you know, who are late in their career, middle of their career, early in their career, gets a life being mentored as a lifelong endeavor. I’m still getting mentored.

Eric Green: I, I got news for you when I became. The, The CMO I’m in a whole new world. I’ve been having conversations with some of my lifelong mentors just ’cause I think bouncing ideas off of them. What, it’s not cookie cutter. And the other thing is the most important thing for a mentor to realize is their goal is not to replicate themself in the mentee and make a mini me, to help guide a person who let them be who they are and even if they’re radically different. In fact, what I always tell people when I give ’em advice is have role models and you should have anti role models. and even your role models, there may be half the things that you wanna emulate in your role model, and half the things absolutely not emulate in your role model. You should pick and choose and feel what’s comfortable for you and pursue that.

Eric Green: So I, I just think there’s sort of an open-mindedness that you can’t, and, and I think if a mentor is way too much about I’m trying to make widgets, and this is the parameters of that widget, that’s just the wrong approach to mentoring as far as I’m concerned.

Grant Belgard: What question do you wish people ask more often?

Eric Green: What question do I wish, you know, you mean like when they’re entering their career?

Grant Belgard: Yeah. Yeah.

Eric Green: Yeah I wish, people would ask, or just be show I I actually, maybe I like it when you question the journey about how you got to where you are. As opposed to, because what I sometimes find that’s humorous is they’re, going through the process, they’re so fixated on asking questions like: take a third semester of calculus? Should I take physical chemistry or not take physical chemistry, especially those who are really trying to get into competitive programs, either medical school or PhD. And I just, I just think some of those are sort of the, the wrong question and I just wish they would ask more people about their journeys so that they realize that everybody’s journey is different and that they shouldn’t try to put themself in a trajectory that is well-defined because there’s no such thing as a single route to get to a destination.

Grant Belgard: And to wrap up what are you most excited to learn next?

Eric Green: To be honest with you, maybe the answer I would give is what I am most excited to learn next is how I can be impactful in a whole new setting, one that is focused on the same goals that I had in the previous three decades. And what I mean by that is, I feel so fortunate by having the career that I had at the National Human Genome Research Institute and I, laser focus, if I had to summarize what we were trying to accomplish, especially me as the director, was, can we make genomics truly improve the practice of medicine? I am now in a completely different role in a completely different part of the ecosystem. And yet I’m, we’re trying to do the same exact thing. And, so what I am most excited about and what I really most wanna learn is what can I do to, to help Illumina in their role in the ecosystem. Truly see genomic medicine and precision medicine become a reality.

Grant Belgard: Eric, thank you so much for joining us.

Grant Belgard: It’s been a pleasure.

Eric Green: Absolutely. It’s been a great conversation and good to see you.

Transcript of Episode 83: Jenny Yang

Disclaimer: Transcripts are automated and may contain errors.

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Grant Belgard: Welcome to the Bioinformatics CRO Podcast. I’m Grant Belgard. Today I’m joined by Dr. Jenny Yang, co-founder and CEO of Outpost Bio. Jenny works at the intersection of biology, machine learning and precision medicine. At Outpost, she and her team are building a platform that pairs automated experimentation with machine learning to better understand how microbial communities shape drug response, nutrition and health.

Grant Belgard: Before starting Outpost, Jenny studied engineering, physics and bioinformatics at UBC and completed her doctorate at Oxford, where her work focused on clinical machine learning. We’ll talk about what she’s building now, the path that brought her there, and what she’s learned about building important things at the edge of science and computation.

Grant Belgard: Jenny, welcome.

Jenny Yang: Thank you Grant, excited to be here.

Grant Belgard: I’m excited to have you. So for listeners just meeting you, what are you spending your time on right now and what are you trying to build?

Jenny Yang: So really we’re trying to make human microbiology computable. So what that really looks like day to day is we have team members in the wet lab and team members on the dry lab side working on machine learning models. So in the wet lab we’re actually, sourcing human derived microbial communities, running perturbation assays and taking multi omic measurements.

Jenny Yang: So think, metagenomics, sometimes transcriptomics, definitely metabolomics. So really trying to understand communities of bacteria before and after. With different chemical compounds and how those microbial communities actually break down these compounds. For example, microbial communities from the gut.

Jenny Yang: How do those break down a drug chemical or a food molecule? And then in the dry lab, we’re building machine learning models on top of this to help create tools that will allow other people to do their own analyses on these microbial communities.

Grant Belgard: What problem keeps you most intellectually stimulated right now?

Jenny Yang: I think I’m definitely motivated by the question of. How can we make meaningful pushes forward in the field of personalized health? I’ve definitely spent a lot of my last 10 years of my adult career looking at human genomics, and I’ve seen incredible advancements in that field. We can identify, exact mutations that lead to certain subtypes of disease and even choose targeted therapies towards that disease. And I really want to understand why despite all this progress, we still can’t push forward improvements in clinical trials and drug development. So the metric I like to show is that 90% of drugs failed 40 years ago and 90% of drugs are failing during clinical trials today. So why have we not pushed forward that metric despite all these huge advancements in the field? That definitely does keep me up. And I feel like the next addition of biological information that needs to be added to this picture is really all the microbes that are in and on our body that affect how we all independently experience health and disease.

Grant Belgard: So for what you’re doing what is the most difficult aspect of the problem from the biology side and what’s the most difficult from the data or a modeling side.

Jenny Yang: Definitely on the biology side it is reproducibility and scalability of these experiments. So when people have been doing microbiome based analyses in their own respective labs, there’s bias that’s going to exist. So it’s been really hard to reproduce findings in one lab to another lab. And then also scaling up these experiments is hard.

Jenny Yang: So if we specifically focus on the gut microbiome, these are anaerobes that we’re dealing with. They have to be in a oxygen free or really oxygen low environment to keep them alive and actually perform experiments. So scaling that process up is very difficult. So when we first started the company, we knew we wanted to focus on both developing a high throughput method that could perform these perturbation experiments, but also make sure we cross validate findings in the lab.

Jenny Yang: So not only do we generate our own data in our lab, but we’re making sure to generate external data sets with other partners just so we can demonstrate that our findings in our lab can be reproduced elsewhere. And in the, on the computational side, we’re dealing with a very high dimensional space.

Jenny Yang: So even compared to human genomics where there’s only about 20,000 genes, the gut microbiome can have up to 150 to 250 times more genetic diversity there. So it’s already a much more. Complex space that we’re dealing with. And again, bringing it back to human genomics between you and I and everyone else in the world, we share 99.9% the exact same human genome.

Jenny Yang: But if we look at our gut microbiomes, we can be up to 90% different. So not only is there huge individual variability, that multiplied with the diversity of bugs that exist in our guts. That is a huge computational challenge. So without the sophisticated machine learning models that we now finally have, as well as the cloud compute infrastructure that we now have, this is just such a huge problem that we couldn’t have tackled before. So that, that level of complexity, I think is what makes it very challenging on the actual computational side.

Grant Belgard: And can you tell us more about the stage you’re at right now with Outpost Bio and what your role actually looks like week to week at this stage?

Jenny Yang: Yeah, absolutely. We have been a company for one year. We raised our pre-seed last July. So that was a 3.5 million round and really the focus of the past year and. And the rest of this year as well was validating our wet lab method and starting to build initial machine learning models and really benchmarking against current state-of-the-art models and benchmarking specific problems. Just to demonstrate the usability and the accuracy of both the data we’re generating and the models we’re, we’re building. My day to day has. Changed significantly from when we first started the company to now. So really when we first started the company, a lot of it was making sure we build up a vision for the company that could inspire people, but also we could see ourselves growing into over the course of the company.

Jenny Yang: And that really is trying to make human microbiology computable so we can improve personalized health. And then it moved into building up our values. So when we hired, we really wanted to make sure that we built up the culture that we were looking for. So not just look for the technical skillset, but also just the cultural fit for the company we envision having.

Jenny Yang: ’cause when you have such a small team, at the beginning, culture is really everything. And I still believe that one year down the road, and now it’s really transitioned into. Just a little bit of everything. We have so many different things going on at the same time. So we have a wet lab in-house that we just opened last week. We have multiple models being trained. A lot of partnership conversations with potential customers, so I have my toes in everything. But the team, is fantastic on, on staying organized, so it’s been very exciting.

Grant Belgard: What decisions do you feel you still need to hold closely, and which ones are you happy to let others own?

Jenny Yang: I very much believe in this quote that I think Steve Jobs and probably a lot of people have said, which is, basically you hire incredible people and you shouldn’t be telling them exactly what to do because you hired them to tell you what the right thing to do is.

Jenny Yang: And I, I really believe that. So we wanted to be very rigorous on the scientific side. So we hired a VP of RD with a lot of experience in microbiology. This is Heidi. She’s trained in incredible labs and she’s just so good at what she does, and I would never want. Want it to be me telling her how to do good science.

Jenny Yang: Like I can point her in the direction that we’d love to go as a company, but I really trust her to be the expert in what the position that we’ve hired her for. Same with Seth and Nathan on the data engineering and machine learning side of things. I’m very happy to let them do the tasks that they think are right to reach the milestones we want to reach. And I think that’s really important because especially at a startup where there’s so many things that need to get done as one person, you just can’t do it all. And you’re gonna have to have trust in your team to, to do the tasks that they’re the best at.

Grant Belgard: What tradeoffs are you navigating between scientific depth and execution speed?

Jenny Yang: I think a big one is the trade off between generating a lot of data really quickly, really broadly, or generating a bit less data, but focusing more in depth on specific verticals. And that is a trade off because we are trying to build a foundation model. And that term in itself suggests that you have a lot of data to build this large machine learning model that’s going to be generalizable. But I do believe because we’re tackling such an important problem that has to do with pushing forward human health and our understanding of it, we have to be scientifically rigorous, especially if the tools we’re creating are meant to be used by other scientists. There’s a level of validation. And scientific rigor that’s really needed for people to trust that you’ve built something that is usable and accurate and if they implemented it into their own work, which is very important that being rigorous and deciding to use our tooling. So especially at this stage of the company where we are trying to make sure we prove that we can do what we say we can do, We are making sure that we focus really rigorously on validating specific verticals, so we won’t go hugely broad and generalizable at the beginning. We’ll demonstrate that we have a method that can lead us there down the road but we need to be more rigorous on proving the science in specific niches first.

Grant Belgard: On that note. How do you think about robustness, bias, and generalizability when the biology itself is so variable and complicated?

Jenny Yang: Yeah, so I think about this a lot. When I did my PhD, I specifically focused on bias mitigation and machine learning generalizability. So from the wet lab side, we are generating data in-house. But we’re making sure to have additional partners generate subsets of data for us. So we’re working with a West coast US institution as well as a CRO, and we’re making sure that they generate buckets of data so we can validate findings externally across sites.

Jenny Yang: And that is really to demonstrate the reproducibility of the wet lab methods we’re using. We’re also. We’re also making sure that we validate machine learning models, so having external data sets from different sites can then demonstrate the generalizability of machine learning models. And we are making sure that we evaluate both metrics of accuracy and metrics of bias because we wouldn’t want to see model performance being dependent on where data is generated.

Jenny Yang: Ideally, it would be based on the actual science itself.

Grant Belgard: What would a truly meaningful win look like for you over the next few years?

Jenny Yang: I think something meaningful would really be demonstrating that the systems we’ve built both in the wet lab in vitro and the in silico systems we’ve built in the dry lab translate to actual h uman outcomes. So another form of validation that we really think about is how can we validate on actual human cohorts or clinical cohorts. And that is something top of mind. So we are making sure we’re working with scientific advisors that are actually running clinical trials or working with groups of patients. We have a project coming up in, in the summer specifically focused on a cohort of patients that we’ll collect samples from, and then make sure that we validate our, both our in vitro and in silico methods again.

Jenny Yang: So I think a huge win would be demonstrating that translatability into the real world. Another win that I think a lot of the team is really excited about is demonstrating that we can actually generalize between, a community of bacteria interacting with a molecule and leading to a certain biological outcome.

Jenny Yang: I think that would be incredible to see that microbiology does follow, some sort of pattern that can be predicted.

Grant Belgard: What turns a biological data set from merely interesting to decision grade?

Jenny Yang: I think that’s a super good question. And it might depend a lot on. Also the question you’re looking at and the industry that you’re trying to implement this in, for example, like there’s a lot more rigorous testing that needs to be done within drug testing versus maybe developing a consumer good. But I think for us it’s making sure that we do focus on certain verticals and then. Validate and calculate metrics that are needed at proof points that are needed for the specific problem, its itself. So there is a little of bespoke kind of tailoring needed for some problems, but I. I feel like it’s in general across all spaces, we would wanna be able to generalize across multiple data sets that are coming from the field, multiple problems that are related to those data sets and demonstrate it with really external partners because we can do a lot of testing ourselves, but when you actually bring it into the real world and it’s in someone else’s hands and not really in your control, that’s where you would wanna be able to demonstrate usability and, a certain level of accuracy there.

Grant Belgard: What does a strong feedback loop between wet lab work and computational work look like in practice in this space.

Jenny Yang: This is super important to us. So when we first started the company, a lot of people told us, make sure you keep your wet lab and dry lab close together and make sure communication is good between the two. ’cause it’s like completely different languages that these scientists would be used to speaking. So for us, we very much believe in having this quote unquote lab in the loop. So the experiments we generate in the wet lab, we make sure people on the computational side understand these experiments are part of the decision making process. Because they need to understand the data that they’re getting and what kind of problems the data can actually solve.

Jenny Yang: Like what kind of outcomes are coming from this wet lab data that they can build a model towards. And then the findings in the wet lab will inform a lot to the to the scientists in the wet lab because. The people from the dry lab will be able to communicate the quality of the data that’s coming out the accuracy of the models where bias exists.

Jenny Yang: So if bias exists in one section, maybe we need to be generating specific data sets targeting that. So we, we definitely believe in just really good communication all across and making sure everyone’s involved in understanding the overall experiment.

Grant Belgard: When you evaluate a possible collaborator or a partner, what signals make you excited?

Jenny Yang: I think people who are really interested in getting to a mechanistic or causal understanding of their food product or their offering. So one example or really any ingredient manufacturer, they wanna understand how, their ingredient or molecule will perform differently across different populations based on their microbial makeup. And also people who are trying to add another level of personalization and provide more of a personalized understanding to their clients. So you can think of people trying to come up with personalized diets for different individuals. Companies that are, that have an app that help you understand your gut microbiome and how that affects what you should eat. So really anybody who’s trying to put a molecule in or on you and wanting to understand the effects.

Grant Belgard: Where do you think the field still confuses correlation with something more actionable?

Jenny Yang: I think there’s definitely a lot of difficulties getting to that causal or mechanistic level. So I think a lot of the field previously has been just focused on correlations. They’ve been saying these communities of bacteria exist and they might lead to better or worse health. They might suggest that you should have these foods versus others. And I think it’s just still very present at that level. We’re really just at the cutting edge of being able to start getting down to the mechanistic level at a scale that just wouldn’t have been, we wouldn’t have been able to do before. So I think there, there is a little bit of an onus on us to demonstrate that this is scalable.

Jenny Yang: ’cause I don’t think people will necessarily be able to implement this high throughput until they’ve seen it demonstrated to a level that they believe they can trust it. So I think there is a lot of work to be done there.

Grant Belgard: What do people building tools for life science often misunderstand about adoption?

Jenny Yang: I think something that I’ve realized over my time in working in machine learning is that. A lot of people immediately expect machine learning models from one place to work really well when it’s brought to an external setting. And I think the attitude with foundation models is one that I believe in a bit more, which is that a foundation model is a starting point to help you fine tune to creating that really high quality model for your own application or your own purpose.

Jenny Yang: I think. Getting to generalizability in such a complex and diverse field, like anything related to biology or microbiology especially. It’s gonna be really difficult to assume that there’s one machine learning model that’s going to work for all. It’s analogous to what we’ve said about the one size fits all model in, in medicine as well.

Jenny Yang: It’s hard to believe that there’s one medicine that’s just gonna work across. Everybody and work every time. I don’t think we should have that belief for machine learning as well. So I think the foundation model space has really opened up the understanding that you start with a model that’s going to bring you to 80% of the way of solving your problem.

Jenny Yang: But if you have your own data sets that are built in the context of your own setting and the problem you’re trying to solve, if you fine tune on that data set, then you’ll be able to build a really strong machine learning model for your own purposes. So I think bringing tools into the life sciences, should not be like just flat out expecting that there’s one tool that’s going to work perfectly across every every team, every problem, every setting.

Jenny Yang: I think there needs to be care into fine tuning these models.

Grant Belgard: Couldn’t agree more. If you could instantly fix one part of the big data ecosystem, what would you change first?

Jenny Yang: I think language modeling, so like chatGPT and all these different large language models that have come out has demonstrated that you can scrape the web of its data and build really strong models that are general purpose and can be used by a lot of people. I think that is it’s a really effective problem and it works for language modeling, but that’s not something that necessarily translates to biology.

Jenny Yang: So I think you see a lot of companies coming out and people building models on all the biological data that they can scrape from the web. And I’ve definitely seen this in the field we’re in right now with the microbiome, but there’s so much bias that exists depending on where you get this data from, that I think it would be very hard to say that you could scrape the web of all this biological data and get to a general purpose model that will understand the problem. Because a lot of these data sets have their own scientific processes. The measuring tools are different. There’s just so much bias that is not controlled that I think it’s a hard attitude to bring into the life sciences. I think you can leverage public data, but I think at the end of the day you need control and confidence over the biological process that you use to generate this data. I very much believe that, especially in machine learning, it is garbage in, garbage out. So as much as you can leverage the public resources, you should, but you should take care into, again, fine tuning, using high quality data that you genuinely are very confident in for the problem you’re solving.

Grant Belgard: What first pulled you toward biology computation and the overlap between them.

Jenny Yang: I’m honestly not too sure. When I started undergrad I was in engineering physics and really working on like robotics and systems engineering. And this was around the time where machine learning was really starting to ramp up and there was a lot of hype around it. And I think naturally I’m just attracted to novelty and learning new things. So I wanted to try machine learning and when I first stepped into it, I was essentially just scraping the web of a genomics database, building a small program that would analyze it, like really simple analysis. And then I just cold emailed 20 different professors at UBC and then. Asking if I could demonstrate what I’ve built. And then Steve Jones he actually just offered me a job after he saw that program and he runs a research lab at the Genome Sciences Center and works very closely with clinicians all working on personalized medicine for oncology. So I spent a summer there and then just fell in love with the intersection of getting to actually work with clinicians to develop something that’s usable by them and would benefit patients but also bioinformatics and machine learning teams on big data challenges. And ever since then I basically asked Steve for a different position every year. I was still in school at this point, so like I would ask to come back in the summer or do a directed studies program with him, and I just kept coming back to the problem and falling more and more in love with it.

Jenny Yang: So that’s just what started me on the journey. It felt like just a positive flywheel that I’ve never jumped off of.

Grant Belgard: Looking back, what early experiences most shaped the way you go about choosing the problems you work on?

Jenny Yang: I, I think I always start with the clinical significance. So when I was at the Genome Sciences Center, the clinicians would always tell us about the problems that they or like the way that tooling could help their processes. There were models that were being built that would try to take genomics information and then predict the subtype of cancer. There was, so that’s like a decision support tool. There were teams that were working on creating annotation systems for automatically annotating histology images and marking out where tumor cells were. And that was part of my Master’s project as well. And I really believe that translational AI can be so effective.

Jenny Yang: You do have to make sure that it works with the clinicians or the people that would actually be using these tools like you. It’s if you come in as just a machine learning researcher, create a tool that you think is useful, it might not actually work with the workflow of a clinician that would be using it.

Jenny Yang: So I think I’m always driven by, let’s start with what can help the people that would be the end user of this tool. And as I’ve moved forward, like through my PhD. And then now with Outpost. I think another thing that really interests me is where are we starting to generate new data sets that we couldn’t have generated before that can unlock insights for more people, more broadly.

Jenny Yang: So I, I definitely have seen kind of the AI for drug discovery and all other biotech fields move towards data-driven analysis. So I know high- quality data that could be used for a lot of different downstream tasks is very valuable because that’s what that’s really where I believe the field is headed. so the microbiome field was really an interest to me at this point because the field of, for example, metabolomics has allowed us to actually study biochemical reactions and get down to a mechanistic level of what’s happening in the microbiome. So that means we can potentially unlock new data sets that we wouldn’t have access to before, at least not at the scale that we could have now which can help solve a lot of problems in a lot of different fields. So I think that’s been a more recent excitement for me.

Grant Belgard: What were some forks in the road that turned out to matter a lot more than they seemed they would at the time?

Jenny Yang: Ooh, this is a great question. I think one decision that we really had to decide on was at what point do we open our own wet So when we first raised our pre-seed funding, we did have the thought that we would just outsource all the experimentation, part of that is cost savings and just efficiency.

Jenny Yang: We assumed that CROs would have the capabilities to just do the experiments we wanted to them to do, and we ended up opening our wet lab t his year. And that’s not something we planned on doing for the first fundraise. And it ended up being really an important decision because what we learned is that what we were trying to do is really specialized.

Jenny Yang: I think we talked to over 60 different CROs and just couldn’t find one that could do what we did. And we had to really work with the CRO that we ended up working with really closely to develop these experiments. And yeah, bringing it into the wet lab, I think it’s really allowed us to speed up. Both data generation ended up becoming a cost saving because we could just move faster. We’re not paying for like external labor of doing the work as well, and we can just test a lot of different variables that we wouldn’t be able to really do with a CRO without adding costs and like extending the time of experiments. So that ended up being a really good decision for us. I think there is something to say about having control over, just what gets done and at what time and what speed.

Grant Belgard: What made you decide that building a company was the right vehicle for the problem you cared about?

Jenny Yang: I had I, so I’ve always been someone who’s been very motivated by the mission that I’m working on, so I’m one of those lucky people where I found a field that I liked really early on in undergrad and have been through that throughout my entire adult career. And I also am someone who had a really good experience during my PhD, so I came outta my PhD still with a positive view of academia.

Jenny Yang: So I was very fortunate for that. I think I would’ve been very happy, doing this type of work in academia, doing it in industry, or doing it in doing it at a startup scale. What I really cared about when it came to making the decision was, how much ability would I have to create vision that I see because I’ve spent a long time building up the skillset and the confidence that I have, I ideas that I can actually follow through on, which meant I really wanted to make sure I was working on a problem where I could have some autonomy over decisions that were being made. wanted to make sure I worked with a team that I really I’m really passionate about what I do, and it’s really made much more enjoyable when you’re around a team that inspires you, that you admire and you trust and are also similarly motivated. And I think if I found, an academic lab that met all those criteria, I would’ve been very happy. And if I, it just happens that I got dragged into the startup world. So definitely a decision that I’m happy I made ’cause I’m having so much fun doing it and I’m working with people that are incredible and on a problem that I think is very worthwhile. But I think one part that maybe I didn’t appreciate earlier on that there are certain constraints within being in an academic lab that I think we don’t have necess, I haven’t felt the same being in the startup world. So for example, like academic labs can really focus on a specific theme. But when you jump into the startup world, I think it really is just what you choose to do as. As a company. Of course there’s other disadvantages, but it’s been a great setting for what we wanna do right now.

Grant Belgard: What parts of your earlier training or work turned out to be unexpectedly useful once you started building?

Jenny Yang: I think one of the biggest, I think one of the biggest advantages of some of my early work that’s helped me now was actually seeing machine learning translated into the real world. So when I worked at the Genome Sciences Center, I could actually see people building the models and then clinicians using them literally the next week. And that was very rewarding. I saw people developing automated tools for annotation, and then clinicians were actually using those tools immediately. So seeing that translation was incredible. Even through my PhD, I worked on a project really closely with clinicians and we actually deployed that AI tool across hospitals and saw clinical validation of that tool in real time.

Jenny Yang: So as people came into the emergency departments, we saw them being triaged using AI and that I think is an incredible experience. ’cause I do think there are a lot of people who build AI models, they publish a paper on that model, and that’s the end of you hearing about that model or seeing the progress of it. And I think that’s a shame because I do feel like are so many ways that AI can help people and support people in their jobs. So by actually having seen multiple examples of that, especially in a field like healthcare and medicine. Gives me like a certain mindset of what kind of rigor needs to go into building AI models that we want to deploy at Outpost.

Grant Belgard: As your responsibilities have changed over time, what did you have to unlearn?

Jenny Yang: That’s a great question. And I think a big thing that I had to unlearn was, I can’t do everything on my own. So I had a very independent

Grant Belgard: PhD

Jenny Yang: where I really got to choose the projects I worked on, drive those projects, and I had to do them from beginning to end. I did all the coding, I did all the research on it.

Jenny Yang: I wrote all the papers, et cetera. I did all of that quite independently, and I of course I had my supervisor and like clinicians and other people on the projects that I could talk to, but I really made all those decisions and something that I’ve had to. Not necessarily unlearned, but like a new skill that I had to learn was delegating, being more organized and combining different people’s outcomes to create the final outcome. It’s very different than being an academia where you’re like much more of an independent researcher. Now we have a team with people working on different aspects, on a really big So That’s been a change.

Grant Belgard: Who or what most shaped your taste in science, leadership, or risk.

Jenny Yang: I think it’s a mix of two people. So Professor Steven Jones at the Genome Sciences Center. I feel like he leads with a lot of trust. He is also someone who lets the work speak. I think he is, someone who doesn’t say a lot necessarily, but everything he does say just is very inspiring, has purpose, has weight and I think that’s a really thoughtful leadership approach.

Jenny Yang: I think it’s also a person, like a personality thing as well, but I really like how he leads with trust. When I was at Oxford doing my PhD, my professor David Clifton, I also think he leads with a lot of trust, which I appreciated. He also was just so efficient. If I needed anything and I emailed him, I would get an email back in a really, like within 10 minutes probably, unless he was in the middle of a meeting. And that just made me realize how important it is. To give people the things they need to do their work really well, especially if you’re in a leadership position. You don’t wanna be the person blocking your teammates from moving quickly or being able to do their job to their best of their abilities.

Jenny Yang: So being present and trying your best organized and answering emails like e even now, like when I see my email fill up. Or my inbox fill up. It can be a little anxiety inducing and I would love to procrastinate it, but I know as a leader especially I gotta just be on top of that because there are gonna be certain things that I just have to answer to keep the machine running smoothly.

Jenny Yang: The other thing about David Clifton that’s really inspired me is that I think he’s he’s a very, he’s a very good listener. And I think Steve is like this too. I think they really enjoyed listening to what other people have to say because if you can understand the people around you, you can make better decisions, especially in a leadership position.

Jenny Yang: I think one of your main jobs is just taking the information you have and making the best decision you can at that time, and that does require more listening than speaking.

Grant Belgard: Was there a point at which your definition of success changed, and if so, what caused the shift?

Jenny Yang: I think my definition of success has not necessarily changed. And what I mean by that is I’ve always been someone who’s just having a growth mindset. I like setting small goals that are achievable along the way, but I feel like there’s always, and celebrate those goals. But there is something exciting to look forward to next.

Jenny Yang: So I think my definition of success is, and when it comes to completing tasks, it really is just finish what you start. Even if you get an outcome that isn’t great, wrap it up. And you can celebrate those small wins. And I think that’s been nice. I’m not of the mindset that you always have something else to look forward to, so you should never feel like you’re finished.

Jenny Yang: I think you should celebrate the small wins along the way, but I do success knowing that you can finish something from start to beginning, even if it’s not necessarily the preferred outcome. You can wrap it up and learn from it and then move forward. And I think now working with a team. My definition of success probably has changed a bit more because now it’s also about keeping team morale up, seeing how motivated other people are, seeing other people’s abilities to do their tasks from beginning to end, and hopefully being part of the support system to get them there. So if anything, the definition of success has just become more of like a we thing than just a independent thing.

Grant Belgard: What advice would you give to someone who wants to build at the interface of biology and computation?

Jenny Yang: I think one piece of advice would be making sure that you bring on the experts in the respective parts, because I really think if you build at the intersection of AI and like biology, healthcare, et cetera, are a lot of important components to it, and. It’s not gonna be able to be tackled by just machine learning engineers or just clinicians or just biologists. I really think it is going to be a mix of all three. And you need to tightly couple the understandings between everyone, like high level enough that people understand the overall goal and how the components connect, but in depth enough that you have the depth of knowledge for each individual component.

Jenny Yang: Because. It’s not a, it’s not a single faceted a field. And every one of those components will be just as important.

Grant Belgard: How should early career people think about depth versus breadth?

Jenny Yang: I do believe in if you’re going to take the leap into building something yourself, I think you should build up a mastery of a, at least a skill set that will contribute to that. So I think when you’re building up that mastery, it’s okay to be very focused on a specific niche but understand where it fits in the general problem a general context of the field. because as one person, you can really only tackle really well, I think, a specific component of something so big, but understanding where it fits can help you, or at least what I’ve found, help you decide maybe what the next step could be or what the next application of what you’ve done is because you’re really building modularly in that sense, rather than maybe immediately having to pivot to a new area. I really wanted everything that I did over the course of my career to build on one another. So it always felt like I was compounding with the skillset I was building and the effect it could have within the greater space.

Grant Belgard: What mistakes do smart people make when they first enter this world?

Jenny Yang: I think entering specifically the AI and biology space and probably other adjacent spaces, but entering it from a startup perspective, I think a lot of people hear that you have to maybe cut corners or take shortcuts and just move fast and break things in order to survive in the startup world.

Jenny Yang: And I think. There is some truth to that. You only have a certain amount of runway and you don’t wanna like waste time in one area and not be able to enough to know the correct direction to go. But especially with biology where experiments matter so much and like a millimeter, a milliliter of incorrect to an experiment will absolutely derail you. I think there is some care that needs to be taken in doing things in an organized fashion at a more steady pace because at the end of the day, that experiment is going to do its own thing. Whether you did it quickly or not. And wanna come out of for example, the first year of company building saying, okay, we have data and that’s all we have.

Jenny Yang: I wanna be able to say we have meaningful data that’s high quality. So I think there’s more caution that needs to be taken coming into this field from a startup perspective than maybe what you typically hear of maybe just a purely software product.

Grant Belgard: What habits or practices have helped you keep learning while the field keeps moving seemingly increasingly faster as time goes on.

Jenny Yang: That’s such a good question, especially we seem to see new AI developments every day, every hour. I think for me it’s, listening, so definitely listening to the people around me. I have incredible AI scientists and microbiologists around me. And my co-founder Alex, our COO, is also just very interested in all the novel advancements coming up, that being able to listen to the people around me really keeps me up to speed.

Jenny Yang: I also like reading. I have news on my phone that I’ll read every morning. I get an update on the news every afternoon, and I just personally. To keep up when I have a little coffee break. The other thing is even though I’m more in a business position now, whereas before I was doing hands-on coding, I’m still very involved with the experiment planning and like reading some of the new articles coming out. I think having some sort of active, component o f my day actually being a little bit more hands-on not to the extent that I was before, keeps me really up to date on what’s happening.

Grant Belgard: How do you think about credibility when the vision is bigger than the proof you can show today?

Jenny Yang: I think it’s very much about how you present the work you’re doing and how you communicate it. So I very much want people to believe our vision, and it’s a huge vision. Like I would love to see a world where can have personalized health outcomes based on our microbial communities in our gut, which is where we’re starting with, on our skin, in our mouth, et cetera.

Jenny Yang: Like I, I think we’re all so unique in that sense that our personalized health recommendations should consider that. And that’s a huge vision saying I’m gonna create some kind of generalizable model to be able to make these recommendations. Huge vision. But I think people believe in that vision.

Jenny Yang: But when we communicate the science we’re doing, we communicate it to the level that we’re achieving it at, which is we’re starting with a focus on the gut microbiome. We’re starting with these classes of drug molecules, these type of food molecules. And we’re doing it, we’re running these type of experiments, so we are going to post open source and we are gonna publish. So we’re gonna be very open with the field to allow other people to evaluate us in peer review. I think credibility is all in how you communicate what you do have. And I think you have to be very responsible there because I would hate for, anyone in the field to put out like, false statements about the truth of the science, especially when it’s in a field that’s so important for human health.

Grant Belgard: What question do you wish more people asked you?

Jenny Yang: Ooh. I think I’m not too sure. I think a lot of what. motivates me are the people that I, I work with and feel like I, I would love to have more opportunities to get to highlight them because especially as a founder of the company I tend to have to naturally be the face of the company and be the person in interviews or answering questions, but I. I think we wouldn’t be where we’re at without the team we have, and everyone is so individual in what they’ve brought to the team that it’s always nice to have more opportunities to, to highlight them because then naturally I can even go more in depth about certain aspects of the company. ’cause I, like I mentioned, being on the intersection of AI is, there’s many components to it.

Grant Belgard: What part of your work still gives you the most curiosity or wonder?

Jenny Yang: I think it is the the translation of real biology, digital form. Because to me I think it’s a very interesting problem to see whether or not we can really digitize or make certain aspects of biology, computable. I think we’ve seen a lot of bodies of evidence that suggest we can. and just really a fascinating problem to me ’cause it feels like you’re taking something that’s this is a poor analogy, but the only one I can think of right now.

Jenny Yang: But you’re taking something that is very 3D and trying to binarize it. And there’s only so many patterns you can represent. Although I do feel like with the rate that. AI is moving maybe this will be really possible, but getting there, I think it is exciting to watch that progress.

Grant Belgard: What belief about the future of biology do you think more people should wrestle with?

Jenny Yang: I think one, I think it really is that. A lot of these biological processes can eventually be automated in the way that we research them or develop data them. I think there is gonna be a very tight interplay between how biological experiments are being done from like the transition between just like humans manually doing it to some automated approach and then looping that in with AI.I think that’s like. It is something that I do believe in. I’m not sure to what extent it’ll be fully automated, but I think people should really wrestle with the idea of which parts can we start automating to make things a lot more efficient. And then where do we still need a human in the loop or how does that kind of evaluation work? And I definitely still, when I think about where Outpost is going in the future, I would love some aspect of automation to really scale up quicker and certain processes to be more efficient. It is something I wrestle with then, where do we make sure we have a human in the loop and what should we automate just yet ’cause we’re not gonna be there?

Grant Belgard: What would you say to your younger self at the very start of this journey?

Jenny Yang: I think one thing I would say to myself is to trust my gut and make decisions, make the best decision you can, even if you don’t have a full understanding of what the outcome will be. I think that’s very important. I think just naturally in a lot of different leadership roles, you don’t have time to get all the information you need, but the quicker you can make a decision and act on it, the quicker you can pivot if you’ve made a mistake.

Jenny Yang: But if the worst thing that could happen is you don’t make a decision at all and there’s no progress being made because it’s better to make the wrong decision, but you’ve learned something and then you can immediately move to the next kind of kind of solution. so I would say. Just move quicker on some decisions even if you don’t have full information.

Grant Belgard: And lastly what do you hope listeners remember from this conversation a week from now?

Jenny Yang: I think it, I think one thing I would love people to really take from this conversation is maybe like an additional peek in their curiosity on how. As humans, we’re not just human DNA, we’re actually these ecosystems, there’s trillions of microbes in and on us. They really affect how we experience health and disease. Yeah, not to creep them out or anything, but maybe just like the curiosity around like how you eat. If you eat something, all these microbes are also eating them. When you use a skin intervention, there’s a bunch of microbes that are dealing with it as well. So maybe it’s just thinking about us more on the systems and ecosystem level than just like a static human being.

Jenny Yang: We’re actually very interesting in that sense.

Grant Belgard: Jenny, thank you so much for joining us today.

Jenny Yang: Thank you so much, Grant. Really appreciate the time.

Transcript of Episode 82: Manuel Corpas

Disclaimer: Transcripts are automated and may contain errors.

Grant Belgard: Welcome to the Bioinformatics CRO podcast. I’m your host, Grant Belgard, and joining me today is Dr. Manuel Corpas, a genomicist, entrepreneur, and educator working at the intersection of genomics, AI, and health data science. Manuel is a senior lecturer at the University of Westminster, founder of Cambridge Precision Medicine and the originator of ClawBio. His work has also included contributions to efforts and tools such as Decipher and BioJS. Manuel, welcome to the podcast.

Manuel Corpas: Thank you, Grant.

Grant Belgard: So for listeners meeting you for the first time, how do you describe what you do right now?

Manuel Corpas: I have been doing bioinformatics since 2000. First as an MSc student at the University of Manchester, then I did a PhD in bioinformatics. Then I moved to the Sanger Institute where I developed one of the leading sort of databases for diagnosis of rare genomic disorders. I did there at Cambridge like four years. Then I started the company, Cambridge Precision Medicine, which was part of the Cambridge University incubator. I did that for a few years. Then COVID came and the wife said, oh, we need to move to London because I want to be closest to my family and so on. Then I moved to London where I got this back to academia as now as a senior lecturer at the University of Westminster in genomics. I lead this program on a new MSc on AI and digital health, which is second year and yeah, with 20 students. So I think that gives you a little bit of an initial set up.

Grant Belgard: What led you to create ClawBio?

Manuel Corpas: So I think the prelude for ClawBio was the bio JavaScript projects, which was an open source community I led around 2014. And the idea was at that time to basically come with a way for stop reinventing the wheel in terms of reusable components that people would need, would want to use for biological data on the web. So fast forward into the internet revolution where we are today, where the idea is that, at least from where I see it, the future looks agentic and knowledge currently in the biological domain, but you could say from many other domains, but I am based on the biomedical domain. So all knowledge tends to be captured by publications, PDFs, which are non native for discovery by agents. And by agents, AI is a software that runs continuously and Alexa, you’ve heard of Alexa, right?

Manuel Corpas: It talks to you and you can ask her questions and it’s able to do specific tasks and it’s all the time on. So the extension to that is that we have now the possibility to use AI powered agents or robots which leverage the power underneath of frontier models, such as ChatGPT, Claude, perplexity, Gemini, you name it. The idea around ClawBio is to come back really to the same situation. So we have bricks of knowledge, which currently are not discoverable. They’re not reusable. They are not reproducible. So how can we make a sort of central repository registry where anyone who is developing this sort of discrete skills can find them in a way that there’s no restriction, MIT license. So anyone can see the code, can push the code. Obviously anything, there’s some guard rails, I look at the code and make sure that it’s audited.

Manuel Corpas: And at the end of the day, ClawBio stands for the idea of using this incredibly adopted new tool called OpenClaw. And I’m going to explain what OpenClaw is. OpenClaw really is the planning between the large language model and then the communication that you have via chatbot, via telegram or WhatsApp or Discord. So the planning in between is done with OpenClaw. And OpenClaw has been gaining a huge amount of traction. So I think it’s like in three months, it’s been the most starred and downloaded in the history of GitHub. And it has, right now, it seems like it’s the sort of base technology on which an agentic AI is going to happen. And so everyone, if you are in the sort of AI domain, you will have thought about agents and agentics all the time.

Manuel Corpas: But if you are not in that sort of domain, the sort of hype around or the sort of heat around agents is that for the first time we have enough sort of capacity via some of the big providers, GPT, Anthropic, and so on, whereby for the first time, they give you the possibility to be able to develop code in a way that basically is hands-free. And that code development, when you transform it into specific tasks and chain them into specific skills, problems, whatsoever, you can then very easily develop a library of repetitive tools, which you can automate without having to be there. So a lot of the sort of vision is how can I automate as much as possible of tasks that normally before we had this sort of elements together. Now we can actually have your agent running them without you having to basically be on the computer all the time.

Manuel Corpas: And you can talk to the agent because it will have already pre-programmed the skills necessary to be able to chat with you. And you can see via your chat and you can ask it questions and it can do and spark code and it can change things just with plain English. So I think that’s really the key of ClawBio. So it’s the application of that kind of paradigm into the biological domain, specifically around reproducibility and also this open source community aspect to be able to share, to be able to reuse.

Grant Belgard: So noting that it’s early March 2026, and this was really just very recently launched, what would you say are currently the most mature skills ClawBio has?

Manuel Corpas: None. I wouldn’t say that there’s any that is mature. The project only has a few weeks and so I cannot claim that. What we do have is some minimal viable products. So some minimal functionality that actually proves the point that you can really do something useful. And I guess for me, the coolest application is a robot, which is currently accessible. It’s called RoboTerri. So RoboTerri’s soul is inspired on my Ph.D. supervisor and Professor Teresa Attwood with whom I did my Ph.D. in Bioinformatics at the University of Manchester. And you can basically talk to RoboTerri, who has already had preloaded my personal genome.

Manuel Corpas: One of the things I tend to demo now is that I can now take a picture of a drug pack that if you could go to the pharmacy and then you say, if you’ve been prescribed this drug, and you would like to know whether that particular drug is compatible with your genetic metabolism for processing the drug. We know that the pharmacogenes influence significantly your ability to respond well or adversely to the normal prescription guidelines. We know that most of the prescriptions and the dosages are based for the average population. And then you have, you know, if it happens that you are not white, northern male European, you’re going to have, and the further you are from that sort of population, you’re going to be more likely to have an adverse drug reaction. Out of those adverse drug reactions are included in your genetics.

Manuel Corpas: So if you are able to just take a picture of your drug, which has your genome preloaded, and then RoboTerri is basically able to identify the active principle in the drug, in the medicine, compare it against FDA approved guidelines for dosages based on your genetics, and then against your current genetic variation, the appropriate dosage based on those guidelines. And then it gives you back a report there in your telephone specifically saying, oh, avoid, or yes, this is good for you. So that’s a lot of minimum viable products I currently have that I demo most.

Grant Belgard: And looking forward to say the end of the year, what would your best guess be about where this project or successors of it go?

Manuel Corpas: Yeah, the reason why I’m now in this place, I’m now in an incubator building. And I’ve been invited by a number of potential investors who are interested in getting further with this project. And so the priorities for me at the moment is that we’re talking not about a sort of normal type of data, we’re talking about very highly sensitive data as it is your health data, your genome data, this is data which is incredibly sensitive. So if you are going to reuse any of those components, you have no idea who the heck have developed them. You have no, the trust component from having a library is very beautiful. Yeah. But when you are now talking about your own personal data or data which is highly sensitive, like patient data, you’re just not going to reuse that.

Manuel Corpas: So what I want to build around now is a little bit like you have seen, for instance, in some of the social media profiles where you have this sort of blue badge where, you know, that person has been certified, that person has, so we could have some kind of certification aspect where if we have that blue badge for any given skill, we can guarantee, obviously for a fee, that specialty skill has been audited against regulatory systems, the European regulatory system and it has compliance 2730001, for instance, that way building that trust for specific skills, which people will pay for, then we can add that extra layer of certainty and trust, which then I think would enable a much more trusted resources. So I think for me, it’s not a question about how big this is, which we’ve already had at least 40 contributions, and we can see that the project is really being very popular.

Manuel Corpas: But I think the issue now is how do we make this into something that can be trusted? That’s really where my current thinking is.

Grant Belgard: What do you find people most frequently misunderstand about AI within the bioinformatics community?

Manuel Corpas: That they have no idea of how quickly things are changing and the power of new versions from 5.2 to 5.3 people think there’s a small incremental change. No, this is 10 times better. People don’t understand two things, the exponential growth in terms of capability that we’re experiencing every three months. And I don’t know about you, but I work completely different as I was working three months ago. Yeah, if you are like me, we’re running like tech agents at the same time, any given time and all these instances. I don’t look at my emails first. Now I look at what was the way I left it with that agent last night and see where we are at. So that’s one thing. And so I gave a presentation at the London Bioinformatics Meetup on the 26th of February. Yeah, that’s nearly a month ago. And I raised it. It’s meant to be a community of bioinformatics practitioners, right?

Manuel Corpas: You have people from major institutions that you know their names. I’m not going to say any names. I asked them, does anybody know what Claude code is? No one. And I was like, oh my God. And this is meant to be it. The top people in my field, I think that, or maybe I’m just mad. That’s why I said I was mad because the relentlessness, the pace, the acceleration of at least how I live on a daily basis, how things are changing, it’s just absolutely, I don’t even sleep because I have this sort of situation where I see this coming. And to be honest, I made a very conscious decision. I have two options. I either stay, unless somebody else makes the decisions for me, as it is happening right now, and I’ll give you some examples in a minute, or I actually invent something and I shape somehow in my own very little small niche, what’s going to be the future.

Manuel Corpas: Because otherwise, unless I invent it, I’m going to be out, as simple as that. And for me being out, that to me is, I can’t live with that though. The example. So I was doing a benchmark of the main frontier models. Yeah. Gemini 3.0, Claude Opus 4.6, Sonnet 4.6, GPT 5.3, Deep Seek 3.1. I think it was a 3.0. And I was basically benchmarking for each of the main World Health Organization diseases that give greatest value to humanity, how well each of these models are able to query back some sample research, output research I had taken from biomedical data is called PubMed. Basically, PubMed has all of the biomedical literature index and you can query PubMed for Ebola, let’s say, or for type 2 diabetes or for ischemic disease or whatever.

Manuel Corpas: I was like, I was actually looking at the 170C global burden of disease, World Health Organization diseases, which include Zika virus, Ebola, I don’t know. So Claude wouldn’t let me query them for those diseases. I know that they’re doing it in the right way. Okay. So these are guardrails. But I’m like, who are some anonymous software developers, Silicon Valley, to decide on what I think I should be doing? Because I’m sorry to say, I’m a bona fide researcher and you cannot or should not dictate my freedom. I know this is a very silly example, but I think this is just a taste of what could happen very soon. We’re not talking about two years. I’m talking about months down the line because one month is a year in AI speed.

Grant Belgard: So in this very rapidly changing environment, how do you decide when a total workflow is trustworthy? What do you look for?

Manuel Corpas: So first thing is transparency. Can I, can I actually look at the code or can I, is it being, are there any black boxes basically? Yeah. So if there are black boxes, then I don’t trust it because there’s no transparency. And unfortunately, most of the LLMs I use, they are black boxes. So how can I trust something which is a black box? Transparency is one. Secondly, I want to see the faces of the people. I don’t trust a project where it’s just an anonymous community. I want to see the people behind it. I want to see who are the developing, who is making the decisions. Because if I have a problem, I don’t want to have your LLM power chatbot to give me one of your recommended arbitrary sycophantic answers. Third, I want to see, is this scientifically grounded? Is it, what’s the thoroughness criteria? I want to see the track record of the people. I want to see their LinkedIn profiles.

Manuel Corpas: And I guess the irony of this is that suddenly the human side of their project becomes so much more important. And I was having this conversation earlier with one person here at this, and suddenly trust becomes paramount for anything. It’s all about trust now, but it’s not about technical prowess. For me, non-negotiable asset, which is cause, is trust.

Grant Belgard: How do you think that will evolve over the next few years? Because the kind of technical side of things is, yeah, I feel like the kind of presentable on this is massive for anyone paying attention.

Manuel Corpas: To be honest, I have a lot of difficulty even predicting, understanding the present, let alone the future. I think that for me, yeah, because I don’t know about you, but I think we are all drowning and that we’re all unable, humanly impossible to keep up with everything that is happening. I, so I can’t predict technology, but what I can see that what would be the tools that will help me be better prepared for the future is something that I live on a daily basis. And to be honest, these are things which I had not paid too much attention until now, but the principles that I know will help me are the following. One, don’t get overwhelmed. If you can just do 1% of catching up every day, you are doing fine. I’ve seen it because in three months time, that is not 1%. It compounds.

Manuel Corpas: And I have seen that just by every day listening to podcasts like this one, where you have trusted people, whoever you feel trusted, yeah, you can trust that. And you keep your own environment because right now it’s becoming less and less important on where you are at, as long as you have access to the right information channels and you keep connecting on a daily basis, that’s good. The second thing is that I have, I’m training this sort of gut feeling that my personal intuition. Whenever I get a result now from an agent, from an LLM, it’s not, I don’t even read it. I don’t even necessarily, it’s more to do with the gut feeling. So I am now having a lot, making decisions a lot more with my gut than my brain. Because I feel that the logical part is sorted now and it’s more to do with, not so much with the logic of intelligence, but how it feels.

Manuel Corpas: And then the other aspect that I have now accepted, and I think it gives me a tremendous competitive advantage in terms of the principles for the future, for how things will evolve, is I feel unstoppable in the sense that for me, the intelligence is now, is not the limit anymore. It’s my capacity to ask questions. For the first time ever, I can ask, and this is already cliche, Peter Steinberger says that the creator of global, you have an infinitely patient machine that will be able to explain things at your own level. There’s no excuse now not to want to learn. And also I find another thing that is becoming cliche as well is you have this situation where some people say, oh, this is going to atrophy your brain because it’s making all these decisions for you and they’re thinking, well, that’s a valid option.

Manuel Corpas: But I can tell you that you can flick the side and harness it to even encompass problems that you would have never thought you would be able to develop before. Because now if there’s something you understand, you can always ask. And so that’s for me, my strategy, I cannot predict the future. I cannot understand the present really, but I have this sort of inner guide compass, which is now more important than ever, that I think keeps me, to be honest, ahead of the curve. And at the end of the day, the adoption curve is here. So as long as I’m ahead of the adoption curve, I’m going to be fine.

Grant Belgard: And how do you think about maintaining scientific rigor in this world? It seems like it takes more time to consume and digest outputs than it does to create them.

Manuel Corpas: Yeah. So obviously we’re being swamped. So my approach is very simple. Have you heard of the dragonfly method? Right. So dragonflies are the most terrible predators you could ever think of. They were human size. We would all be dead. They wouldn’t be humans, right? They are so precise. Why? Because they have 10,000 lenses. In other words, they have 10,000 different perspectives from which they can really calibrate their environment. The way to survive this sort of lack of validation or verifiability of having your work, you can train your LLM to judge it as a reviewer. Then you can have the perspective. You have another lens that comes, which is the founder, another lens that is the patient, another lens, which is the general party.

Manuel Corpas: And so I’m going to give you complimentary perspectives that allow you to, for the first time have really, if you trust your model, I guess that for me, the trust comes from what model do you trust? So if you have a model that you trust, and the only way to trust that model is by using it and by tinkering, by testing it, by seeing, oh, this one is better for emotional empathy. Oh, this one is better for generating figures. This one is better for integration with this particular tool. And that’s the kind of knowledge that you can only guess if you are invested into embracing all these different technologies. And you need to stop being a user. And now if you really want to ride the wave, you must become a builder. That mentality has to change and that will give you the necessary confidence to be able to understand what the shortcomings are. What’s the best way to prompt?

Manuel Corpas: Because as I said, every tool is going to have their own quirks and not even the providers of these tools understand it, they don’t even understand it. They can only have a, some kind of general frameworks and they have their guard rails, that there’s a huge space in between that remains unexplored. And that is the right strategies because all of these models are all going to be generalists. But if you have that specific, very specific expertise that you had in my case, bioinformatics, let’s say, that I’m going to win in bioinformatics for these very specific genomics tasks, whatever. I’m not going to win at the many other general things that are out there. And that’s where I see for myself anyway, the opportunity.

Grant Belgard: How can others get involved in ClawBio?

Manual Corpas: So just go ClawBio.ai and then it will have pointers to the repository where the code is and then just tell your favorite LLM or tool to help you understand what the code is. And so you have your own personal tutor and that will be the way. The other thing is that obviously we’re now developing channels, we’re doing hackathons here next week in London, we’ll develop ways for people to become community and through email lists, through Discord, through, as I said, we have not even had time to have all of these different options, but I think that the best way is simply to just go to the website and tell your favorite chat book to walk you through it and then start question. Break it. If you break it, I’ll give you, I’ll buy you a gift. This is meant to be, stop thinking about messing up, please messing up. That’s the only way you’re going to learn.

Grant Belgard: So changing track here to talk a bit about you and your own career. Was there a moment when your work stopped feeling like a series of separate projects and started feeling more like a mission?

Manuel Corpas: It’s always felt like a mission since I had very clear, I wanted to become a scientist and the current projects are simply an expression of this relentless need to somehow express the all of this energy and all of this feeling I have for the world. I think it becomes like really like my own temperament. I must say that I’m a little bit in the autism spectrum, so I get quite obsessed with things. And right now I’m obsessed with AI, I’ve been obsessed for several years now on AI and now I’m obsessed with global and really harnessing the power of agentic AI. Because as I said, I see a lot of potential, I see a lot of danger, and I see a lot of people who very in a very, in a good way, they’re trying to impose their values, which I know I may not necessarily agree. And some people talk about super intelligence as the end goal.

Manuel Corpas: I don’t think that’s necessarily one that really excites me because super intelligence for me, it sounds a little bit like you exclude some people. What if these people are disabled? Some other people are talking about super abundance as the end goal for this revolution. I don’t agree with that. That sounds selfish and materialistic. For me, what really the purest purpose for me to pursue this obsession is what I call super enlightenment. If we take into the history, into account the industrial revolution, which is the closest thing I can think of to what’s happening today. You had these people like Nikola Tesla, Immanuel Kant, or even slightly earlier, Isaac Newton. So these were people who saw advancements as a way for growth, not in terms of wealth or power, but as wisdom about really a better understanding of yourself and the world around you. And I know that there are real dangers.

Manuel Corpas: And then this is the fact that you could have super intelligence ruling the world. I understand that there have to be people thinking about those problems. For me, frankly, it’s a bit of a distraction. If I focus on the negative, I prefer to focus on the things that are meaningful to me. It’s more of an integration of the technology, even with a spirit, even if I can say that. And it’s weird because you have these new agents that are so [?]. It’s becoming somehow spiritual, even if we don’t mean to do that. Not that I’m necessarily a religious guy, but I think that this meaning aspect, this need for me to be authentic, value oriented, which sounds obvious. I think it’s now ever more important than before.

Grant Belgard: Looking back, what risk are you glad you took?

Manuel Corpas: I don’t think I have risked enough. I wish I had. I’m a risk taker, but I don’t think it’s enough. I guess for me, I had this sort of pathological state of mind when I’m never satisfied. So I have a constant sense of dissatisfaction, and that sort of drives me to want to improve, I guess, combined with my obsessive behavior for things I feel really passionate about. I am not taking more risks because of people I love, whom I care, and I would be taking more risks if I was on my own, but I think I would probably be dead by now.

Grant Belgard: What skills matter most now that AI is changing how technical work gets done?

Manuel Corpas: I think some people say curiosity and inquisitiveness and asking questions. I’m going to go one level beyond that. And I actually want to say it’s about your attitude, and it’s about your own grounding and having a very, very clear sense of compass in terms of what matters to you and why. So your internal compass, why should you be doing what you are doing? Finding the right motivation drive that gives you that inner fire that keeps you going is for me the most important thing, not just from now. This is just a new reincarnation, but I think that that is something which will never change regardless of what technology we’re surrounded by.

Grant Belgard: What makes someone genuinely strong at interdisciplinary work?

Manuel Corpas: Really, not being afraid of showing your vulnerabilities and being prepared to swallow your ego again and again by people who know more than you. And I think it’s also an essential appetite for learning.

Grant Belgard: Speaking of learning, there are lots of ways to learn. What specific habits in that space have compounded the most for you over time?

Manuel Corpas: Studying. So for me, a day that I don’t spend, I don’t mean studying on the computer. I need my physical book, smelling, it may sound a little bit old school, but if I am on the computer, I get distracted a lot. And so having that sort of discrete physical medium I can touch, there’s this connection, a physical connection, a spiritual connection with that work. And so for me, a constant habit of, one of my vices is I keep buying books from Amazon, which I never read, but it’s one of the things that gives me most pleasure, just buying books. I know that I’m going to read maybe 50% of them, but I have them everywhere. I have one book in my car. If it happens that I’m in the underground and then I don’t have anything to read, I have another book in my, in this wallet, I have a book in that. So I always have a book around me, which will bring me back to my origins.

Manuel Corpas: And the origins is scholarship at the end of the day. And that scholarship for me is not given by the computer. It’s given by that sort of quiet, calm, no noise place. In this case, in the early morning, 6 AM, 5 AM, when everyone is sleeping, everything is quiet. I have my little lights, my pile of beloved books there, and just enjoy that sort of moment of solace and connection with learnings, new, old, ancient, which to be honest is for me, was the essence of civilization or our civilization. That’s why I don’t think that AI necessarily is going to make us less intelligent or less able. Obviously, some skills like having a calculator, now, if I want to have a sort of complex sum, I use a calculator. Yeah. Okay. But that doesn’t mean that I’m going to stop being less intelligent because there are other things, as I said, this gut feeling, which I’m constantly training.

Manuel Corpas: So you are that, you harness that technology and internalize as a new Swiss knife artifacts, which now becomes part of him.

Grant Belgard: And lastly, what advice would you give your younger self?

Manuel Corpas: Don’t doubt yourself so much.

Grant Belgard: So Manuel, this has been a great conversation.

Manuel Corpas: Yeah, absolutely.

Grant Belgard: Thanks.

Manuel Corpas: Thank you.

Transcript of Episode 81: John Connolly

Disclaimer: Transcripts are automated and may contain errors.

Grant Belgard: Welcome back to the Bioinformatics CRO podcast. I’m Grant Belgard. Today, I’m joined by John Connolly, Chief Scientific Officer at the Parker Institute for Cancer Immunotherapy, also known as PICI. PICI’s mission focuses on accelerating breakthrough immune therapies by bringing researchers, tools, and collaboration structures together to move faster from scientific ideas to patient impact. In this conversation, we’ll cover what John’s working on right now, how his career path shaped the way he leads, and practical advice for anyone building in translational science, especially where data, bioinformatics, and real-world complexity collide. Let’s jump in. So, John, for listeners meeting you for the first time, how would you introduce yourself and what you focus on these days?

John Connolly: Yeah, first of all, I just want to say thanks, Grant. It’s a real thrill to be on the podcast with you and to catch up. John Connolly, as you heard, CSO of the Parker Institute for Cancer Immunotherapy. I guess the way I’d introduce the Parker Institute is, first of all, by saying it’s a 501C3 nonprofit. We’re a cancer charity. So we, as you heard, our mission is really to make all cancers curable disease. And the organization really lives to that mission, very much focused on funding fundamental research in the field of cancer immunotherapy, and then really creating what is the highest concentration of immuno-oncology expertise in the world, pulling all of these experts together, betting on these people, not on projects, but on the people and what they do, and creating these 14 centers around the US. They’re full centers or what is known as EMR centers.

John Connolly: And this really gives a lot of autonomy to those sites to do that fundamental research. But in describing the Parker Institute, it’s not just a grant agency that gives money out. What we’ve done is we’ve really knitted these organizations together, sort of a network of networks together above each of the individual institutes. What we’re trying to do is break down those barriers, break the silos, so you’ll be able to exchange data, information, projects, people between the different institutions. So we pre-negotiate confidentiality agreements, material transfer agreements, everything is there. So you can just stand up in the middle of a presentation and send a vector to the next lab just immediately, or open up and really have these substantive discussions about what’s next in the cancer space.

John Connolly: And that’s really a major part of the institute is that funding, is that research, is finding those young investigators, building out those centers around the US. And then the next part really is translating that into real clinical trials in the real world space. And so to do that, I think there’s no better place for blue sky ideation than academia. I mean, this is kind of what it does well. But one thing it doesn’t do well is prioritize programs and execute in the clinic. So what we’ve done is we basically created a venture philanthropy arm that spins out biotech companies based on the technology that’s coming out of the network. So getting best in class from Stanford, MD Anderson and Dana Farber and pulling them all into one company and then putting that under project management. So we’ll fund those companies and actually staff them.

John Connolly: We’ve got a new co-build team that can jump in in operational roles and then push that technology out and really test it in the clinic under project management. So you actually see it executed there. And we have a business development arm that can then work with pharma to get this out to a much broader community. And so with that, I think you really do have to have that. If you want to accomplish such a ambitious goal like all cancers curable disease, you really need to have a line of sight from the blue sky kind of science all the way to commercialization. And when I say line of sight, you need to have operational efficiencies in each of those areas. And that’s really what the Parker Institute does. It’s been around now for 10 years, 2016 we started it. Really everything I just described was the idea of Sean Parker.

John Connolly: So Sean really saw this vision of there’s, these silos are really preventing the immunotherapy from really reaching its full potential. And there has to be a way to break down these silos so that people, the best people at MD Anderson can be working shoulder to shoulder with the best people at Cornell or Memorial Sloan Kettering.

Grant Belgard: What’s the problem you find yourself thinking about repeatedly right now?

John Connolly: One of the biggest problems is we’re in the middle of kind of a strategy review for the next 10 years. And so it’s thrilling to really talk about that. I’m working with Ira Mellman and who’s recently joined the Institute from Genentech and to just think about what that 10 year strategy really looks like. And it’s funny to be on this podcast, what I’m thinking about is how we recruit more kind of AI native people into the immunotherapy space. And I think the way the approach that I think works and that we’re taking is not to train people to become kind of proficient to think in this AI kind of first integration, but really grab people that are in the tech space here in San Francisco or in Asia or other where and then turn them into immunotherapists. I think that’s for me the biggest thing.

John Connolly: So we’re excited, but it’s something that’s because of the way we’re thinking about strategy, we’re really pushing forward. So that’s one big one that we’re thinking about.

Grant Belgard: What’s something about cancer immunotherapy that’s widely misunderstood outside the field?

John Connolly: Yeah, I think one of the things for cancer immunotherapy is this idea that, so there’s a lot of expectation with it. I think the, and it’s that you just simply sort of induce an immune response against the cancer and the cancer would suddenly go away. It’s a difficult thing to do. As much as we’ve created incredible successes in the field, and I really mean that, I think the advent of checkpoint blockade is arguably the biggest advance in cancer in 5,000 years since the advent of surgery. I mean, like really. So it works broadly across multiple tumors. It’s curative in late-stage metastatic disease. There’s just nothing else like that. This chemo doesn’t do that, nothing else does that. So it’s phenomenal. And when it works, it works spectacularly. The downside really is that checkpoint blockade works in 20 to 30% of people, and that’s it. In certain cancers, it works very well.

John Connolly: In others, it doesn’t. And so getting a better understanding of why that is, being able to predict, requires a deeper understanding of how the immune system really works. And so I think that’s a big one. The other is this idea that it’s a free ride, right? There’s any kind of novel therapy that comes in that overactivates your immune system. There are obviously side effects, and mitigating those side effects and amplifying the effective nature of the tumor, anti-tumor effect, is totally essential. And that’s another obviously big area of research.

Grant Belgard: What’s a recent moment where you thought, this is why we do the work?

John Connolly: Oh man, this is, luckily for me, this happens a lot. But we’ve recently taken, a lot of efforts gone into immunotherapy, tackling big cancers, man. Lung cancer, all over the place, right? So we’ve got tons of programs and projects in that. Big efforts in breast cancer and others, and they’ve made true progress, like phenomenal progress. But what I’ve recently done is taken a step back and challenged the network to live to the mission, what I said was all cancers curable disease. Not all cancers, just treatable disease, okay? So, I mean, let’s see what we can cure. And so actually doing a scoping, looking at cancers that are highly responsive to immunotherapy, right? And saying, let’s move beyond just treating those cancers. Like rare subtypes of melanoma with Antoni Ribas at UCLA and Paul Nghiem doing Merkel cell carcinoma up at the Hutch.

John Connolly: Actually saying, guys, what if we actually took all of these incredible tools that have been developed for these very common cancers, like lung disease, like lung cancer or breast cancer, and instead focused on rare cancers that we know are gonna be responsive, and actually cure these things. Let’s tick some boxes here, let’s get these things off the list. And so phenomenal work, again, from Tony Ribas, recent publication in rare subtypes of melanoma showing just cures. It’s really, really spectacular. And I’m proud to say we’re putting a clinical trial together at Dana Farber now, which is a combination cancer vaccine for Merkel cell carcinoma. We really dove deep into, can we induce a really potent immune response against this thing that’s highly responsive to checkpoint blockade?

John Connolly: Can we then clone the T cell receptors, ship those to the Hutch and have cells ready for those patients so that if they do recur, they can be treated immediately and cured. So I think just eliminating cancers, like truly curing a whole class of cancer is something that is really near and dear to my heart. I think it’s just on the horizon.

Grant Belgard: How do you translate such a big mission into a concrete research strategy?

John Connolly: Well, I mean, the first thing is some humility, right? So saying that there’s so many things we just don’t know yet, and we don’t know about the immune system, about how cancer interacts with the immune system, and going to find those people that are really focused on those questions. I think in building that networked based foundation, I think this is an essential portion. It’s really the value of the Parker Institute. It’s just the people and the incredible investigators. And then asking them, guess what is it about the current funding mechanisms or the current mechanisms within your university that are holding you back? You talk about all these projects, but it’s been 10 years and we still haven’t seen something come out. And a lot of this has to do with grant funding, review process, bureaucracy, the slow nature of all of this.

John Connolly: And you and I both know that just the way the concentration of expertise works is these centers attract good people that attract good young people to kind of get there. And so what we’ll do is we’ll come in and bet on those people and say, look, your area of focus, let’s give you a block gift, largely discretionary funding, right? With some obviously project guidance through a steering committee. But that’s it, it’s really up to you. How do you want to spend this money? What do you want to do? And then do it in perpetuity. So they know they’re never going to have to worry about that money again, because it’s coming every three to five years, there’s another gift coming, another gift coming. So that takes that constant grant writing off the table for these academics. The second is when we do have steering committees, at the end of the committee, the money immediately goes out.

John Connolly: So it’s just a review, quick review, and then yes, no, modify it, yes or no. And then the money’s out the door at the end of the meeting immediately. So for all those funded projects. And so that kind of speed, it just changes things. I can just speak from experience, if you’re a PI in a lab, and you want to have the ability to, you’re thinking all the time about what your areas of focus constantly, 24 hours a day. And you want to be able to go out on a bike ride and come up with an idea and immediately hire two postdocs to work on it. Like this is what the institute’s kind of funding brings. And it’s just an essential kind of thing that just changes the dynamic.

Grant Belgard: How do you decide what not to do, even if it’s scientifically exciting?

John Connolly: So, I mean, the focus on immunotherapy, even if immunotherapy kind of is turning out of favor in like the investor community or the pharma community, I think this is staying on mission. This is really extremely helpful. So no matter whether it’s a project that we’re funding, or if we’re building a company, or we’re looking at an investment opportunity, or doing a partnership with pharma, the first thing I always ask is, is this mission? That’s all, is this mission? And if it is, then we’re aligned. So we can work together as companies, we can move forward, we can invest in that company or build that company, we can invest in that project or that person. And so I think that that really is a North Star for us, is this idea of all cancers curable disease and a focus on using the immune system to get there.

John Connolly: The other is, there’s a certain, staying in touch with the network, doing regular site visits, getting out there, is really essential to understand where the momentum in the field is going, and where the early results from early stage clinical trials, the innovation in this space is going. So that also kind of helps an idea of which direction and funding is going to go. The other is, I think some of the best ideas out there are coming outside our space. I mentioned AI and other things, but there’s those inventions that come in sideways to try to solve problems that people have been banging their head on for a long time. I look for those all the time. I also look for contrarian troublemakers too. I love those people that’ll jump in there and the worst thing you can have in a network is just everyone saying the same thing.

John Connolly: You definitely want people that’ll go against the grain and shake things up.

Grant Belgard: What are the biggest friction points that slow progress in multi-team science and how do you try to reduce them?

John Connolly: That’s a great question. So I think the biggest kind of hurdles that you have to overcome, and this is probably true for any organization of our size, is that bureaucracy that I talked about. In worst case scenario thinking, this idea that you have to constantly worry that you’re working with another investigator and they’re going to take your ideas or the IP or something like that, or that that university is going to have a better position than a new company build. That kind of worst case thinking just sort of breeds mistrust and what it does is it eliminates opportunities because you end up just taking a defensive position. You see this across a lot of organizations. This is why it’s really essential.

John Connolly: When you understand the Parker Institute, you understand that it’s a network of people, people that trust each other, the people that get together twice a year in these really intense retreats that we do, sharing unpublished data and just getting it out there and really trying to show the best in class. So that trust within the network, it’s kind of a secret sauce. It’s almost impossible to kind of recreate just with money. It’s something that these guys see each other as Parker Institute investigators before they do Harvard professors. And I think that that’s just an important thing that came with the great work of Jeff Bluestone when he built the network, as the first CEO of the Parker Institute, Sean’s vision of building this and pushing it out. And I think the work that my team and I have done pushing it forward.

Grant Belgard: Yeah, how do you design incentives so that collaboration is real and not just a slogan?

John Connolly: This is, so it’s really matching, it’s kind of impedance matching on capability. I think that’s really what it is. Because I don’t think that collaboration all the time is such a great idea. We fund projects that are very similar to each other in individual labs, like real competitive projects that I’m happy to fund if we think we need to double and triple down on the idea. One lab’s not gonna solve this problem. So even if there are very similar ideas and things like AI based protein design or TCRT therapy, there are programs that are extremely competitive labs. These guys have been competing for decades and I think the Parker Institute isn’t gonna solve it. But I think this impedance matching concept that I was getting to is really the real deal. So if you have someone like Chris Garcia at Stanford, Chris is a genius and he was successful long before the Parker Institute.

John Connolly: But one thing that the Parker Institute brings is, now what Chris is doing is he’s building these incredible proteins, these incredible systems, but then they’re immediately getting transferred over to Carl June in Penn, who’s then taking them into the clinic and moving those forward and really seeing Chris’s work applied to medicine. And I think that that kind of matching of capability where you’ve got the people that just live in structural biology that then pass it off to someone who’s a development expert who then passes it off to someone who’s a clinical execution and do so seamlessly because it’s exciting. This is how those projects really move forward. And again, touch base, just always going back to that touchstone of mission, is this something we wanna work on?

Grant Belgard: How do you measure if your strategy’s working, what metrics matter and what metrics can be misleading?

John Connolly: Sure, for sure. So one metric that can be misleading, I think, is publications, so nothing against it, but if you sort of get the absolute top people in the field, you’re gonna get a lot of publications. I guess just kind of, because that’s a metric of universities. And it’s a good one for universities. So it’s very important to get out there to communicate, to spread the word and to excite and attract other people. But for us, I think that some of the key metrics are this sort of full circle. So I mentioned the idea of moving blue sky science and pushing things forward and paradigm changing kind of ideas into execution in the clinic and then into distribution through pharmaceutical companies or through large biotechs to the greater patient community.

John Connolly: So for us, the first thing really has to go back and ask how many patients are actually benefiting from the research that’s happening at the Parker Institute. For me, that’s a big one. And that’s just really looking back on, and we have hundreds of clinical trials with ideas and therapies that have come out of fundamental research at the institute. We keep really good track of that and just see how things are going. I think that’s, for me, that’s probably the biggest one. And I think this is, it takes a lot of time, unfortunately, to get something that someone that’s City of Hope or UCLA comes up with and then translate that into a phase one clinical trial, execute that into the clinic, and then really begin to push it forward, benchmark it in a phase two or three trial and actually see that applied to patients. But this is really what it’s all about.

John Connolly: There’s wonderful organizations who are here to fund just sort of, just fundamental research, right? And the NIH is clearly the global leader and the actual backbone of all research funding and progress that we’re making in the field. And that’s an important and incredibly amazing thing, but that’s not what the Parker Institute is doing, right? Mission is all cancers curable disease and we do what it takes to get there. And so for us, when we go back and check, we ask that question, how well are we doing by looking at what kind of impact in the patient population we’re making?

Grant Belgard: What are the failure modes of cross-sector collaborations and what guardrails help?

John Connolly: Yeah, I think, I mean, some of the failure modes, I mentioned that trust idea, right? So anything that threatens that, because when it’s working, when people are openly sharing data with an expectation and understanding that working together is better than working in silos, that anything that kind of comes in and threatens that is problematic. I mentioned that I love taking contrarian troublemakers, but I don’t want a room full of them. So it’s like, for me, that’s really the big take home is making sure you maintain that network effect. And to do that, you have to listen to the network too.

John Connolly: So one of the most important things about the job at CSO is getting out to the sites, meeting regularly with the center directors, meeting regularly with the young investigators that are coming up, and talking to them about what their hopes and dreams are, but most importantly, like what the problems are. So part of this job is representing not necessarily PICI or the sites, it’s representing the network, this effect that’s happening. So if there’s a problem that we’re doing back at Central, then we need to know, I need to know, so we can go back in there and fix it and really maintain this network-based effect.

Grant Belgard: What role does bioinformatics play in your strategy?

John Connolly: Oh, it’s huge. So one of the big things with the big opportunities we have at the Parker Institute is really to become kind of a central database for all of this scientific and clinical data across the network. And it’s important that it’s written into the master collaborative agreement that knits these centers together. And so in doing so, we’ve really collected some amazing cohorts that are out there. We have the world’s largest cohort on adverse events in checkpoint blockade, just looking longitudinally at thousands of patients that are treated with checkpoint blockade. We had our RADIOHEAD cohort. And then we just published very recently with Mike Angell at Stanford, a large consortium on the BRUCE cohort, which is the largest collection of brain cancer spatial data that’s out there.

John Connolly: And all of these things are analyzed and we work at Central to make sure that that’s accessible to the network and that’s out there. And there’s many other cohorts that are like this across the network. And what that gives us is it gives the network an ability to dive in and to ask questions, whether it’s a target discovery question in the BRUCE cohort or better understanding of myeloid responsiveness in glioblastoma, for instance, or it’s something like we can predict adverse events or response to checkpoint blockade across multiple different clinical indications. All of this is available and they can dive in and really work closely with the informatics group, as well as their own informatics team. So we really are talking about the top centers in the world with some of the brightest informatics groups internally. So I think that’s one of the major areas.

John Connolly: The other is from this seat as a CSO is to push and encourage to get up there at these retreats and say what I was saying to you, which is we need to start turning the questions away from small questions to big questions and applying both informatics and large language models to the data that we’re generating. And if there’s something that’s missing, come and tell us. Like what is that data set? What is the problem that you want to solve and what’s the data set that’s needed to solve it? And so this, at Parker Institute, we can actually pull that together very quickly, put together a data strike for us to try to build that cohort. We can immediately fund large projects like that to get them off the ground. And these projects can be multi, multi, multi-year projects in order to answer really important questions.

Grant Belgard: When you’re working across multiple sites, what are the hardest data standardization problems you face?

John Connolly: Oh, so for sure. So this is my informatics team is pulling their hair out like every day, right? So always trying to stand, I don’t know, the hardest standardization. A lot of it’s probably, first of all, the simple stuff, right? If we’re doing clinical studies across real world hospitals, then it’s going to be data entry, coding, what you call like this chemo versus that chemo. Going in there, it’s actually kind of hard to, you have to go in and standardize that. The others are real batch effect things like blood processing effects. So we try to control all of that by providing templates to the hospitals prior for data entry.

John Connolly: We have our own red cap system and some of these cohorts they can enter immediately into so they’re familiar with the interface and they can put it in and it standardizes how they’re calling things like the over-the-counter meds that the patients have prior to therapy or the outcomes. The other is we use a lot of centralized core facilities when we put together these big cohorts and that’s, I think, really important. And it was a decision made really by Fred Ramsdell when he was CSO to do this. And I’m just completely benefiting from that when I’m looking at the quality of the single cell RNA sequencing on these cohorts is spectacular. It’s really, really good.

John Connolly: So being able to just take that first step, build the infrastructure to standardize that and saying, guys, for the proteomic analysis where everything is going to one site or the single cell sequencing, one group is running all of it and the samples are centrally archived and curated and we make sure that that’s taken care of. So yeah, I think that we try to tackle those problems. They’re the same problems I think that others have that are out there. But it’s important to do really.

Grant Belgard: How do you think about analysis readiness in real clinical trial data sets? What must be true before you trust downstream conclusions?

John Connolly: So I think one of the terms I just said before is real world. So one of the things, we’ve got a lot of cohorts and you and I have been involved in clinical translational studies where you’re doing deep analysis of say a phase two clinical trial, like this long data analysis where you get multimodal proteomics, flow cytometry, tumor biopsy, spatial, all of it and you get this incredible data set that’s just around each of those patients. The downside is that the patients in those academic medical centers that have those resources to do that, these are really highly selected patient populations. So when you then translate that out into the real world, those biomarkers, they don’t really translate well into real world settings. And so starting off and starting your large scale studies that you want to train these models on in the real world.

John Connolly: So go to set up in community hospitals and put the staff in there to actually pull those samples out. There you’re getting people that are checkpoint naive, they’ve got a job, they’re showing up at, you know, they’ve got real world problems. They are not the highly selected patient population that’ll make it into an academic medical centers clinical trials. So we’ve done that across 50 different hospitals for one of our cohorts now that the data is just, it translates much better into the real world. I think that this is, that’s a big one. But you do have data readiness problems when you start to do that, because these hospitals are not staffed to do any of this stuff, nor do they want to. So there’s not even an enthusiasm to do it.

John Connolly: So the other thing you won’t get is, you know, advance multiple biopsies and things that an academic medical center would do that your local hospital is just, if it didn’t have to do with care, they’re not doing it. So it’s, and they’re not funded to do it. So what we’re doing is, this is where we’re really putting in place resources at those hospitals to really acquire that data. And the other is to recognize them too. You know, when we publish these papers, we make sure that those physicians are authors on those papers, that this is moving forward. When we present the data, it’s always with those 50 hospitals in mind, the work that they did, even through COVID, to collect a lot of the data on that cohort. So, and then pulling that forward, I think, into PICI Central, where we do do a lot of QC, QA on the data sets themselves. This is, so far, this has been a, that’s a heavy process.

John Connolly: You know what I mean? This is what we hope things like AI algorithms can help with and they have to a degree, certainly for the QA they have. But, and the other, of course, is sample archiving. So, and biobanking. Always challenging when you’re doing that at scale. It’s a full-time job. We subcontract a lot of that out to CROs that I think do a pretty good job at tracking them. But, you know, there’s always the spurious sample that people are mislabeled or whatever. So, keeping on top of that, making sure you’re project managing all of it. This is, these are challenges. But I can’t emphasize this enough. The value of real world data in real hospitals is enormous to translating to something that’s actually effective in clinical setting.

Grant Belgard: What data types tend to drive the most useful decisions right now? Genomics, transcriptomics, proteomics, imaging, clinical notes, something else.

John Connolly: There’s no doubt. In the clinic right now, genomics does, of course, because we’re entering this kind of era of genomic medicine and targeted therapies. So, anything that has a matching therapy to it that’s easily available can be, that’s in the US is approved and can, you know, can be used in a doublet combination. So, this is where genomics comes in. Because everybody is getting, you know, a Caris report or a foundation report or, you know, you name it. And there’s all of this, or if you’re at some of the big academic medical centers, they have their own, you know, MSK impact or something, which does similar things. And so, with that information, you do get a bunch of really nice genomic data that can be used to guide care. And I think that that’s hugely valuable, particularly in combination with immunotherapy.

John Connolly: Right now, we’ve got, you know, tests like PD-L1 positivity in the tumor microenvironment. So, okay, well, you’ve got lung cancer, you know, it’s PD-L1 positive. We know you may, you’ve got a high likelihood of responding to checkpoint blockade. And so, that’s why, you know, it’s first line. But the questions that we want to know are not just what’s right for the median of the population, you know, but what’s right for the you personally, right? So, what is that genomic kind of workup that says, hey, maybe I should be, maybe I should start with another therapy. So, maybe I should like a MEK inhibitor or something or platinum based chemo plus, you know? I think that that’s, and then personalizing that journey is really valuable. So far, that’s really come from genomics and just sequencing for sort of driver mutations.

John Connolly: As we move forward, we’re starting to see things like, as I mentioned, what does the tumor, what does that tumor neighborhood look like, you know? So, is it PD-L1 positive? Is it rich in leukocytes? Is it, you know, what does it actually look like? Is it highly fibrotic? All of that can guide care, you know? So, and what I’m most excited about is not so much the research grade, highly multiplexed analysis of the tumor where we get huge amounts of information back. I’m really excited by the large language models that are going in and looking at just H and E stains and they’re trained on outcomes data and the genomics data that’s, or in the transcriptomics data that’s already there to actually predict, hey, this is a KRAS G12V mutant, you know, like just by looking at the H and E stain. These models are getting better and better and better at giving us more and more information.

John Connolly: And so, for me, I think I need that for immunotherapy. So, I want to, you got to move beyond just PD-L1 high, which is really just a interferon signature to not, is checkpoint blockade going to work? Yes or no? But this, your checkpoint blockade won’t work, but NK cell therapy will, or a targeted cytokine will, or an innate immune activator will. Being able to use these models to begin to predict the quality of response to immunotherapy would be absolutely, absolutely thrilling. And then from the transcriptomic side, I think there’s a lot there from the research stage, but it’s just not yet applied to medicine, you know? The biggest thing I run into is you can get a huge amount of information about these patients, but then you go and look at what therapies are available now to actually, you know, actionable therapies that are there to move on that information.

John Connolly: And there’s nothing there, or there’s maybe just one thing that’s available. So, the Parker Institute, our push, if you look at the companies we spin off, they’re a vast majority of therapeutics companies. You know, there’s like very few that are in sort of the diagnostic space. And I think that’s really because that’s where the need is. We just need more options and opportunities based on the huge amount of data that’s really coming out and a deeper understanding of that tumor.

Grant Belgard: What’s a common trap in translational interpretation where people overreach from interesting biology to clinical claims?

John Connolly: So, one is that the last thing you said, which is interesting, biology. You become just enamored with the cool idea, right? So, these ideas, I don’t wanna bash on the NK cell guys, but I’m just gonna use that as an example, that this really works incredibly well in the mouse models that we’re working on, and even in some of the tumor organoid systems or PDX models. But when we then go to apply that to someone that’s actually gone through three rounds of chemo and their immune systems beat up pretty well, and the tumor has been immunoselected to resist the immune response for the past seven years it’s been growing inside of you, this is a totally different world than a transplanted mouse or cell line that you’re trying to kill.

John Connolly: And so, this kind of dependency on clinical data, on preclinical data and this belief in it, and you become enamored with the mechanism and understanding of how it works, this leads you then to misinterpret responses on your phase one trial. So, you’re coming in, doing a safety study in phase one, you see two partial responses, you jump up and down and think this is the best thing in the world. What you missed was the eight non-responses. So, it’s one of those things that’s having, and it’s really because the mechanism works so well in preclinical data. And so, you push to the phase two, again, maybe some, and those patients are heavily selected at your academic clinical trial, so you’re just picking the patients you kind of think will work. And then, once it hits phase three, it’s 50-50 on every clinical trial, it’s a coin flip.

John Connolly: And it shouldn’t be, because you’ve been through so much to get to that point, you should have seen that this thing was gonna miss. And so, again, this is a great place for AI to come in and to remove a lot of that subjectivity from that. I think one of the most exciting things about the path I just described is, even if the drug doesn’t work, you start to, you learn a lot. There is something to be said about experimental medicine. And I think some of the best innovation in this space is really coming from clinical trials that didn’t work the way we expected them to work. It’s throughout the history of science, its serendipity has been an essential portion of it. And it continues, it’s incredibly valuable when it happens in a clinical trial, where you really say, hey, hold on a second, I’m not getting what I want, but I’m getting something here.

John Connolly: It really teaches you a lot that mice and in vitro organized just don’t.

Grant Belgard: Switching tracks now, what did you originally think your career would look like and how did reality diverge?

John Connolly: That’s a funny question. I think from a career standpoint, I’ve always wanted to be, obviously be in science. And someone had asked me a couple of years ago this, I don’t remember a time where I didn’t want to be a scientist. There’s never, never, even when I was a little kid, I had my test tubes and things like that, chemistry kits and microscope and everything in the just bedroom, even when I was six years old. So it’s always kind of gone in that direction. I think the track, as I was coming up, the traditional track would have just been an academic professor doing great things, but very siloed, where you’re doing your thing, you’re kind of in the corner of the lab, you’ve got the main project that’s driving, but you’ve got these side projects that keep you excited. I think that for me was always the track that I think people, you’d always go on.

John Connolly: I think most people that came up even now have that in mind as a potential. I think the difference really came with, as always, with the mentors that you have as you’re coming up. And I think just pointing out some great ones in Mike Fanger of Dartmouth. Mike was head of the department, but he also started a company called Medarex and a number of other companies as well. But Mike had this kind of entrepreneurial spirit, and I think that was highly inspiring. So just to watch him run the department, to do his thing, and to also run this big company at the same time, and almost seamlessly, when he’s thinking about it, he’s thinking the same way. He’s the same guy in both places. He’s just interested in solving the problem. The company, the academic position, the friends, the networks, the service that he has on profits, all of that was toward one thing.

John Connolly: And each of these different things was like Dartmouth, medical school, and the company. These were all ways to get there in service of his greater kind of vision, what he wanted to accomplish in the cancer space. And so he went on to develop CTLA-4, PD-1, all of these great breakthroughs, identified them, and then internally developed them within Medarex, which was then acquired by BMS. But I think that that, the way he worked and the way he thought was really important for me. And then moving on, I think working with Jacques Banchereau at the Baylor Institute for Immunology Research was big for me, because Jacques thought he was very much a high-energy company person. You know what I mean?

John Connolly: Getting into an environment where teamwork was essential, you had to work together with each other to get anything done, and think purely about the human disease, not so much about the mouse models, about really getting things into the clinic and testing them there. That was a change that moved me away from this idea of just the lone professor in the corner, more toward this team-based biology. And so I think those two people were highly influential. That and everybody else, you go through life. But it definitely changed the way I was thinking and the direction. You come to realize that to get anything really substantive done, you can’t do it alone. That’s all, there’s only 24 hours a day. You might be the best at everything, but there’s still only 24 hours in a day. So you really need to have a team of experts and collaborators and networks.

John Connolly: And that really led me to what I think is just a great network in the Parker Institute.

Grant Belgard: What skills turned out to be career compounding, the kind that kept paying dividends?

John Connolly: Oh, it’s mostly, it’s just the ability to work with people, you know what I mean? And enjoy it. I think some of the true, for me personally, one of the true joys in life is working with people to build things. And that for me is absolutely, it’s probably true across most careers. I said, if you like to work with really smart people, you hire people that are smarter than you and empower them and recognize them, this is really essential to building effective teams. And I don’t say that from kind of a business book. I only say that looking back on my life and what has, continues to be a really successful formula. It’s just that the ability to have joy in the successes of others and the rest of your team is really what drives this and has worked out.

Grant Belgard: What did you have to unlearn as you moved into broader leadership?

John Connolly: I think you had to unlearn the idea that you could be, I may be the best CFO, legal guy, CEO, whatever, it just doesn’t matter because again, that concept of 24 hours in a day, if I can only put four hours on that project, then it doesn’t matter if you’re the smartest guy in the room, you only put four hours on it, that’s it. And it requires 12. And so building a team of effective people that you trust, that you work well together, this is something academia does not teach you at all. I tell this story, but in my academic lab, there’s kind of no problem that’s too small for me to have an opinion on. Somebody asked me, what color paperclips? And I’d be like, it’s blue, like everything, it’s your lab, so you’re running the whole thing.

John Connolly: And that’s great because it allows you to deeply explore big ideas, but going into companies and I think probably one of the good examples when we built Tessa Therapeutics and working with a really effective team there, I knew I could walk out of a room and the right decision would be made because the people that were there, they are doing their job as well as I do my job. They are just as effective, they’re really good. And once you have that trust within the team, it just amplifies everything you can do. And again, I think that that’s something academia does not teach you. You really have to learn that in the real world or in certainly in the biotech setting.

Grant Belgard: How do you maintain scientific depth while taking on more organizational responsibility?

John Connolly: You just got to go and talk. First of all, you have to have some enthusiasm to the science, but you got to love it, right? Because you’re going to be hit with a lot of it. It’s really talking to the investigators, going out. Part of this job is to travel around to the sites to talk to them about their projects. But I don’t really want to talk to them about their projects as it relates to funding. We already gave them the funding. They have the money and they know the money’s coming. It’s about how cool the science is. And I want to kind of catch that, the excitement. And you can say it’s the young people that are going to give you the excitement. That’s not always true. These guys have been at this for 50 years that still jump out of bed and get super excited about this cool new idea. So it’s just looking at that.

John Connolly: And then from the standpoint of my own personal excitement, it’s also talking to all of those people who are ultra focused on their own projects and then knitting together those ideas. You know, like, all right, that was cool at Dana Farber, but you know, these guys at UCSF have this other thing. Maybe we should get them to talk and kind of work together. These are observations that are coming at the problem from two different angles. And so that I think is being there, talking to the people. This is what keeps you aligned.

Grant Belgard: For people who have worked across different environments, academia, industry, nonprofits, what mindset shift helps them to adapt quickly?

John Connolly: I think in academia, it’s this sort of mini monarchy that you get in your own lab. You can shift anytime you want. You know, somebody once told me, this was years ago when I was thinking about moving to a company when I was at Baylor. They said this guy named Don Capra. So shout out to Don, passed away, but he started so many great things. He’s an amazing, amazing guy. But had the good fortune to have lunch with Don. I was just asking for his advice on this company. And he said, look, academia, there’s almost no better job in the world. As long as you’re publishing papers, getting things out there, and publishing good papers every few years, getting grants in, you can study anything you want. You can wake up in the morning and suddenly decide to study turtles. And that’s what we’re gonna do. And as long as it keeps going, is there’s no job in this world that has that kind of freedom.

John Connolly: And it allows you to truly explore deep ideas. There’s huge value in that. I think from, I talked about this earlier, when it comes to the lessons from companies are very much teamwork lessons. You know what I mean? I couldn’t have done a global pivotal phase three trial in multiple countries alone. It’s ridiculous. But we could do that at Tessa with 1,500 shipping lanes and centralized cell therapy manufacturing because the expertise that we built together and the trust we had in each other. So I think that’s another one. In the nonprofit space, I think that the lessons there are that concept of mission. So as much as the lab and the company, those are very what’s going on today. You know what I mean? You’re always focused on today. Like what’s going on, we’re kind of putting fires out or keeping things moving.

John Connolly: And you’re enjoying the growth that you had when you look back on where we were and where we are now. But in PICI and I’m sure in other nonprofits, it’s really about where we wanna get to. This vision of this mission and how close are we? It’s right around the corner. And that belief is really quite essential at being effective in a nonprofit. So yeah, I think that’s kind of the take is that that’s what the nonprofit really taught me is that to have this longer term vision and to talk about mission and to constantly check back on everything on whether it’s getting us one step closer to that mission.

Grant Belgard: What does good taste look like in choosing problems?

John Connolly: Oh, wow. That’s a cool question. I think when it has to do with cancer immunotherapy, I can tell you it has to do with like, how close is this to actually curing someone? There is something else though, you know what I mean? And for me, it is that a little bit of that contrarian nature, which is, how unique is this idea? You know what I mean? Like, is it, and sometimes those ideas are, everyone’s doing this. So on that 1% chance that everyone is wrong, let’s take a deep look the other way. Like that let’s assume the sun doesn’t come up in the West. Yeah, I mean the East, it’s coming up in the West tomorrow and that’s just it. And what would that mean? How can we explore these kinds of ideas? So, and it’s absurd and the vast majority of time it doesn’t work, but it gets you to think a little bit of a different way. So for me, ideas that are audacious, I think have value.

John Connolly: And then the ones that, and when you kind of lead your way through or the ultimate kind of end point where you’re gonna get to with those ideas, if it’s leading to real effective impact in the clinic, like if this is right, then we’ve got something totally different here. Then going back and checking the data, not your data, but all the data, everything that’s out there in the field, diving deep saying, well, I can’t be right because this is going another way. So for me, it’s not following along with what everyone else is doing. Those ideas are not that exciting. Because my assumption is there are smart people that are working 24/7 on this and they’re gonna get to where that ultimate path is gonna be. But if you’re going in a different direction, you’re thinking differently, you take a big swing, that I think is an exciting idea.

Grant Belgard: How do you recommend building credibility across disciplines, especially for computational people working with wet lab and clinical teams?

John Connolly: Yeah, sure. So I mean, this team idea is essential right, but it’s also from the computational side, and this is actually even from the wet lab side, the credibility comes with the kind of end result, of course, and the track record is the end result. But to get there, and I think you know this even better than I, Grant, is you’ve gotta have an understanding. So you’ve gotta get in there and understand the biological question that you’re trying to solve, that’s all. Even if you’ve never done this before, you say, all right guys, walk me through this, let’s talk, teach me.

John Connolly: And so constantly learning, constantly engaging the wet lab scientists and learning what are the key, why is this an important question, not just what it is, to the same degree to be able to communicate, your solution to that has to be explained to the wet lab scientists as well so that they understand where this one’s coming from. It’s like, okay. And then you can really start working together, mostly because they’re gonna ask you what you think is a stupid question, but then you’re like, all right, hold on a second. There might be something there. And to the same degree, you’re gonna have this wealth of experience working with so many wet lab scientists that you’re gonna bring excellent questions to the table there too. But ultimately that credibility comes from the relationships you’re forging with these people, but also the outcome from that collaboration.

Grant Belgard: If someone wants to move towards scientific leadership, what experiences should they actively seek out?

John Connolly: So I think there’s a, I mentioned there’s a big difference in sort of this leadership role, but I think versus say your own, just a PI in the lab, there’s just so many different kinds of leadership. So one is just, is be a good leader, right? So focus on yourself. That’s the biggest thing, honestly. This idea of, I mentioned this a little bit earlier, but finding good people that are extremely talented, that are engaged, they’re energized, that share your enthusiasm for what you’re doing, that are better than you at certain areas, absolutely hire those people. And then, as I said, recognize and build. So to be a good leader, just work on yourself. That’s a huge thing. And once that happens, you’ll begin to create incredibly effective teams. And those teams will, the product of that output is really gonna kind of launch you in the right direction.

John Connolly: I think that also translates whether you’re running a small lab somewhere or you’re moving up to a dean of a medical school or you’re head of a pharmaceutical company or even just a division head within a pharmaceutical company that you’re being good leader is, people select good leaders to become good leaders. So that’s kind of how it works. And a lot of that is just focusing on your own behavior, expectations, and sort of, there’s another aspect of this, is it sounds a little Pollyanna to say that, but I think honestly, you also have to kind of filter out the noise. All the organizations I said have issues and problems and real world stresses. You just got to learn to filter that stuff out, focus on what that ultimate goal is. And this is why having a mission and about what you want to do is really important.

John Connolly: Whatever barriers come up in front of you, you’re just keeping your eye on the mission and just weaving your way around those barriers, eye on completely all the time and doing that with your team. That’s really best advice. And that’s from smallish leadership role to head of the NIH.

Grant Belgard: John, this has been fantastic. Thanks for walking us through how you think about strategy, data, and translation, and for sharing the career lessons you’ve gained along the way. For listeners who want to follow your work, where’s the best place for them to do that?

John Connolly: It’s definitely the Parker Institute website, but we also have a really active social media. So please follow everyone on Parker ICI, our Parker Institute for Cancer Immunotherapy, on Twitter, on X, on LinkedIn. There’s a good comms team. So they’re always putting out great output from the network. So, and keep an eye on the immunotherapy space too.

Grant Belgard: And is there anything you’d like to leave the audience with as a final thought?

John Connolly: There is one thing I think, I mentioned this idea of believing in the mission. You know what, I think there’s certain times in the history of science when you kind of look back on things where science doesn’t just work progressively to help society. You know what I mean? It’s not like you see like these sort of increases in lifespan over years and years and years. The way science works is inventions, people, the adoption of new procedures and technologies launch the field forward. There was a time where you were pre-antibiotics, pre-vaccines, pre-germ theory of disease, where half of kids died before the age of 11, half. And this was terrible and everybody hated it. And they felt just as bad now as then as they do now. But you couldn’t imagine a world where that didn’t happen. Well, we live in a world now where we’re living with cancer and everyone’s dying of cancer.

John Connolly: Everyone has this touch to their lives and their families and it’s a huge, huge, huge, huge impact on society. Well, we’re entering a world soon with the advances that are happening where it would be look like, it looks like childhood mortality. You’ll look back and say, how was it possible that we lived in a world where everyone died of cancer? It’s like, this just makes no sense to me. And that comes with funding this research and pushing it forward, but it is just around the corner. It truly, truly is.

Grant Belgard: John, thanks.

John Connolly: Thank you, Grant. Appreciate you.

Transcript of Episode 80: Diane Shao

Disclaimer: Transcripts are automated and may contain errors.

Grant Belgard: Welcome to The Bioinformatics CRO Podcast. I’m Grant Belgard, and today I’m joined by Dr. Diane Shao, an attending neurologist at Boston Children’s Hospital and instructor of neurology at Harvard Medical School. Dr. Shao is a physician scientist whose work focuses on understanding the genetic causes of childhood neurodevelopmental conditions, including how newer single-cell approaches can help answer questions we couldn’t address before. She’s also an investor. Diane, welcome to the show.

Diane Shao: Thank you so much, Grant. And it’s such an honor to be here and also reconnect with you after our long-time friendship from college.

Grant Belgard: Indeed. So what’s been most energizing for you lately in your work?

Diane Shao: Well, something I really like to think about in my work is how to span across disciplines. So, you know, based on your introduction, I think the listeners can understand I do some very fundamental research in genomics. I also really think about how that research applies to patient translation. I actually see the patients and have to involve sometimes not yet solid data in terms of making a then firm clinical decision.

And then as an investor, thinking about how to assess that landscape. And so all of these, I would say, require a different vision and goal in mind. And so I think a lot about for any given application, what is my vision of translation or patient care or understanding fundamentals, et cetera, and how to generate the data, work with the data, apply that to really further that vision, kind of like big picture goals.

Grant Belgard: What’s a question you’re hearing more often now than you were a few years ago?

Diane Shao: The question I’m hearing more, you know, more and more people want to translate, from the time a PhD student starts working in the lab to post-docs graduating thinking, or post-docs trying to think about what’s next in their careers, wondering about industry versus academia. There is such a strong focus on translation, making that impact on humans versus I think, 10 years ago, as I was still going through training, it was more, you were doing a PhD, a lot more students were thinking about an academic path, fundamental biology.

And, you know, I don’t know if this shift is good or bad, but it certainly brings new questions to the table. And then the, you know, way far past academia had this idea that, you know, going to industry is, you know, maybe a sellout, you know, you’re not asking us interesting questions, but I think there is a growing realization that those questions are also extremely interesting, extremely impactful and need really, really smart people to be involved.

Grant Belgard: What does a good week look like for you? What kinds of activities make you feel like you made progress?

Diane Shao: Yeah, I do think stepping back and seeing where have things gone from, maybe you get some data that is really uncertain and murky. And then this week it’s, hey, we can draw one small conclusion from that. Or it’s thinking about, hey, this data, which is applied to fundamental biology, may be able to be reanalyzed in some small way to give us an insight on an actionable clinical impact. Or thinking about like, could this have implications for which companies we think could really be really strong in their market spaces? And so even one small 1% insight, I think is a good success because it’s building on that, 1% in all different directions that ultimately leads to where we’re going.

Grant Belgard: So since you have this kind of dual role of physician scientist, how do you think about differentiating between this is something interesting and this is something actionable, right? Because for your patients in the real world, you have to make decisions now, you can’t wait five, 10 years for something to maybe be firmed up. So how do you approach that?

Diane Shao: Yeah, those are really, I think, questions that the field of let’s say genetics is always constantly grappling with. So I’ll just give you an example from my clinic from this week just to make it a little more pertinent.

So this week, I saw a case in my neurogenetics clinic at Boston Children’s Hospital, a two year old that has a condition called lissencephaly, which is their brains are smooth and they had clinical sequencing that comes back with a rare variant that’s homozygous, meaning it’s in both the mother inherited and father inherited alleles of a particular gene and records the variant as variant of uncertain significance which means on a clinical lab basis, they cannot provide a diagnosis. And if you search the literature for this gene, there are exactly four patients reported worldwide that have other variants, not this exact variant in this new gene, but their features are all extremely similar to the given patient.

And so there is a practical matter of how many people need to exist in the world for you to have confidence that the fifth variant in mother and paternal inherited alleles of a gene is now diagnostic. And so that’s a clinical lab question. And on their end, they said, hey, we can’t call this disease causing, we have to give it this variant of uncertain significance label. And then there’s a whole other decision to be made on a clinical level. So when the patient comes to see me and I’m like, okay, the lab is not gonna be able to change your classification, but I can tell you your brain looks almost exactly like the four other brains that are out there. Your kid is manifesting all the symptoms that those other four are. We have a very good sense that we should be worried about the things that those other patients have.

So if they have, for example, those other patients had problems with their eyes and so I’m saying, hey, we gotta check their eyes, we gotta check their hearing. These are the things I can worry about now. And those are really practical clinical decision-making matters. And then there’s a whole interesting aspect of, well, what do we do in this gray zone? And those are kind of boundary pushing now research questions. So I then spoke with one of the residents who was very excited about this potentially new gene and this new presentation that we’re seeing. And so they’re saying, hey, can we write this up? I’m like, yeah, it would be great.

And it would be great if we found 10 other people so that we now have the statistical informatic confidence to provide this diagnosis. We can then go back to the clinical lab, change their classification, who would change therefore the classification of other patients that come in with a similar presentation and new variants in that gene, which otherwise wouldn’t be diagnostic. And so we can then go back to the research realm and really make a difference. And so I don’t know if that kind of showcases how the different elements of clinical decision-making, gray zones in what is known in a diagnostic laboratory, and then what can be brought back into the research side are clear from my description.

Grant Belgard: Oh, that’s great. What kinds of uncertainty are you most comfortable with and which kinds do you work hardest to reduce?

Diane Shao: Yeah, so in terms of, we can talk about a couple of different settings here. So maybe in the clinical setting that I, currently in this example, continuing on the kinds of decisions that we can make are interventional. Does this child need therapy? That’s a pretty certain yes. And I can probably give a good sense of how much therapy they need. Do I need certain screening and certain organ systems based on what I know? The answer is yes. And the risk that I’m going to be wrong, or even if they don’t totally need it, that screening will be negative. Okay, those are tolerable risks.

But other risks are not so tolerable. For example, if I am wrong about the variant interpretation and the family is doing prenatal genetic testing for embryo selection for their next child, at that level, I may stop at my confident assessment that this is absolutely the disease-causing gene until I have more of my research statistical evidence that I’m going to gather with my resident, let’s say. And so those are various arenas where I may or may not be able to make a solid decision. And then in the stepping back into the research space, these, the confidence in a research diagnosis is a little more clear.

Because on a research basis, you don’t need to have an assessment of any patient with any variant in that gene that comes in. You just need to have a sense of, is that particular variant causing a functional change? And on a research basis, there’s a lot of other modalities that can give us confidence. You can do, look at the RNA changes. You can see how that variant affects gene function. Structurally, you can do other types of statistical testing if you enroll patient cohorts within your cohort to do, for example, linkage analysis or other types of confidence-building metrics. And so in different settings, there are different ways to really increase confidence in different types of interpretations.

Grant Belgard: How do you think about measuring success when outcomes can take years to show up?

Diane Shao: Yeah, yeah, that’s a great question. You’re kind of thinking about as we, let’s say, push forward our research agenda on a given genetic condition, what the success is.

Grant Belgard: Well, or I guess, or in the case of investment, right?

Diane Shao: Yeah, okay, yeah, no, I think that’s a great question. So why don’t we jump to the investment for just a moment? So right now, for example, not all rare disease genes are good even current targets for investment. To even embark on starting a company, there are only certain, you’ll see this mentality where people will invest in only a handful, let’s say, of rare diseases that are broadly of interest. And partly it’s because those are the diseases that we know the most about.

There is a lot more research dollars, there’s a lot more research interest. Maybe the patient advocacy groups have been really promoting or focused on getting a therapeutic out and there’s enough support interests that finally there’s enough data and understanding so that initial startup can even be conceptualized for investors to be interested. And so not every, let’s say, genetic condition in this moment in time is ready for research translation.

And so pushing that long-term envelope from the fundamental discovery of a gene to when is it ready to be even considered a therapeutic target to actually pushing out the company to then now assessing that market landscape and seeing whether or not it’s worth funding, et cetera, is a really, really long pipeline as you’re suggesting. And so in any given moment, there are many different people from investigators pushing their visions and agendas to the NIH pushing their research vision agenda to the business development people pushing their agendas and the investors pushing their agendas.

And I kind of really see the progress for each individual needs to be unique. As an investor, I am really interested in pushing the investments that we make into rare diseases more broadly, but that doesn’t mean every rare disease that’s presented to me with the potential therapeutic target is a good investment to make. And so a progress on an investment front means having grasped, let’s say, further the landscape of a particular genetic condition, grasped maybe the market space, what are the FDA regulations?

Those are things are progress in an investment space versus in a research setting, I may be a little more agnostic to which disease I’m looking at and promoting. And that research space may be promoting, let’s say, like progressing new techniques for gene discovery. It may be figuring out how can I collaborate better with others. And so for people in any given phase of all of these different intersecting sectors, I think progress at the end of the day is very, very individual. And I hope that collectively across everyone, this will really push the boundaries of treatment for any disorders, you know, rare or common.

Grant Belgard: So across all the domains in which you operate, what is your expectation for the impacts AI will have in the near term, right? Looking out over the next one to two years?

Diane Shao: Yeah, after this conversation, I’d love to hear your thoughts on that too, Grant. But for me, I feel like AI has touched every aspect of both what I do and also how I assess both the research spaces I want to go into as well as investment spaces I am considering. At a high level right now, I would describe my usage of AI as increases in efficiency. So increases in data sourcing, let’s say to help me find relevant papers and subject matter and people and spaces, et cetera. I also feel it as efficiency in terms of helping me integrate across different, let’s say, perspectives.

Right now I have all this data that describes this biology. Now I want to understand how to change this into a clinical risk assessment model, et cetera. These are kind of, I would still consider efficiency spaces. That being said, I know that the AI field really wants to do new discovery, pushing the envelope, idea creation from AI. I don’t feel that it’s there right now and I’m not really engaged in tool development to know how close are we to that. I think that pushing efficiency and data interpretation, management, et cetera, is already a really, really large task.

It takes off so much from my plate to be able to outsource a lot of those tasks to AI for it to also hold that information for me across, let’s say, these are the grants I’m writing and this is all the data that I need you to store for me. And as I re-synthesize into a new grant with a slightly different focus, how can you help me shape that? And then so it lessens my work a lot. And I’ve found it tremendously beneficial. And to me, that’s really important because it means I can leave my mind space, let’s say, open to big vision problems. I can be the one leading idea generation and then using AI to kind of curate these spaces. So I would say that’s my perspective. I think AI is transformative, but I don’t feel like AI is transformative in the way of taking the place of human creativity and pushing the boundaries of, let’s say, the unknown, unknowns in the world.

Grant Belgard: When you’re designing a study, what decisions early on have you found most impact downstream data quality and interpretability?

Diane Shao: Yeah, so the types of study that I design most are in the realm of human genetics. So I do some human gene discovery research for which I would say the pipelines for that are probably pretty well described. And then I also do single cell technology development for the purpose of understanding how mutations arise and in particular, understanding the variation in the DNA within or between individual cells of an individual, what we call somatic mosaicism.

I’m part of a pretty large consortium from the NIH called the NIH Somatic Mosaicism Across Human Tissues Network, where analogous to other large consortium efforts, one of the most notable ones being the Human Genome Sequencing Project back in the 2000s, the idea is that by characterizing the full intra-individual variability in genetics, that tool can be extremely useful across many, many different areas of biology and life sciences. And so for single cell technology development, that experimental design really affects the downstream.

So for example, I have been working on understanding human brain development and the single cell copy number landscape. Copy number changes are structural changes in the DNA where whole areas of regions of chromosomes either get amplified or deleted or lost. And so to detect structural copy number changes uses fundamentally different techniques than detecting other types of variations, such as single nucleotide variation, where you’re just changing, let’s say C to a G or a single nucleotide, and also uses totally different techniques than identifying, let’s say, repeat expansions in single cells, which are also highly mosaic across an individual.

And so the study design choice of tool becomes really critical to say, is it even possible to analyze my genetic change of interest? And that decision comes down to a matter of, what is the goal of the project? And also has some practical considerations of cost, and also has some technical considerations of do I have the informatic support to analyze the type of variation I’m interested in?

Grant Belgard: How do you communicate uncertainty to different audiences, scientists, clinicians, families, leadership?

Diane Shao: That’s a great question. Depending on the audience, I try to do things differently. Most people do a lot better with the things that are certain than the things that are uncertain. I think that for me, always trying to portray first what we do clearly know can be really, really helpful to then give a framework to all the things that we still don’t know or still exploring.

So just to give a concrete example of that, in my work in mosaicism, I really think that there will be totally new possibilities for genomic biomarkers or different possibilities for precision medicine that are related to the genetic landscape when we look across all the cells in the body. But of course, we’re still in early days of that on a research basis, so I don’t know if that’s true. But what I do know is true is that we have, for example, in our brain, in our neurons, hundreds of single nucleotide variation per neuron, times six billion neurons in our brain by the time we are born.

So that is a biological fact. And so I can hang on that certainty and share with people that certainty and then describe what I think we can do with that level of genomic data. And just so the audience kind of understands where I’m going a little bit with this thought, think about, for example, the difference between when the Human Genome Project first came to light and they sequenced one human versus what we can do with the genetics now that we’re sequencing hundreds of thousands of humans across different countries and across different disease modalities, et cetera. That type of data, while we don’t know yet what will be revealed about ourselves and tissues and how they all work together from a DNA perspective, I think is also inevitable to shift how we think about disease and how we think about diagnostic possibilities.

Grant Belgard: What is the current state of the evidence on the impact of mosaicism on clinically relevant phenotypes and the prevalence?

Diane Shao: Yeah, that’s a great question, Grant. So in certain diseases, it is a fairly actually commonplace now to think about mosaicism. There are a number of disorders where it’s pretty common to now look for mosaic genetic causes. So for example, epilepsy, there is a subset of patients with epilepsy which will get surgical removal of the epileptic lesion and often somatic mutations are found in those lesions. They follow particular biological pathway principles and so those are pretty clear.

Another realm which is pretty common to think about now is vascular disorders. So localized cavernous malformations, there’s a pretty common precedent. Vascular disorders like Sturge-Weber syndrome which is a capillary malformation over just one part of the body now are pretty commonplace. So there are certain disorders where it is common to now think about somatic mutations as the primary cause. There are other disorders that is coming to light that even while they can have both causes in the germline and at a mosaic level, that many of those individuals actually are mosaics.

And just because think about generating a human, how many cell divisions that you went through to generate this entire person from the time they were an egg and a sperm meeting each other to the huge five to seven foot human being, there’s just a lot of mosaicism to be had and that causes disease and sometimes they look like germline presentations even if the person themselves are mixed genetically. And then there’s a whole realm of things that we don’t know which is maybe a subject of research but things like there are diseases where certain cell types are lost.

So for example, in Hirschsprung’s disease, a very particular neuronal cell is lost from the gut intestine. And so to me, that’s a high likelihood place that there is likely a somatic localized cell-specific component but when it’s lost, how do we use genetics to actually determine what it was that was lost to begin with? So a lot of questions but I hope that answers your question on the areas that we do currently know which is I would say a tip of the iceberg.

Grant Belgard: So how do you think about future development of precision medicine and so on in a mosaic condition?

Diane Shao: Yeah, so I’m really excited about a couple different areas. One area is simply leveraging the power of essentially what I would describe as let’s say a saturating mutagenesis experiment within an individual. So thinking about what we’ve learned from human populations. So when we sequence hundreds of thousands of people from human populations, we can see, hey, these genes never have a mutation and the other genes have mutations that are just scattered all across the genome.

And those genes that never have a mutation, they’re actually important to humans in some way. There’s a reason why we never have a mutation usually is because either they were embryonic lethal or they affected reproductive fitness in some way. And so that’s actually a huge part currently of gene discovery to compare to population databases and say, hey, those areas are constrained, this may be an important disease gene. And so similarly, you can imagine that there are lots and lots of disorders which don’t have a strong reproductive fitness component.

Think about cancer, for example, in old age, it’s not necessarily gonna be selected against the population level. Think about eye conditions like strabismus where you’re not really gonna have a strong reproductive fitness signal or autism even, nowadays many people are getting diagnosed when they’re already lived full lives. And so while some forms of autism will have reproductive fitness constraints, others will not.

And so then the question to me starts to be, well, if we can now get information on genomic constraints, so which areas of the genome are
really, really important just in a particular cell types, like in neurons or in the lung cells or in something like that, is that now new information on what genes are really critical for biology and does that tell us something about disease? So that’s one area I’m really excited about.

You can also think about that the same way in terms of modulation, how do individual genetics within a cell either drive a phenotype or are still collected against the phenotype. So for example, let’s say a person with a neurodegenerative disorder where some of their neurons will die with age. Well, it’s not that these neurons die uniformly, some will die earlier, others will die later and there’s genetic variation between that.

So can we leverage that to somehow understand what is it genetically about those individual cells that are surviving longer? And I think in the past, the view is just, oh, it’s stochastic. Some are just gonna die sooner, some are die later. And yes, probably it is stochastic, but stochastic doesn’t necessarily mean random. Stochastic is a distribution that is related to some underlying biology. And so these are open questions as to the genetics that drives these stochastic processes. And so these are some of the areas I’m interested in and I think they have really strong translational potential and also the therapeutic potential. Yeah.

Grant Belgard: When did you first realize you wanted a career at the intersection of medicine and research?

Diane Shao: This is a great question, Grant. I think it actually goes back to our college days. When we were at Rice University, I started working for a PI at Rice who’s now left that university, but he was my first significant research experience and I realized he was kind of a remarkable person in that he was a trained astrophysicist who then became an HHMI investigator, which is a very prestigious award funded investigator who studied slime molds, Dictyostelium.

And then when I was in the lab, was going into human immunology and had created a compound to treat fibrosis, which is I was working on in the laboratory as like he had one postdoc and, I guess, me the undergraduate working on this at the time. And then he turned that into a company that was sold for $1.4 billion, ultimately for trials in fibrosis. And so that mindset of the fundamentals of science can be leveraged across astrophysics to slime molds, to human immunology, to translational medicine, I think already came to me maybe through this experience by osmosis maybe as an undergraduate in this space.

And I think that mindset really resonates with me as in at the core, science is science and those principles apply no matter what realms you’re looking into. And also as scientists or people engaging with life sciences in any way that many people do, you also don’t have to be limited to the one dimension that you’re trained in, that all of these realms are possible and so, for me, that is what also made me think doing a MD/PhD career path would be one for me because it was one where I got to see both the research perspective, the translational perspective, the clinical perspective and then in my early 20s, in my past couple years have added this investment and market space perspective as well.

And while some people feel that they’re really disparate and indeed they’re really tackling very different problems at the core, if you go to core principles, there’s a commonality.

Grant Belgard: What’s something you intentionally didn’t do or stopped doing that made your path a little easier?

Diane Shao: Oh, that’s interesting. Yeah, it does sound like I’m just accruing things, but to be honest, I drop things constantly. I actually think that’s a critical part to maybe going back to your question on what drives progress. Progress does mean constantly cutting out everything that is not leading to your vision of progress.

So even in, let’s say my work on single cell technology, I was developing some technology, applying it to a number of different settings and when I found one that seemed like it’s particularly interesting in terms of its understanding of the biology and that we could really gain traction with the tool and stuff, it meant I just dropped everything else and I don’t have any intention of picking them back up unless they further my vision in a given direction. And so I think that there is always this fear, like the sunk cost fear of like, oh, I’ve invested all this time, I gotta finish it, it’s gotta be a thing, but I don’t buy into that at all.

So I actually need to constantly drop things along the way and to me, that’s a huge driver of success because it means we focus on our energy, on the things that go toward a vision.

Grant Belgard: If you could go back and give your earlier self one piece of advice, what would it be?

Diane Shao: Oh, probably don’t stress so much. You know, I think that especially as a trainee or a student, it was so easy to worry about how things would unfold and try to control them, but honestly, simply because we didn’t know, for example, writing a first paper, you don’t actually know what it takes to even write a paper or, you know, what are all the steps, what are all the pitfalls, what is everything you wouldn’t even need to think about?

And so I think I spent a lot of time stressing and let’s say strategizing and things like that, but the reality is you just gotta do it and then you’ll learn from it, as in nothing needs to be perfect that first time. And to allow for that, allow for the learning process, you’re gonna get more out of that than trying to make it go a particular way each time.

Grant Belgard: I guess on that note, how do you avoid burnout?

Diane Shao: Drop everything else that you don’t feel like doing. But in some ways, I really believe that burnout is a combination of what we’re holding, all the different aspects that we’re holding, and also how we feel about it. As in, if we’re aligned, like if I’m holding a lot of things that I’m doing and those are the things that get me up in the morning, I’m so excited about them, I can’t wait to discuss them with people and share them with the world, that’s not burnout.

That’s just me holding a lot of things that I like to do. But burnout is having a particular interest, but also feeling like I’m obligated to do all these things I don’t wanna do, I’m supposed to be finishing XYZ thing in this other realm that I’ve sunk all this time and effort in. And so to me, preventing burnout is pretty continual, like every few weeks renewal of what is my actual vision, what is actually driving me, and am I doing the things aligned with that? Because if it’s not, and you’re doing that and having that conflict internally long-term, that’s what burnout is. So yeah, so if you are aligned, then that will feel good. Everything will feel like fun and flow.

Grant Belgard: What’s an effective way to build competence across disciplines?

Diane Shao: Competence or confidence?

Grant Belgard: Competence.

Diane Shao: Competence. Oh, that’s a great question, Grant. The biggest thing is to not be afraid and to not be afraid to not know. There’s no reason you would know. And I find that what people really orient around is a strong vision. So for example, maybe with my own interest in mosaicism and thinking about how that can push our boundaries in precision medicine, I work in child neurology, I work in pediatrics, brain development, et cetera. I’m very interested in maternal influences on childhood brain development, but that’s not a space I know at all.

I don’t know a single OB, I don’t know nearly anything about obstetrics or what happened, all the actual biological principles of pregnancy, et cetera. And so, as I delve into that space, that is a totally new space for me. But what I do orient around is how important I think understanding this phenomenon is. And if I can share with people my vision, what I know in a very clear way, others are going to wanna help me and that will build my competence. As in, I don’t go in pretending I know anything about these other spaces where I don’t.

And that’s actually where true collaboration lives. It’s not, we both know everything about the other’s field, it’s knowing exactly what do I know that’s valuable between us and exactly what do you know that’s valuable between us and then putting those together. And competence is not always getting to know everything in a different space. Competence is sometimes being able to know where the gaps are and know how to ask questions and get help.

Grant Belgard: What mistakes do you see smart people make when they try to do interdisciplinary work?

Diane Shao: Oh, that’s a really good question, Grant. You’re full of good questions. So one thing I do think is really important to recognize is that there’s always a difference in culture, no matter what. Research culture, medical culture, even as I’m talking about neurology research versus obstetrical research, there’s a difference in culture. And if you are not recognizing that and respecting those cultures, it’s just not going to work out. So for example, in the biological space, samples are really critical. I work with post-mortem tissues, those are really important. And PhD scientists are also really interested in studying human tissues.

But why do PhD scientists have a lot of trouble integrating with MDs? It’s because they kind of speak different languages, right? It’s the way they’re talking about the samples is different. The PhDs are talking about the samples as a biological utility. The MDs are talking about them like the boy they took care of for 10 years and then passed away for some reason. And so to understand that culture is critical. If you go to the MD and say, hey, I’m looking for samples for X. They might say like, oh, okay, I have some. And then you’re going to say something like, okay, well, I want to study protein. Proteins A and B and how they interact and blah, blah, blah.

The MD is not going to connect with that, right? So thinking about, well, protein A could be a therapeutic if it interacts with protein B in this way as a much more viable start. And then also thinking about, it’s easy to start thinking about, okay, the doctor is just the one who’s going to just be retrieving the sample and et cetera. And the minute you start reducing some other person’s role to just a task oriented sample retrieval role, you’ve totally lost the collaborative interdisciplinary engagement there. And so I think about these things a lot and I encounter them constantly.

For example, even in my example of, what do I do as a neurologist who wants to think about obstetrical tissue? Well, when I started, I’m used to paying $0 for my tissue because I get them from biobanks. I get them from patient groups that are really trying to get people to utilize the tissue for studies, et cetera. But obstetrical tissues are different. They pay a lot of people healthy pregnant women money to collect samples to be part of studies, et cetera. And so even engaging on costs, what is value?

I was running the risk of devaluing all of their tissues simply because I’m used to paying $0 for my tissues. And so these are all cultural nuances between disciplines, the same way going to a different country, you really have to consider those cultural nuances. Understanding them is non-trivial. I do rely on saying things like, hey, I don’t know what the typical way things are done in your field is, this is what I’m used to. And having that humility upfront allows people to also share with you their culture and being open to that, whatever that culture is and not just judging it as unreasonable or too hard just because that’s not the culture you’re used to.

Grant Belgard: What’s a good habit you find most strongly compounds over time?

Diane Shao: Oh, good habits. I find that, I think this may be going to your burnout question, finding the things that are going to make you feel passionate and excited every day. And sometimes they’re not always scientific questions. Like for example, I find a good habit that I have is taking a break at 2:30 PM every day. Either that break could be taking my 2:30 meeting and asking the person if they’d rather take a walk around and have a discussion instead of sitting at a Zoom screen, or that break could be meditating for 10 minutes by myself in a quiet space.

And so I guess I mean that as in, not to say that everyone needs to take a break at 2:30, but just if that is something that you need and will make you feel good about your day, that’s something you need to do for yourself. Similarly, if there’s a particular question you need to answer to feel excited, engaged in science, you just need to go down that route regardless of if it’s exactly the right time or if you have 10 other things you need to finish first or whatever it is, because it’s doing those things for you that is really gonna make everything worthwhile.

Grant Belgard: And where can our listeners follow your various threads of work?

Diane Shao: Oh, that’s a wonderful question. I am in the middle of building my own lab website, but for now you can find me through the
Boston Children’s Hospital. I have a research page there. I’ll provide the link for your notes. And then also my venture capital firm is at LegacyVentureCapital.com.

Grant Belgard: Well, Diane, thank you so much for joining us. It’s been
lovely.

Diane Shao: Thank you so much, Grant, so lovely to be here.

Transcript of Episode 79: Yang Li

Disclaimer: Transcripts are automated and may contain errors.

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Grant Belgard: Welcome back to the Bioinformatics CRO podcast. I’m your host, Grant Belgard. Today, we’re joined by Professor Yang Li from the University of Chicago, a computational genomics researcher working at the intersection of genetics, gene regulation and disease. Yang, welcome.

Yang Li: Hi, Grant. Nice to see you.

Grant Belgard: Good to see you again. So what’s been energizing you most recently in your work, scientifically or operationally?

Yang Li: Well, since the New Year’s, I’ve been playing a lot with Claude. I mean, everyone’s, I think, playing with Claude. And I think both in terms of the science that he can help me produce and also, you know, just managing my schedule, that has been a game changer. And I’m still exploring what he can do. But yeah, so I think that’s basically what’s been what I’ve been thinking about most of the time.

Grant Belgard: What have you put into practice so far? Like what’s kind of, quote unquote, in production?

Yang Li: Yeah, we’ve been writing the revisions for one of our papers. And I’ve been using that extensively both to help me write some of the response, making it a little bit friendlier, but also rewriting some of my old code and checking for bugs and things like that. And it’s amazing. The number of things that I can do in just an hour far exceeds what I can do within a day at this point. So things like producing a plot in a slightly different way. As you know, it’s very difficult to rerun your code, especially if it’s not the best practice in the sense of software engineering. I’ve been self trained in terms of programming, mostly, and so the comments are not necessarily the best. But with Claude, it helps me comment, it helps me name my variable, right?

Or at least improve the naming of my variables, and then produce plots very, very fast, right? And so as you know, a lot of the way we check that the code is doing its job is to visualizing the underlying data in many different ways. And so Claude helps me do that. You know, as soon as I have an idea, I can just ask it to do it. And then I would see the visualization and I would sometimes I would find error. But most often than not, it gives me exactly what I expect.

Grant Belgard: When someone asks you what you do, what’s your favorite way to describe it without using jargon?

Yang Li: Well, lately, I’ve been trying to steer away from that because I’ve been doing things that are pretty technical. But in just a few sentences, I think I would just describe it as I’m trying to understand how proteins are expressed. And there are many different ways by which we can control the expression of these proteins and focusing on this regulatory mechanism called RNA splicing. And this is highly regulated. And I want to understand what is the function in different system and how to modulate it using drugs.

Grant Belgard: What makes this the right time for that?

Yang Li: Well, I think the reason why I chose this and I stuck to this ever since I think I was in grad school, really, is because almost nobody talks about genes in terms of how many proteins each gene can be producing. And so and it was clear when I was researching, even the things I was researching in grad school, which is, as you might remember, the cichlids, it was clear to me that every single gene produces many proteins or many isoforms. And to me, it felt like this has had to do something. Right. And my perspective has changed slightly since then. But because of my earlier work and the fact that no one, almost no one was really researching that, I became really interested in that topic.

Grant Belgard: So what is your current perspective on splicing?

Yang Li: Well, when you read the textbook, it basically tells us that every single gene, every single human gene can produce many different proteins and many different protein isoforms. So these are isoforms that are essentially the same, but with slight differences. So it could be one protein domain that is included in an isoform and in another isoform, this same protein domain is excluded. And so often textbook or in literature, it would be described as something intentional, as in the two version of the proteins have very different function. So one would be performing function A and the other would be performing function B. And both are very important for the survival or the proper function of a cell or the organism.

But what I think now is that the vast majority, and by a vast majority, I mean really over 90% of these different isoforms is not really to have a different function, but really as a regulatory sort of switch. So again, to fine tune, very similar to gene expression level, right? So when you regulate gene expression levels through enhancers and promoters, you’re not changing the final output or the function of the gene. You’re just changing the activity by a little bit. And I think splicing most of the time is doing that, is doing exactly the same thing. The regulatory input is a little bit different, but the outcome is very similar.

So it’s able to change the protein and have a different function, but those are really the minority of the cases rather than the majority of the cases, as is taught by literature or the textbook.

Grant Belgard: How do you decide if a problem is method worthy or just something you’ll apply existing tools and move quickly on?

Yang Li: So do you mean in terms of developing a tool or just using a tool to solve a problem? Right. So I think it takes me a long time to convince myself that I need to develop a method for something. And so in general, I try to use methods that exist already or previous method that I or my lab has developed. In some very rare case, I think, hey, we need to develop a method because there’s really something that hasn’t been done. And we really need to do that and also that we can do it. So all of these checkboxes has to be checked in order for me to move on to method development.

And I should say that we’re not particularly, I don’t think my lab is particularly good at developing methods, but we’re pretty good at identifying, I think, problems that can be solved by an older method whose goal is not necessarily for, well, hasn’t been developed for the specific question.

Grant Belgard: What are the most common bottlenecks you run into today? Is it a matter of data, compute, annotations, study design, interpretation, something else?

Yang Li: Yeah, that’s a pretty good question. I would say for me, it’s my time and getting a sense of what to focus on when there’s just so many people that I think needs my attention, so many projects that needs my attention. I think one thing that I’ve heard a friend tell me was a good example that I often talk about. It’s this context switching time. I’ve heard that the grape vines that Terry Tao, the famous mathematician, is extremely good at context switching. So he basically could switch from one problem to the next within seconds. And for others like me, we need more time to context switch. And so our schedule, when I guess you become a faculty, is that it’s spreading blocks of one hour. And I find it pretty hard to switch context from one hour to the next.

So I try to block more time, but then there are fewer blocks of the longer period of time. And so I think that’s somewhat of a bottleneck for me, is to find a longer block of time so I can have the time to context switch and then do deep work instead of just trivial work in order to make progress. It feels a lot of time I’m trying to just keep afloat and that doesn’t give me enough time to do enough deep work, which is the thing that I think I’m good at and also the most happy in doing. Yeah.

Grant Belgard: Have you found using tools like Claude impacts that in any way?

Yang Li: Yeah, yeah. So I think previously it was very hard to, I had a lot of questions about a data set or some topic and it just never felt like I had the time to do it. And with Claude, all of a sudden you could do things that would take a few hours. It would just take you a few minutes because it had the context, it remembers the context in which and you would ask and then you would remember the context and then you would just do it. So for example, plotting a figure about a data set and then it remembers where the file, where the raw data was. It would have taken me maybe 10, 20 minutes if I came back to this specific project after a week. It would take me maybe 10, 20 minutes to even recall where was the file that I was using and what exactly I was doing essentially.

I can ask Claude or summarize what I was doing or just scroll up a little bit and then ask questions and then he would give me the answer within a few minutes and then that would get me back on track much more rapidly than he would me by looking at my own code and browsing and recalling. So that has been extremely useful. I think also Claude might be able to help me manage better. I haven’t implemented this, but I’ve sort of joked around that I would have my trainee talk to an agent or Claude and then Claude would tell me, you know, summarize all of their things. And then I would only have to read through the summarized version.

Grant Belgard: So you could be like the nurse at a doctor’s appointment before you see the doctor, right?

Yang Li: Yeah, exactly. And then five minutes before I meet them, I would review that and I would think a little bit to just get into context. And then it would be, I think, a lot more productive, right? So, yeah, I often tell my students to prepare some slides or some notes before I meet with them so that it helps me switch, get into context, because oftentimes I hear about their problem on the spot when they come to me during the half an hour or the hour period. And then I have to think about it. And oftentimes when I think about it, I find it’s not really awkward, but it’s still some pressure to answer, right? I can’t think if I thought in silence for five minutes, even two minutes, right? It feels a little bit long, right? Let alone 10, 15 minutes.

But oftentimes that’s the time that you need to bring you back into context, to recall all of these different information, right? To have a very effective conversation. But the reality is that it’s also hard on them to come up every time with a few bullet points. Or at least, you know, I don’t know if it’s hard for them, but they don’t do it essentially. And this would, I think, speed up tremendously our meeting or at least make it extremely productive because everyone’s on the same page.

Grant Belgard: What’s a recent result or direction that surprised you and how did you respond to the surprise?

Yang Li: I can’t say that there’s a recent direction that really surprised me. I think I plan my projects long in advance and I can see points of failures pretty early on. And oftentimes the project or the direction does indeed fail. But then I often have a backup plan. And so I don’t think there’s anything, any direction that surprised me, I would say. And unfortunately, there hasn’t been anything like a sudden discovery that changed everything, unfortunately. So I’m either a very good planner or just not super lucky in terms of unexpected findings.

Grant Belgard: How do you think about reproducibility in practice? What’s good enough versus gold standard?

Yang Li: Yeah, I think there’s a lot that can be improved in terms of reproducibility. Unfortunately, when I think there is some amount of pressure to understand the system, the biology. I mean, there’s a speed component, right? You want to dig into the biology more rapidly. And oftentimes the solution to that is to do what you know best to do. And we’re not trained as software engineers. We don’t do these kind of unit tests. And so reproducibility and there are bugs, right? So I’ve developed LeafCutter many years ago and I still find bugs there. So in that sense, these things can be improved drastically. On the flip side, I don’t think any of these bugs or these issues affect our results, our biological interpretation of things.

Very rarely there would be a very important result that are affected by these. It does happen that it affects a very minor result, right? Or the interpretation of a minor result. And to prevent these bugs or these lack of reproducible findings, we essentially try to poke holes at our major, what we call major discovery. So the things that would, for example, break a paper or the main finding that we think we made. We would look at many different data sets and we would design tests that would essentially break it in one way or the other. So we have very orthogonal ways of trying to confirm a result. That would include, for example, looking at a just completely different data set or deriving some corollary. So based on these, if this were true, then this other thing must be true.

And so we would do more tests on whether this downstream result should be true, will be true. So we do a lot of these type of analysis. And then at some point, everything makes sense. And if something doesn’t make sense, then we have to explain this. Right. So I think this is a scientific process. And I’m not going to claim that this is foolproof, as in I will never have anything that is later falsified. But I think from my track record, I think this has worked so far.

Grant Belgard: How do you decide what to delegate and what you personally stay close to?

Yang Li: Right. So I try to delegate as much as possible. I try to delegate anything that I think a trainee or someone else or a collaborator can do to them. But I obviously weigh by importance. So the things that are the most important, even though I also try to delegate those, depending on whether I think they can do it, I would pay attention to the outcome. Yeah, in my minor things, I would just trust them to do the correct thing. And sometimes, you know, we have to backtrack when later on we find a problem.

Grant Belgard: How do you help your trainees develop taste, knowing what to do and what’s not worth the effort?

Yang Li: Yeah, that’s a very good question. It’s a little bit like asking me, how do I teach creativity, someone to be creative? And yeah, I hate to have this fixed mindset view, but I think it’s something that’s very difficult to teach, right? I think we can encourage creativity, but it’s something that has to do a lot with personality. I think I’ve noticed some type of personality that are, I would say, not as creative or don’t have as much taste and more rely on other indicators. So, for example, sometimes I notice it as not just my training, but in general, right, that a paper that’s published in Nature, right, or in a high impact factor journal, they sort of rely on that to be as a measure of what’s exciting and what’s good.

And others, they don’t rely on this and they have an internal perception of what’s exciting and what’s not. I think the one way that you can help is to read a lot, right? I think it’s, I always tell my trainees to read a lot. I don’t know if you remember, but in grad school, I just tried to read at least one paper a day and I would go through my RSS feed with, you know, hundreds of abstract every day. I mean, now it’s getting even harder because, well, much harder because there’s just a lot more papers that’s been published. But at least back then I had all my journals that I generally read and an RSS feed and I would go through all of the abstracts, title and abstract. I would do this every morning and I would read at least one paper that interests me.

And so I think that helped a lot in terms of both creativity. I mean, creativity is not just, you know, whether you can come up with new things, right? You can come up with new things to you, but someone might have done it. So you also have to know about what’s out there, right? And taste, I think, is somewhat similar as well, right, to creativity. If it’s just, if you like a paper or if you like a project just because it sounds good to you and you don’t know that much, then maybe someone might not call that a good taste, right? So I think these are linked together.

So the more you know, the more you’re likely to have good taste and you have to have your own sense of what’s worthwhile and what’s valuable and not just use some kind of, you know, external, I mean, what someone tells you, right? Obviously, at some point you have to rely on someone, right? So someone that you respect, someone that you know have good taste, if they like it, then you can maybe up weight something a little bit. But then at the end of the day, you need to build your own, you know, scoring function.

Grant Belgard: So let’s talk about your own career track. In your own words, how did you get here?

Yang Li: That’s a very interesting question. I did mention that I like to plan things ahead in terms of my research project, but my trajectory, I think it’s been, yeah, I’m reminded of the quote by Bertrand Russell. I don’t remember the quote, but essentially it goes like, you know, my life has been like great waves, right? Or great winds, like it blows me here and there. And I really feel that way, that, you know, there are periods of my life where that changed me a lot, right? And that has depended a lot on luck or maybe we shouldn’t call it luck, just circumstances that I guess I viewed favourably and therefore I called these luck. But it could have also been misfortune, right, if it didn’t end up very well. And I think these periods are what, these few periods are what took me here.

And the first period was during the last few years after high school. So right before college, I grew up in Montreal, in Quebec, and there’s this period called CEGEP, which is two years before university, but after high school. And at that point, I met some very good friends who introduced me to coding, but also hacker culture, not in terms of, you know, black hat, but more just, you know, coding hacker. And I remember that I started to also become interested in philosophy a lot and asking, you know, bigger questions such as what is the meaning of life, obviously, what is consciousness and all that. But really asking the question of, you know, what am I doing here, right? And at that point, I started to code and to read essays.

I think many of us have been influenced by essays from Paul Graham about, you know, being a little bit more intentional about who your friends are, who you hang out with. And I think this really has started this trajectory, right, being very humble, always trying to look for people who are smarter, who are more, you know, who are more knowledgeable than me. And so without that perspective, I don’t think I would be where I am right now. I mean, grades don’t really matter, but my grades were very average. I wasn’t particularly interested in anything other than video games, obviously. But at that point, something switched in me, right? So being a lot more intentional about how I use my time, who I’m friends with, or who I hang out with. And I think that worked out, right?

Immediately during university, I just identified people who were really excited about their work, excited about their craft. It didn’t have to be anything particular. But at that point, I majored in mathematics and computer science. And I met very good friends, again, that were really excited about the work that they did. And they were really passionate about something, right? So you can be passionate about video games, which I was about, right? But it’s very easy to be passionate about video games. It’s a lot harder to be passionate about something that’s very difficult and that no one cares about. And so I was looking for these sort of phenotype of people who really cared about mathematics, right?
Something that I didn’t particularly care about, I enjoyed, but I didn’t particularly care about. But then, you know, I started to model things that I cared about and use their intensity on these, I guess, passion, right? And so just recognizing the fact that real usable things like mathematics or coding or these things that are hard and tedious can be something that you really enjoy, right? Was something that’s quite new to me. And then, as you know, I got really interested still through my philosophical angle about aging, the aging process. And so I followed these passions and essentially all through that experience, changing from mathematics and computer science to biology, my main goal was to follow what I was passionate about and to do things as rigorously as I could.

And so essentially that led me to where I am right now, which is not studying what I initially set myself up to do, which is aging. And there’s plenty of reasons for that. But essentially following a passion that not everyone cares about, right? But I care about and applying the same fundamental values to these problems.

Grant Belgard: What’s something you learned early on that still pays dividends today?

Yang Li: Early on, as in how early on? I think one thing that I mentioned a lot to people is doing a degree in mathematics. And I don’t think that you have to do a degree in mathematics to get that. But this is where I got it, is this sense of what you don’t understand is actually very important, right? I don’t know if it’s, it’s definitely not a muscle, right? But it does feel like a muscle that you can use to know gaps in logic. And I think even, I wouldn’t say extremely good scientists, but because I do think that very extremely good scientists, they have this muscle, but I would say maybe many, many trainees and many faculty, I would say, and leaders, they still struggle with some gaps in logic. It’s very easy to jump, to have this logical jump.

And that impacts a lot of things, impacts the science, but also the writing a lot. That’s what I observe. That I think is one aspect that I see the most apparent when I see someone’s writing and I observe that there’s a gap in logic. So you just assume that, well, first of all, you assume that everyone knows what you know, but you also assume that one sentence followed the next sentence, or rather the next sentence follows the previous sentence. And I often see that there’s a gap in reasoning that I think is pretty hard to fix, right? Essentially, you have to say, well, why does it follow? And then a student might say, well, it follows because it’s obvious, but it’s actually not obvious. But how do you know that something is not obvious?

How do you distinguish something that’s not obvious from something that’s obvious? And especially when you’re talking about biology, for something to be obvious, there’s often a stack of unstated assumptions. Exactly, exactly. And in mathematics, when you do a lot of proofs, you’re sort of trained to always question every single step. And so I think doing this has really taught me, or at least it made me extremely careful about these steps. And in biology especially, I thought it was extremely useful because, well, sometimes you just can’t overcome, right? You cannot prove every single thing, right? In fact, the first few years when I transitioned from mathematics to biology, it was extremely difficult, because I was just hung up with the simplest thing, right?

But then I found utility in this because you can stash it, right? You can stash this gap in logic. So you notice them, and then you have to convince yourself that, well, it’s true that I can prove it, but it’s probably right in this system, right? And then you can move forward. But also at the same time, you understand what is this gap, right? And by understanding this gap or this condition, right, that it works only in one system, I think you start to understand the system a little bit better, and you start to understand how can this information that is supposedly only applies to this specific system also apply to another system. And so it helps me transfer some of my understanding from one paper, for example, to another paper, right?

So how might these be similar across papers or across cell types, right, or across disease transferred to another cell type or across another cell, another disease? So I think, I mean, this part helped me a lot, I think, in my thinking and in how I transferred knowledge across disease cell types or anything really. And I guess this was a little bit unexpected. I use very little mathematics right now, very, very little of the things I actually learned during undergrad. But this obviously has stuck with me.

Grant Belgard: What are some things you had to unlearn when transitioning between stages, you know, student to postdoc to faculty?

Yang Li: Right. I mean, I wouldn’t say that it’s unlearn, but change definitely very much so. All right. So when you’re a student and a postdoc, you’re very self-centered. You drive your project forward, and there’s some sense of the truth is the only thing that matters. The results are the only thing that matters. There’s less, I would say there are some, but much less personal touch, right? There’s some collaboration, obviously, but you’re really focused on your own project. At least that was my experience. And whatever I did was a lot focused on just obtaining the truth, obtaining, you know, understanding the way it works. What I had to, I would say, unlearn is maybe be less obsessed with the truth and how things should be done versus, you know, how it will be done by someone.

So it’s hard to force your way of doing things, even though if you still believe that it’s correct onto someone else who might not do the same way as you. Right. And so, as you know, we’re not taught to manage as faculty. And this is something that you learn because you see either students struggle or you see other people struggle. And then you notice that, hey, this is not, I mean, this is not productive, right? You cannot tell someone to work the same way as you did, even though you think or you strongly believe that this is how you would do things. And even if you could prove that this is the more efficient or the better way. So I think this is something that I think about.

Everyone’s different and some personalities are more likely to accept some ways of doing things and some other personalities are unlikely to perform well if you tell them to do it in a certain way.

Grant Belgard: What’s something a great mentor did for you that you try to replicate for others?

Yang Li: Well, I think all my mentors have been extremely kind. I think that’s something that, and at no point I felt like that the mentor just was using me in some ways to get a paper out, for example. And I’m mentioning this because I have witnessed that some mentors, they essentially think trainees, even though maybe they think it’s justified, I mean, using the students as a means to an end. And so I always think of the trainee as a person that is here to grow in terms of their ability, in terms of their knowledge. And so I think that’s something that I’m very careful about. I never try to have a student do something that is not beneficial to them.

Grant Belgard: Given the rapid changes in the field driven by AI, what advice do you typically give to early career bioinformaticians in navigating that?

Yang Li: Yeah, I think that’s a great question. And it really depends on your own personality. I think one aspect is to understand yourself, like what kind of personality you are. And I truly believe that personality matters a lot, right? And it’s really, some might say, oh, well, you have to change your personality. But I find that extremely hard. There are some personality traits that I know that I should change or that if I change, I would be happier or even more productive. But it’s very difficult to change, right? And so the way that I try to guide my trainees, for example, is to get a very broad sense first of what type of personality that person is. There are some, I think it was Ray Dalio in his book, he used to be the CEO of Bridgewater, and he developed these tests.

I don’t exactly remember the specifics, but I think what he did was for every personnel, every member of the company, he has this test that will classify them into what they’re good at and what are their personality. And one thing that I keep on thinking about is doers and thinkers, right? So oftentimes you can characterize someone as a doer or a thinker. The thinkers are those who like to think and then they’d like less to do. And the doers, they’re more, you know, they have a higher affinity to just start to do things before even thinking, right? So one thing that’s helpful and it’s only, you know, potentially related to personality is to figure out if you’re more like a thinker or more like a doer. And maybe you’re both, right? And that’s great.

But then figuring out these sort of traits for you will help you determine what you should focus on. And one advice was, if you think that you’re a doer, maybe you should team up with a thinker, right? And vice versa. If you’re a thinker, maybe you should team up with a doer and be very, again, intentional about this, right? Don’t let chance decide. If you have two doers, odds are that you’re just going to build a lot of things and it might not be very useful or not very good, right? If you’re a thinker, if you’re two thinkers and nothing gets done. And personality as well, it’s the same, right? And sometimes I also think about this diversity. I mean, lots of people say, oh, diversity is good, is good, is good.

But when pressed about exactly how diversity is good, they would say, you know, that the blanket statement like, oh, well, diversity, you know, you have different ways of thinking about things. I agree with that. I think you need a little bit more to really build a good diverse team, right? And this, for example, this diversity in thinkers and doers, and there’s also other personality traits that I forget to mention, right? So there are also, you know, personality traits about being very pessimistic, right? So I would classify myself as being a very pessimistic person. Careful, I’m trying to improve that, obviously. And then there are some people who are extremely optimistic. Like, you have an idea and they’re on board and then they’re like, OK, yeah, it could work because X, Y, Z.

I’m more of the, but it won’t work because X, Y, Z, right? But you need both, I think, on the team. If everyone is optimistic again, then this is going to be maybe an echo chamber of, well, yeah, it’s going to work and they’re just going to be hyped up. And then it’s great, right? Everyone feels great, but then it doesn’t, it’s not, you’re not going to have a good product, right? Because then you don’t consider what the negatives are. And if you’re all pessimistic, like me, if you have two rooms of me, then nothing’s going to work. So I think you need to figure out who you are and then team up with some diverse people, right, in that sense. And again, there’s lots of different, these are just two axes of variation.

There’s a lot more axes of variation that I think that you can optimize to build a very strong team.

Grant Belgard: What separates great collaboration partners from frustrating ones in CompBio projects?

Yang Li: As in me, is it CompBio or like two CompBio teams, or like one biological and one computational?

Grant Belgard: Yeah, probably a computational and a wet lab.

Yang Li: And a wet lab, I see. I think there needs to be respect, right? Respect for each other’s craft. If one is, again, using the other and without any amount of respect, I mean, that seems obvious, but it’s actually not. And it can go in both ways and often does, right? Yeah, yeah, exactly, exactly. So we, as a computational people, we can treat the experimental as just, you know, a pipette. Like, oh, you’re going to be replaced by robots soon, right? In the same way that the wet lab experimentalist cannot treat us as, you know, Claude Code, right? And in fact, I see it happen, right? Not every day, but I know who these people are, right? And so it’s a lot more prevalent than you might expect, I think.

And also a little bit of effort in understanding the other is, I think, at bare minimum, right? But obviously, accepting the fact that you’re not going to be as good as your experimental or dry lab counterpart. Another thing that is extremely important is that you have to enjoy working with them. Sometimes it could be tempting to work with someone who’s just very good, right? And you just need the resource. But personally, I just don’t think it’s worth it if you really don’t enjoy working with someone. Yeah, personally, I don’t think it’s worth it. The other thing is energy level. I think it’s very important to have the same amount of energy. If one of you is just a lot more excited, you end up being really annoyed that the other one is slacking off, right? And vice versa.

They’re probably going to be annoyed at you, or you’re going to find them pushy if you don’t have the same energy level. So I think these things are the main thing. And I’ve had, I would say, very good collaborators and pretty bad ones. And I think always these three aspects separate these perfectly.

Grant Belgard: What frameworks do you use when helping trainees decide on career paths?

Yang Li: Yeah, I think it also has to do with personality. Anyone who’s very curious and very open minded and maybe like more, you know, just very idealistic, I would try to push them towards academia. Anyone who is very practical and, you know, I don’t mean to say that one is better than other. Anyone who is very practical and have a very good sense of what they want in life and they don’t want to deviate too much. I would say that I would, you know, steer them towards industry. And I don’t tell them that, right? Everyone who goes through my lab, I tell them that I think that they could become good academics. But the fact of the matter is academia right now is not super welcoming in the sense that it’s just very difficult. It’s very difficult to have a tenure track position.

That being said, there’s a lot of position that is not tenure track. And if you’re OK with that, and I think you should totally be OK with that, there’s a lot of possibilities. And I would also encourage that. But obviously, you know, if you’re very creative and very, you know, idealistic kind of person and you really want to change the world or research something that you’re deeply passionate about that not many people might care about, then I still think that academia as a tenure track, having your own lab, at least, is the right place or the right path.

Grant Belgard: Final question. If you could give just one piece of advice to your earlier self, what would it be and why?

Yang Li: Other than buy Bitcoin? Yeah, I think communication is very important to focus on and be more open minded to things to improve. I think when I was young, I was really into doing hard things and technical things. I think you can call it hard skills versus soft skills. And I didn’t think at all about improving soft skills or maybe personal skills. So interpersonal skills. And I think I would give that advice to my past self, even though I strongly suspect that I wouldn’t listen to myself. Yeah, so personal skills is, I think, more and more important, especially with AI, which I think can replace a lot of the hard skills, to be honest.

And so the one who I can see that the one who will succeed a lot more than I will are the one who has the soft skills and know how to get AI to help them with the sort of hard skills.

Grant Belgard: Well, Yang, this has been fantastic. Thank you so much for joining us.

Yang Li: Great. Thanks for having me, Grant.