Bioinformatics Jobs

Principal Bioinformatics Scientist Bay Area, CA 155-165k base Company Overview: This mid-sized, stable, and continually growing biotech company is looking to add a senior-level scientist to their bioinformatics team. The Pitch: Join a well-established and stable biotech company that has consistently expanded its team even during economic downturns. On-Site Requirement: 3-4 days a week on-site work requirement in the Bay Area. The Role: Principal Bioinformatics Scientist As a Principal Scientist in Bioinformatics, you will act as a subject matter expert over data analysis focused around TCR/BCR immune profiling data. The Opportunity: We are looking for candidates who possess: • A Ph.D. in a relevant field. • Proficiency in Python within a Linux environment. • Experience in TCR/BCR sequencing • Wider experience in epigenetics is desirable as well • Strong cross-functional communication abilities. How to Apply: Apply at the link and we will reach out for next steps.

About The Role As a member of our bioinformatics and computational biology team, you will collaborate with colleagues across the company on projects that include data system design, management, analysis and visualization. You will play a critical role in developing cutting edge screening approaches, while designing and maintaining pipelines for large scale molecular screening data. Additionally, you will work as a computational biologist on drug discovery program projects, collaborating on drug discovery efforts as a data analyst, and point of contact for the team’s computational needs. About You You are enthusiastic about working at the intersection of experimental and computational biology. You have demonstrated proficiency in leveraging open source and commercial software to analyze and present ‘omics data. You have familiarity with screening-related assays and the tools used in the field. You enjoy working closely with laboratory scientists to find solutions to difficult biological problems. You are conscientious, detail-oriented, and organized. You enjoy working as part of a team and collaboration comes naturally to you. You thrive in a fast-paced environment where pushing the boundaries of what is possible is the norm. Minimum Qualifications • Ph.D. in Bioinformatics, Computational Biology, Computer Science, Statistics or a related field plus 1-6 years of industry experience. Individuals with a Ph.D. in the Biological Sciences whose research displays a strong emphasis on informatics and data analysis are equally desirable. • Experience establishing efficient pipelines for the analysis of high-throughput screening data from antibody and other large molecule drug development programs. • Significant experience with data processing and data mining in a biological context, including integration of multiple experimental results and databases to produce biological conclusions. • Ability to write high-quality analytical code both independently and as part of a team. • Enthusiasm and experience in software development, with demonstrated expertise in one or more commonly used programming languages such as Python, R, go, rust or C/C++. • Experience with Linux/UNIX environments. • Team-oriented and highly collaborative with a hands-on approach; takes ownership of projects and advances them through both self-directed efforts as well as team engagement. • Demonstrated ability to design and execute computational analysis in accordance with best-in-class scientific standards and practices to ensure robust, reproducible results. • Understanding of statistics relevant to omics data analysis, including experimental design, handling of multiple comparisons, and mitigation of batch effects. • Excellent oral and written communication skills. Ability to communicate complex concepts to audiences with a wide range of backgrounds and technical familiarity. Preferred Qualifications • Experience with building or maintaining scientific software. • Experience with analysis of a range of assay data in a drug development context, including binding (e.g., SPR), display experiments, and developability assays (e.g., viscosity and aggregation). • Experience with AWS or other cloud computing. • Experience building and maintaining Nextflow Pipelines. Compensation The specific compensation package for this role depends on experience, qualifications and level. We anticipate the compensation range to be $106,000 to $167,000 per year. Xaira Therapeutics is an equal opportunity employer. We thrive on diversity and collaboration, and we welcome candidates with diverse backgrounds and experiences.

POSITION SUMMARY We are seeking a full-time Senior Bioinformatics and Data Scientist to join our team at the Buck Institute for Research on Aging to work on projects in academia with a close-knit team, collaborate with experts in the field of aging, and participate in a nationwide effort to further the field. • The Buck Institute for Research on Aging’s Bioinformatics Core is a collaborative group of data analysis scientists who pool their knowledge and skills to provide cutting-edge services for internal and external researchers. Members cross-train to improve their data analysis skills and career development under Dr. David Furman's mentorship. • The Program Projects Grant (PPG) “Cellular senescence and cell fate/interactions as drivers of Alzheimer's and age-related dementias”: focuses on how age-related changes in both neurons and non-neuronal brain cells can drive these pathologies, with the promise of developing effective interventions. • The NIH-directed SenNet Tissue Mapping Center located at the Buck Institute for “Senescent cell mapping, identification, and validation for human somatic and reproductive tissues”: is part of a cross-consortium program to study senescent cells that play positive and negative roles in biological processes. As part of this Center, our Data Analysis Core is the nucleating facility between the Biospecimen Core, Administrative Core, and Bioanalysis Core of the U54 NIH longitudinal study of cellular senescence. • The “Biomarkers of Aging in Human Cohorts Project” is a collaboration between multiple Buck Institute Principal Investigators to investigate biomarkers of aging and vaccine response in human cohorts. The Furman Lab member will help analyze metabolomics and proteomics data to consolidate vaccine response biomarkers. KEY RESPONSIBILITIES • Perform data analysis as part of the Bioinformatics Core including: • Omics Analysis (transcriptomics (single-cell and bulk), proteomics, metabolomics) • Simple/Multiple Linear Regression • Parametric and Non-parametric Statistics • Classification Methods (random forest, SVM) • Neural Networks • Computer vision (Feature extraction) • Biological Aging Calculations (Omics Clocks) • Candidate gene studies and GWAS • Enrichment Analysis • Dimensionality Reduction • Drug re-purpose • Integrative Multi-omics • Analyze and curate data from the SenNet project: • Interact and coordinate between groups to ensure timely collection of data. • Curate and upload data samples to the central repository. • Review and improve Standard Operating Procedures (SOPs) for data transfer and management. • Attend meetings and collaborate with NIH SenNet groups to improve upon current systems. • Analyze and curate data from the PPG project: • Interact and coordinate between groups to ensure timely collection of data. • Data curation and analysis • Collaborate with staff members, research scientists, and principal investigators. • Grant Writing • Journal Article Writing • Figure Creation QUALIFICATIONS Required Education & Experience • PhD degree in Computational Biology, Bioinformatics, or Data Science • Minimum of 2 years professional experience in a biological field • Proficient in R programming, Python, and Bash scripting Other Skills • Knowledge and experience developing and running Bioinformatics workflows • Outstanding analytical, mathematical, and creative problem-solving skills • Excellent listening, interpersonal, written, and oral communication skills • Logical and efficient, with keen attention to detail • Highly self-motivated and directed; works well independently and as a team • Ability to effectively prioritize and execute tasks • Experience in Computer Vision Preferred • Experience with Human data COMPENSATION & BENEFITS • Competitive salary ($95,000 - $105,000) commensurate with experience • Exciting, collaborative work environment at the forefront of science using state-of-the-art techniques • Generous benefits package including health insurance, paid parental leave, generous PTO and 401(k) with 5% employer match & student debt repayment • Work visa sponsorship available for qualified candidates ABOUT US Our success will ultimately change healthcare. At the Buck, we aim to end the threat of age-related diseases for this and future generations by bringing together the most capable and passionate scientists from a broad range of disciplines to identify and impede the ways in which we age. We are an independent, non-profit institution located in Marin County, CA, with the goal of increasing human healthspan, or the healthy years of life. Globally recognized as the pioneer and leader in efforts to target aging—the number one risk factor for diseases including Alzheimer’s, Parkinson’s, cancer, macular degeneration, heart disease, and diabetes—the Buck seeks to help people live better longer. TO APPLY Interested candidates should click the Apply button to complete the online application. Please upload both your CV and a document that includes a brief statement of your interests plus the names/contact information for 3 references.

Caribou Biosciences is a leading clinical-stage CRISPR genome-editing biopharmaceutical company dedicated to developing transformative therapies for patients with devastating diseases. Our next-generation genome-editing technology enables superior precision to develop cell therapies that are armored to potentially improve antitumor activity. We believe the future of cell therapy is off-the-shelf, and we are advancing our pipeline of off-the-shelf, or allogeneic, cell therapies from our CAR-T platforms as readily available treatments for patients with hematologic malignancies autoimmune disease. Members of the Caribou herd open their minds to new ideas and welcome diverse perspectives. We proudly assert that teams do their best work when their members are personally engaged, their ideas are taken seriously, and contributions are recognized. Members of the herd work from our headquarters in Berkeley, California, or remotely. We are seeking a Bioinformatics Intern to support development of our cutting-edge cell therapies. This role offers hands-on experience working in a team environment to design and improve bioinformatics tools that guide our research efforts and improve outcomes for patients. The on-site position reports to a Principal Bioinformatics Scientist. Depending upon the applicant's qualifications, projects include: • Implement AI/ML models to predict protein interactions relevant to cell therapy • Optimize CRISPR design using ML-based approaches to enhance editing efficiency and specificity • Design and benchmark bioinformatics algorithms for genomic data analysis • Analyze single-cell/bulk RNA-seq using short and long-read sequencing to uncover novel insights • Build visualization platforms for R&D and translational applications using internal and public databases • Work with cross-functional teams, including scientists, bioinformaticians, and information technology, to translate computational models into actionable insights • Contribute to research reports, presentations, and publications Preferred Qualifications • Currently pursuing (or recently completed) a Bachelors, Master's or Ph.D. in Biology, Bioinformatics, Computational Biology, Machine Learning/AI, or a related field • Experience with Python or R for data analysis and modeling • Foundation in statistics and biological data analysis • Familiarity with machine learning frameworks (TensorFlow, PyTorch, Scikit-learn) • Knowledge of CRISPR editing technologies • Familiarity with cloud computing (AWS) and workflow automation (Nextflow) • Previous research experience in cell therapy, immunology, or synthetic biology What You'll Gain • Hands-on experience at the intersection of bioinformatics, AI/ML, and cell therapy • Mentorship from leading experts in computational biology and genomic engineering • Exposure to real-world therapeutic development in a cutting-edge biotech environment • The opportunity to contribute to high-impact publications and patents Responsibilities include: • Development of bioinformatics algorithms for donor optimization • Development of robust clinical bioinformatic pipelines to generate automated, reproducible, verifiable results • Prepare high quality documentation to contribute to regulatory filings • Collaborate with an interdisciplinary group of bioinformaticians, data scientists, and engineers to translate research into clinically actionable insights • Occasionally support genomic pipeline development as needed • Leverage internal and external data sources (i.e. IPD-IMGT) to provide actionable data-driven decision making • Present, visualize and communicate scientific insights to internal stakeholders • Provide expertise and technical consultation for internal collaborations Qualifications: • Ph.D in Biology, Bioinformatics, Computational Biology, or a related discipline • Minimum 5 years of biotech industry experience (immuno-oncology preferred) • Proficient in at least one general purpose programming language (R or Python preferred) • Experience developing with workflow management software (e.g. Nextflow) • Cloud-based data science experience (e.g. AWS) • Experience in leveraging data science best practice tools: version control, collaborative analysis and documentation • Experience with common NGS data processing tools and statistical analysis • Knowledge of documentation procedures for clinical-grade software development • Strong communication skills to foster collaboration in cross-functional teams Compensation & Perks • Range for this Paid full-time internship is $26/hour with a 2-3-month duration • Professional development, networking, and mentorship opportunities • A chance to work alongside some of the brightest minds in biotech • Interns are responsible for their own housing and transportation Equal Opportunity Employer Caribou Biosciences is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment where all employees feel valued, respected, and empowered We do not accept unsolicited resumes or candidate submissions from staffing agencies. Any resume submitted without a valid agreement in place will be considered unsolicited, and Caribou Biosciences will not be obligated to pay any referral or placement fee

About Us Nkarta is a publicly traded (Nasdaq symbol NKTX), biotechnology company headquartered in South San Francisco focused on the discovery, development and manufacturing of off-the-shelf, natural killer (NK) cell therapies. Our near-term goal is to bring cell therapy out into the community setting, dramatically expanding access for patients. Founded in 2015 at the birthplace of biotechnology, Nkarta is a fast-growing, fast-moving, clinical-stage company that has built an extensive cell therapy manufacturing operation in anticipation of product commercialization. Our developmental pipeline of engineered NK cell therapies includes clinical programs in B-cell malignancies and autoimmune diseases. Complementing our broad research and development capabilities, Nkarta has also built an extensive cell therapy manufacturing operation. We recently built out a 23,000-square foot clinical good manufacturing practice, or cGMP, facility on-site at our primary corporate location in South San Francisco, California. Nkarta is a people-driven company looking for passionate, collaborative, driven team members galvanized by a paradigm-shifting opportunity to change the cell therapy landscape. Overview Nkarta is seeking a highly motivated, collaborative, detail-oriented Associated Director/Head of Bioinformatics to join our Translational Medicine team. The successful candidate will have experience in leading computational biology and/or bioinformatics teams in a biotech or pharmaceutical setting. This individual will work collaboratively within Translational Medicine and cross functionally to advance, support and execute on biomarker discovery, MOA investigations and data analysis from clinical samples to support translational and clinical strategies in early development. This role is ideal for an individual who is driven and passionate about cell therapy for the treatment of hard-to treat diseases. Responsibilities • Lead, manage and actively participate in the design, development and implementation of computational strategies and hands-on data analysis of clinical and biological datasets, contributing to go/no go decisions • Drive the innovation and oversee the application of advanced bioinformatics state of the art computational tools for analyzing different data types, including large-scale datasets, company metadata in databases, data lakes, Benchling, etc. • Lead and mentor a team of senior bioinformatics scientists, cultivating an environment that emphasizes continuous learning, innovation and career development • Collaborate with senior leadership to prioritize bioinformatics initiatives, delegation of resources, establishment of timelines, to align with company goals and objectives • Foster strong collaborative relationships with experimental scientists, internal and external stakeholders, including Translational, R&D, clinical and regulatory teams to support multidisciplinary projects. • Communicate effectively with internal teams and cross functionally during company presentations to both scientific and non-scientific stakeholders Qualifications • PhD in Biological sciences, Computational Biology, Biostatistics, Bioinformatics, Genomics, or a closely related discipline with 5+ years of industry experience. • Strong foundation in biological sciences with interest in immunology and applying bioinformatics tools and methods to enhance understanding of diseases • Deep-seated understanding and experience in modern statistical methodologies • Expertise in analyzing next generation sequencing data (e.g. bulk RNA-seq, single-cell RNAseq, whole exome sequencing, spatial RNAseq) • Proficiency in Python or R • Strong familiarity with data infrastructure and cloud computing resource implementation and management in AWS ecosystem • Demonstrated ability to oversee external CROs to implement data management and bioinformatics solutions. • Ability to lead teams in ensuring high data quality and integrity • Experience in fostering cross-functional collaboration to ensure alignment of project objectives and seamless executing, demonstrating strong teamwork and communication skills • Ability to multi-task and work independently as well as in collaboration with peers within a fast-paced team environment with a positive outlook and high degree of self-motivation and organization Working at Nkarta Inc. The common requirements of an office environment (computers, computer screens, workstations, etc.) apply when not working in or around the laboratory environment. Car and airplane travel might be required of this role for conferences and meetings. This role is local to the office in South San Francisco; however, the work hours are flexible as agreed upon. A reasonable estimate of the current salary range for this position is $216,000 - $247,000. There are several factors taken into consideration in determining base salary, including but not limited to: job-related qualifications, skills, education and experience, as well as the value of other elements of an employee’s total compensation package. Nkarta also offers an annual discretionary bonus, equity grant(s), medical, dental, vision and life insurance coverage, in accordance with the terms and conditions of the applicable plans. Other benefits include 401K plan, flexible spending account, ESPP, employee assistance program, paid vacation, holiday and personal days, paid parental, pregnancy, and bereavement leave. The 150+ team members describe working at Nkarta through some of the following comments. While getting better work-life balance and improving communications between groups in an early stage start up environment are two areas on which we are working, here are real, anonymous comments about or regarding why people think Nkarta is a great place to work. • “People are always open to ideas. This company provides a safe place for its employees (covid testing, etc.)” • “Exceptionally talented, committed, *kind* & supportive team.” • “The CEO is transparent and honest with expectations for the whole company. There is genuine care amongst the leadership team for their peers and employees. I believe this is unique.” • “Not to sound corny, but the emphasis on people as a valuable resource is something I recognize doesn't often exist elsewhere, and it's here in ample supply, which is great.” • “It's the first place that I've worked where the executive team truly values the employees. It's a pretty amazing thing not to hear that employees can be replaced with someone new. Institutional knowledge is understood.” • “We have a very diverse team with executives that are friendly and accessible.” • “Smart and dedicated colleagues. Mission to make a difference in patients’ lives. Empower us with tools needed to succeed. Open and transparent culture. Transparent leadership. Handling of covid and running the company was done very well.” To learn more about our work at Nkarta and the career opportunities that will drive us forward to serve patients, please visit the company’s website at https://www.nkartatx.com.

About Xaira Therapeutics Xaira is an innovative biotech startup focused on leveraging AI to transform drug discovery and development. The company is leading the development of generative AI models to design protein and antibody therapeutics, enabling the creation of medicines against historically hard-to-drug molecular targets. It is also developing foundation models for biology and disease to enable better target elucidation and patient stratification. Collectively, these technologies aim to continually enable the identification of novel therapies and to improve success in drug development. Xaira is headquartered in the San Francisco Bay Area, Seattle, and London. About the Role As a Bioinformatics Scientist, you will play a key role in analyzing bulk/single cell RNA-seq and other novel NGS assays in support of drug discovery programs. You will work closely with wet-lab scientists to optimize experimental design, ensuring that studies are statistically rigorous and technically sound. Your primary responsibilities will include developing and applying statistical models for gene expression analysis, performing quality control on sequencing data, and translating complex biological questions into quantitative analyses. You will also build, maintain, and run computational pipelines using Bash and Nextflow to enhance scalability and reproducibility. About You You have a strong background in statistics and RNA-seq analysis, with deep expertise in experimental design and statistical modeling. You are proficient in R and have experience working with packages such as dplyr, DESeq2, edgeR, and the tidyverse. You are also skilled in Bash scripting and Nextflow for creating and managing bioinformatics pipelines. You enjoy collaborating with wet-lab scientists and providing guidance on best practices for study design and data interpretation. Key Responsibilities • Perform QC of sequencing and alignment data, critically reviewing MultiQC documentation. • Conduct RNA-seq analysis using DESeq2 and other appropriate methods, handling both UMI-based and non-UMI data, while accounting for experimental factors such as batch effects. • Build and maintain bioinformatics pipelines using Bash and Nextflow to ensure scalability, reproducibility, and efficiency. • Apply generalized linear models (GLMs) and random effects models for differential expression analysis. • Support diverse drug programs through computational and statistical analyses. • Advise wet-lab scientists on experimental design and plate layout, minimizing technical artifacts and facilitating experimental comparisons of interest. • Develop and optimize statistical models and hypothesis tests to extract meaningful insights from gene expression data. • Clearly explain statistical and experimental design concepts to interdisciplinary teams, including wet-lab scientists and project stakeholders. • Contribute to presentations, reports, and publications summarizing methods and key findings. Qualifications • Ph.D. or M.S. in Biostatistics, Statistics, Bioinformatics, Computational Biology, or a related field, with experience in statistical modeling and RNA-seq analysis. • Strong proficiency in R and Python, including experience with scanpy, DESeq2, edgeR, dplyr, and tidyverse for statistical modeling and data analysis. • Experience with bulk RNA-seq data analysis, including QC, normalization, and differential expression analysis. • Proficiency in Bash scripting and experience with Nextflow for building computational workflows. • Solid understanding of generalized linear models (GLMs), random effects models, and experimental design principles. • Strong ability to collaborate with wet-lab scientists, advising on plate layout, controls, and experimental contrasts. • Excellent communication skills, with the ability to translate biological questions into quantifiable hypothesis tests and analyses. • Experience working in a biotech or pharmaceutical setting, supporting drug discovery programs. • Familiarity with Bayesian methods, mixed models, and hierarchical modeling. • Proficiency in Git for version control and reproducibility. • Familiarity with cloud computing environments (e.g., AWS, GCP) for large-scale data analysis. • Prior experience presenting complex computational analyses to diverse audiences. Compensation We offer a competitive compensation and benefits package, seeking to provide an open, flexible, and friendly work environment to empower employees and provide them with a platform to develop their long-term careers. A Summary of Benefits is available for all applicants. The base pay range for this position is expected to be $110,000 - $145,000 annually; however, the base pay offered may vary depending on the market, job-related knowledge, skills and capabilities, and experience. Xaira Therapeutics an equal-opportunity employer. We believe that our strength is in our differences. Our goal to build a diverse and inclusive team began on day one, and it will never end. TO ALL RECRUITMENT AGENCIES: Xaira Therapeutics does not accept agency resumes. Please do not forward resumes to our jobs alias or employees. XairaTherapeutics is not responsible for any fees related to unsolicited resumes.

At Cepheid, we are passionate about improving health care through fast, accurate diagnostic testing. Our mission drives us, every moment of every day, as we develop scalable, groundbreaking solutions to solve the world’s most complex health challenges. Our associates are involved in every stage of molecular diagnostics, from ideation to development and delivery of testing advancements that improve patient outcomes across a range of settings. As a member of our team, you can make an immediate, measurable impact on a global scale, within an environment that fosters career growth and development. Cepheid is proud to work alongside a community of six fellow Danaher Diagnostics companies. Together, we’re working at the pace of change on diagnostic tools that address the world’s biggest health challenges, driven by knowing that behind every test there is a patient waiting. Learn about the Danaher Business System which makes everything possible. The Bioinformatics Surveillance Officer Intern is responsible for establishing a data surveillance pipeline designed to automatically retrieve information from publicly available gene sequence repositories, and evaluates Cepheid test performance against these sequences in silico. This role will provide the opportunity to learn in partnership with Cepheid’s established bioinformatic team and could lead to growth within the Scientific Affairs group. This position is part of the Medical and Scientific Affairs Department and will be located in Sunnyvale, California, although remote positioning is possible depending on the applicant’s experience. At Cepheid, our vision is to be the leading provider of seamlessly connected diagnostic solutions. In this role, you will have the opportunity to: • Develop an automated process to collect gene sequence entries from publicly-available gene sequence repositories such as GenBank and GISAID. • Develop an automated process to evaluate collected gene sequences for allelic variations which may impact performance of relevant Cepheid diagnostic tests. • Develop a process to generate report outs of the Cepheid test performance in Word and/or Excel format “at the push of a button”. • Develop a dashboard to provide summary-level overview of Cepheid test performance. • Aid in the development of outward facing materials designed to communicate the results of Cepheid’s test performance evaluations to customers and/or other external stakeholders. The essential requirements of the job include: • An undergraduate degree with significant training within the domain of bioinformatics, biostatistics, and/or genetics. • Demonstrated 2 years of work experience in a computer script writing function within the domain of genetics, bioinformatics, or biostatistics. Additional training may be considered in lieu of work experience. • Demonstrable proficiency in a biostatistically-relevant computer language and tools such as R, Python, R-studio, BLAST alignment, etc. It would be a plus if you also possess previous experience in: • Infectious disease diagnostics, epidemiology, and/or molecular biology. • Statistical report generation. • Web-based application/dashboard design. The hourly range for this role is $28.00-30.00. This is the rate that we in good faith believe is the rate of compensation for this role at the time of this posting. #earlycareer Join our winning team today. Together, we’ll accelerate the real-life impact of tomorrow’s science and technology. We partner with customers across the globe to help them solve their most complex challenges, architecting solutions that bring the power of science to life. For more information, visit www.danaher.com. Danaher Corporation and all Danaher Companies are committed to equal opportunity regardless of race, color, national origin, religion, sex, age, marital status, disability, veteran status, sexual orientation, gender identity, or other characteristics protected by law. We value diversity and the existence of similarities and differences, both visible and not, found in our workforce, workplace and throughout the markets we serve. Our associates, customers and shareholders contribute unique and different perspectives as a result of these diverse attributes. The EEO posters are available here. We will ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform crucial job functions, and to receive other benefits and privileges of employment. Please contact us at applyassistance@danaher.com to request accommodation.

Stanford Center for Genomics and Personalized Medicine (SCGPM), situated in the heart of SF Bay Area, has an excellent opportunity available for a motivated bioinformatician. This position within our bioinformatics core team will support bioinformatics consulting services for faculty and researchers via the Genetics Bioinformatics Service Center (GBSC). For examples of the projects we support, please visit https://med.stanford.edu/gbsc/services/baas.html. The ideal person for this position is a bioinformatician who lives and breathes NGS data analysis and is passionate about learning. The successful candidate will have deep knowledge of NGS technologies, quality analysis for read alignment and variant calling (secondary analysis), and a large suite of analytical methods for discovering genetic components of human diseases (tertiary analysis). Responsibilities will include: • Meeting faculty members and researchers to evaluate their bioinformatics needs. • Conducting data analysis that meets quality standards of major peer-reviewed publications. • Providing faculty members and researchers with data, analysis protocols, figures, method descriptions, code, documentation, support, and anything else that might be needed to meet project goals. • Managing time and projects efficiently to support the analysis needs of multiple labs simultaneously. • Establishing, refining, and standardizing the process for bioinformatics analysis and validation. Benchmark-driven development is expected, e.g., use of PrecisionFDA/Genome-¬in-¬a-¬Bottle for DNA¬Seq analysis, or the use of well-characterized data or simulated data where commonly-used reference datasets do not exist. • Presenting bioinformatics efforts and best-practices at conferences and symposia. Peer-reviewed publications with and outside of client laboratories are strongly encouraged. • Delivering quick proof-¬of¬-concept feedback on new methods and protocols. • Providing training to researchers to allow them to learn and use new techniques for analysis. • Staying abreast with bioinformatics best-practices (e.g., large consortium Data Coordination Centers like ENCODE and HMP) as well as cutting¬-edge data analysis methods from recent publications. • Meeting 3rd party developers, service providers, and consortium members to stay on top of development of new tools, solutions, and practices in the field. • Observing the highest standards of customer interaction, including maintaining confidentiality when required. The GBSC bioinformatics service team is supported by a group of expert software developers and biomedical engineers who are proficient in a variety of development environments, including large HPC clusters and multiple cloud platforms (e.g., DNAnexus, Google Cloud Platform). Members of this team are expected to participate in activities that are important to the center’s mission, including participation in conferences, arranging seminars, and attending annual retreats and other academic events as necessary. We recommend that interested candidates explore the NIH RePORTER website (https://projectreporter.nih.gov/reporter.cfm : search for organization “Stanford”, text search “Sequencing”, among other keywords) to see the range of basic science research Stanford investigators are engaged in. Our bioinformatics service strives to support the entire range. REQUIRED QUALIFICATIONS: • PhD in Bioinformatics, Computational Biology, Physics, Computer Science or related field. • Ability to define and solve logical problems for highly technical applications. • Deep understanding of next¬-generation sequencing data and bioinformatics algorithms. While Illumina sequencers are the most common data source, it is not unusual to see 10xGenomics or PacBio data. • Provide best-¬practices data analysis, including QC and visualization, employing common NGS pipelines such as RNA¬seq, ChIP¬-seq, ATAC-seq, Methyl-seq, DNA¬-seq, and Microbiome Sequencing. Multi¬omics analysis is often needed. • Proven experience working in a Linux cluster environment. Experience in cloud environments is also a plus. • Ability to select, adapt, and effectively use a variety of programming methods. Strong programming skills in Python and R are expected. Familiarity with C, C++, Java. and Perl are useful. Best practices in coding, including techniques of reproducible and transparent science (github, DockerHub, markdown documentation) will be required. • Excellent verbal and written communication skills with both technical and non¬technical clients. • Stanford offers a supporting learning environment and ability to learn rapidly is a critical need. Our service supports a large and growing customer base and Stanford researchers are engaged in innovative basic science research. We expect our team members to ramp up rapidly to support this innovation. • Strong work ethics are critical in this role, since the individual will be responsible for the highest quality scientific data analysis. DESIRED QUALIFICATIONS: • Postdoctoral training in one of the disciplines listed above is highly desirable for this position. • While a wide background in NGS bioinformatics will be useful, deep experience with DNA¬-seq and/or RNA-seq data is strongly preferred, including whole genome, whole exome, SNP¬-array, tumor/¬normal. • Strong background in one or more of the following: pedigree analysis, machine learning, statistical methods, variant annotation and interpretation, Genome Wide Association Studies (GWAS). • Knowledge of general principles for regulatory compliance, including understanding of the NIH Security Best Practices for Controlled ¬Access Data Subject to the NIH Genomic Data Sharing (GDS) Policy (aka dbGaP compliance). • The core team has developed extensive set of data analysis pipelines on the local cluster and Cloud. We expect reuse of these pipelines. Candidate is also expected to add to this analysis library by developing custom/novel pipelines. • Experience working in academic environments. • Experience with mentorship or project management. Contact information: Please direct all applicants to http://stanfordcareers.stanford.edu/ Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. Stanford welcomes applications from all who would bring additional dimensions to the University’s research, teaching and clinical missions. The expected pay range for this position is $90,000 to $117,000 per annum. Stanford University has provided a pay range representing its good faith estimate of what the university reasonably expects to pay for the position. The pay offered to the selected candidate will be determined based on factors including (but not limited to) the experience and qualifications of the selected candidate including equivalent years since their applicable education, field or discipline; departmental budget availability; internal equity; among other factors. As an organization that receives federal funding, Stanford University has a COVID-19 vaccination requirement that will apply to all university employees, including those working remotely in the United States and applicable subcontractors. To learn more about COVID policies and guidelines for Stanford University Staff, please visit https://cardinalatwork.stanford.edu/working-stanford/covid-19/interim-policies/covid-19-surveillance-testing-policy.

The Department of Medicine, Division of Cardiovascular Medicine at Stanford University is seeking a talented Bioinformatics Engineer to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC). As part of this groundbreaking national research consortium, you will help unravel the molecular mechanisms underlying the benefits of physical activity. Under the supervision of co-PIs Dr. Euan Ashley and Dr. Matthew Wheeler, you will play a crucial role in shaping the future of personalized exercise science and public health. Dr. Euan Ashley's research interests focus on the application of genomics and other omics data to improve clinical care, with an emphasis on cardiovascular disease and personalized medicine. Dr. Matthew Wheeler's research centers on the integration of large-scale molecular and clinical data to understand the genetic basis of cardiovascular diseases and to develop novel therapeutic strategies. By joining our team, your proficiency in applying advanced statistical methodologies, such as multivariate analysis, machine learning, and Bayesian approaches, will be essential for uncovering novel insights and driving innovation in our research efforts. Your strong statistical background and expertise in analyzing large biological datasets. experience in handling diverse omics data will contribute significantly to our understanding of complex biological systems and the development of personalized medicine. You will also contribute to the analysis, execution, and development of pipelines and bioinformatic tools for various omics data generated within MoTrPAC. This innovative project integrates large volumes of clinical and densely time-sampled molecular data, pushing the boundaries of biomedical data analytics. Our portal (https://motrpac-data.org) will push the boundaries of biomedical data analytics to provide insight into the basic and translational science of exercise. Working alongside our multidisciplinary team, you will be at the forefront of understanding how physical activity preserves and improves health, ultimately making a lasting impact on human well-being. To find out more about our studies, you can check our recent publication in Nature and other journals about the endurance exercise training in rats (visit https://motrpac-data.org/publications). To be considered, please submit a resume and a cover letter that describes your interest in this position, and what skills you would bring to this role. Responsibilities: As a Bioinformatics Engineer II, you will contribute to the analysis, execution, and development of pipelines and bioinformatic tools for various omics data generated within the MoTrPAC project. Your primary responsibilities will include: • Collaborate with a multidisciplinary team of scientists and engineers to analyze and interpret large-scale multi-omics data. • Develop and implement innovative bioinformatics tools and methods to further our understanding of molecular mechanisms underlying the effects of physical activity. • Prepare reports and presentations to communicate findings with the team and the larger scientific community. Qualifications: To be successful in this role, you should possess an advanced degree (Ph.D. or M.S.) in a field such as statistics, biomedical informatics, engineering, or computer science along with a minimum of two years of relevant professional experience. They should have expertise in the analysis, execution, and development of pipelines and bioinformatic tools for various omics data and be proficient in programming languages like R and/or Python, as well as Linux bash scripting. Familiarity with pipeline languages, container systems, code management platforms, and systems biology approaches for data integration is also essential. Candidates should demonstrate experience in large-scale data analysis (with emphasis on genomics, transcriptomics, epigenomics datasets), biological domain knowledge, bioinformatics, and software development team-based projects. Additionally, they should be willing to work in a highly collaborative environment, be able to adapt quickly, possess strong communication skills, and have the capacity to work independently. Due to extensive teamwork needed, this is a mostly on-site position. Why Join Us? • Work on a highly exciting and innovative multi-omics project with the potential to revolutionize our understanding of physical activity and health. • Be part of a world-class research team at Stanford University, led by Dr. Euan Ashley, a pioneer in personalized medicine. • Contribute to groundbreaking research with a significant impact on public health and the prevention of diseases. • Enjoy a collaborative and stimulating work environment at one of the top universities in the world. If you are a passionate and dedicated professional with the required qualifications and a strong interest in advancing scientific research, we encourage you to apply for this exciting opportunity. Join us in unraveling the mysteries of physical activity and making a lasting impact on human health. A complete application will include a cover letter. Duties include: • Prioritize and extract data from a variety of sources such as notes, survey results, medical reports, and laboratory data, and maintain its accuracy and completeness. • Determine additional data collection and reporting requirements. • Design and customize reports based upon data in the database. Oversee and monitor regulatory compliance for utilization of the data. • Use system reports and analyses to identify potentially problematic data, make corrections, and eliminate root cause for data problems or justify solutions to be implemented by others. • Create complex charts and databases, perform statistical analyses, and develop graphs and tables for publication and presentation. • Serve as a resource for non-routine inquiries such as requests for statistics or surveys. • Test prototype software and participate in approval and release process for new software. • Provide documentation based on audit and reporting criteria to investigators and research staff. DESIRED QUALIFICATIONS: • Graduate degree (MS, PhD) emphasizing statistics, biomedical informatics, engineering, and computer science are preferred. • Domain expertise in analysis and running pipelines and bioinformatic tools for at least one of the following ‘omes: genomics, transcriptomics, epigenomics (ATAC-seq, RRBS). Knowledge of metabolomics and proteomics analysis is a plus. • Experience in systems biology approaches for data integration. • Proficiency in Python and/or R and Linux bash scripting. • Experience and knowledge of code management such as GitHub. • Experience with pipeline languages such as WDL, snakemake, and/or nextflow. • Proven track record of working with data and infrastructure in an HPC (High-Performance Computing) cluster or cloud computing environments like Google Cloud Platform, AWS, or Azure. • Experience with container systems such as setting up virtual machines and docker instances. • Experience in developing tools and statistical methods for large-scale data analysis is a plus. • Biological domain knowledge (exercise science is a plus). EDUCATION & EXPERIENCE (REQUIRED): • Bachelor's degree and three years of relevant experience or combination of education and relevant experience. • Experience in a quantitative discipline such as economics, finance, statistics or engineering. KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED): • Substantial experience with MS Office and analytical programs. • Excellent writing and analytical skills. • Ability to prioritize workload. CERTIFICATIONS & LICENSES: • None PHYSICAL REQUIREMENTS*: • Sitting in place at computer for long periods of time with extensive keyboarding/dexterity. • Occasionally use a telephone. • Rarely writing by hand. WORKING CONDITIONS: • Some work may be performed in a laboratory or field setting. WORKING STANDARDS: • Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations. • Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned. • Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University’s Administrative Guide, http://adminguide.stanford.edu/. The expected pay range for this position is $104,358 to $128,038 per annum. Stanford University provides pay ranges representing its good faith estimate of what the university reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location and external market pay for comparable jobs. At Stanford University, base pay represents only one aspect of the comprehensive rewards package. The Cardinal at Work website (https://cardinalatwork.stanford.edu/benefits-rewards) provides detailed information on Stanford’s extensive range of benefits and rewards offered to employees. Specifics about the rewards package for this position may be discussed during the hiring process. Why Stanford is for You Imagine a world without search engines or social platforms. Consider lives saved through first-ever organ transplants and research to cure illnesses. Stanford University has revolutionized the way we live and enrich the world. Supporting this mission is our diverse and dedicated 17,000 staff. We seek talent driven to impact the future of our legacy. Our culture and unique perks empower you with: • Freedom to grow. We offer career development programs, tuition reimbursement, or audit a course. Join a TedTalk, film screening, or listen to a renowned author or global leader speak. • A caring culture. We provide superb retirement plans, generous time-off, and family care resources. • A healthier you. Climb our rock wall or choose from hundreds of health or fitness classes at our world-class exercise facilities. We also provide excellent health care benefits. • Discovery and fun. Stroll through historic sculptures, trails, and museums. • Enviable resources. Enjoy free commuter programs, ridesharing incentives, discounts and more. Consistent with its obligations under the law, the University will provide reasonable accommodations to applicants and employees with disabilities. Applicants requiring a reasonable accommodation for any part of the application or hiring process should contact Stanford University Human Resources by submitting a contact form. Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. The job duties listed are typical examples of work performed by positions in this job classification and are not designed to contain or be interpreted as a comprehensive inventory of all duties, tasks, and responsibilities. Specific duties and responsibilities may vary depending on department or program needs without changing the general nature and scope of the job or level of responsibility. Employees may also perform other duties as assigned.

Assistant/Associate/ Full Specialist on Bioinformatics/ Computational Biology study selective vulnerability in human neurodegenerative diseases Assistant/Associate/ Full Specialist on Bioinformatics/ Computational Biology study selective vulnerability in human neurodegenerative diseases Job Summary We are seeking a Bioinformatician to join a multidisciplinary lab focused on neurodegenerative disease. The ideal candidate will bring a strong background in bioinformatics, computer science, or computational biology, as well as general experience in the life sciences. Working with neuropathologists, neurologists, and neuroscientists, the candidate will help design and implement analyses of high dimensional data (e.g., [single- cell] RNA sequencing, genotype or WGS data, proteomics, digital pathology, etc.) from human brain tissue, utilizing bioinformatics tools and databases to reach biologically meaningful insights. Successful candidates should be scientifically motivated self-starters, comfortable working in a highly productive academic environment, and keen on modeling biological processes using rich datasets. This position presents an outstanding training experience for a computational/bioinformatics scientist seeking to break into the neurodegenerative disease field. Neurodegenerative conditions, including Alzheimer's disease and frontotemporal lobar degeneration, selectively target specific neuronal subpopulations, making the identification of molecular signatures of these vulnerable populations imperative for developing new treatments. The appointment will be with the Seeley Lab, which is part of the Memory and Aging Center at UCSF. Required Qualifications: • Assistant Specialist - Master's degree or a baccalaureate degree in Bioinformatics, Computational Biology, Computer Science, Mathematics, Statistics, or a related field with three or more years of research experience. • Associate Specialist - Master's degree (or equivalent degree) in Bioinformatics, Computational Biology, Computer Science, Mathematics, Statistics, or a related field or five to ten years of experience in the relevant experience. • Full Specialist - terminal degree (or equivalent degree) in Bioinformatics, Computational Biology, Computer Science, Mathematics, Statistics, or a related field or ten or more years of experience in the relevant experience. • Strong experience with pipeline development, bioinformatic tools, and data management, and demonstrated competence in programming languages such as R or Python for bioinformatics analyses. • Experience with cloud-based storage and service tools is essential Preferred Qualifications: • MS or PhD degree • Familiarity with the use or administration of laboratory information management systems is a plus. Please apply online at https://aprecruit.ucsf.edu/JPF05474, with a letter of interest, CV, and three references (contact information only). For other inquiries, please contact: bill.seeley@ucsf.edu. See Table 24B for the salary range for this position. A reasonable estimate for this position is $61,300- $188,200. UC San Francisco seeks candidates whose experience, teaching, research, or community service has prepared them to contribute to our commitment to diversity and excellence. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. To apply, please visit https://aprecruit.ucsf.edu/JPF05474 Copyright 2024 Jobelephant.com Inc. All rights reserved. Posted by the FREE value-added recruitment advertising agency jeid-71ad6d9a7a2a6d44819dffe4bb654444