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More Bioinformatics Jobs

Principal BioInformatics Software Engineer

Pleasanton, CA (+1 other)

The Position Impact Healthcare... Roche Sequencing is not only changing science, but we are changing lives! Our team is pushing the boundary of technology with next-generation genomic sequencing. You will develop products that scientists and others in the life sciences will use to diagnose, find treatments, and eventually beat diseases like cancer. Make a Big Difference Do you want a career that enables you to make a huge difference? If so, we want you on our team! We are seeking a Principal Software Engineer to partner with bioinformatics scientists and software developers in support of building the underlying bioinformatics analysis algorithms and workflows to support Next-Generation Targeted Sequencing solutions. Own the efforts to productionize and optimize bioinformatics software working with collaborative and multi-disciplinary teams. Responsibilities: • Develop efficient, maintainable, and documented production software from scientific prototype code or specifications using software development best practices. • Define requirements for sophisticated bioinformatics software applications to develop solutions to complex algorithmic and machine learning problems; such as in the area of secondary analysis (read processing, variant calling) for next generation sequencing. • Conduct system-level analysis of software to include requirements, design, testing, modifications, planning, and performance. • Review software / algorithm specifications and code to provide feedback on potential areas of improvement. Ex. efficiently leveraging accelerated/parallel computing. • Continuously improve software development processes by implementing innovative methodologies and standards used by the Bioinformatics department for software development and testing. • Document work and provide updates at team and project meetings. • Mentor, train, and guide other developers in software standard methodologies including other bioinformaticians in the department. • Represent the project and team at various stakeholder meetings. • Conduct risk analysis and assessment of integrated software projects. Requirements: • Master’s degree in Computer Science, Computational Biology or equivalent technical field; or equivalent combination of education and experience to perform at this level. • 8+ years of experience developing software for enterprise-level customer-facing applications, including 3+ years of experience working as a BioInformatics engineer or computational biologist contributing to Next Generation Sequencing. • Expertise in programming languages such as Python and Java development. • Proficient in microservices architecture and distributed computing in a Linux environment. • Experience with various software development and support related tools such as PyTest, jUnit, Cucumber, Behave, and Command Line Tools (Linux Shell), Maven, Github. • A demonstrated skill set for developing and tuning algorithms is preferred. • Experience with workflow management tools such as Nextflow or Snakemake is preferred. • Experience with Machine learning / Deep learning (used in NGS context) is a plus. • Experience with C/C++ is a plus. • Experience developing for cloud platforms such as AWS or Google Cloud is a plus. • Experience with GPU acceleration architecture and development is a plus. • Experience developing software for diagnostics or medical devices is a plus. • Experience with Behavioral and Test Driven Development (BDD) principles is a plus. Relocation assistance is not available for this role. The expected salary range for this position based on the primary location of Pleasanton CA is $111,000-$206,100. Actual pay will be determined based on experience, qualifications, geographic location, and other job-related factors permitted by law. A discretionary annual bonus may be available based on individual and Company performance. This position also qualifies for the benefits detailed at the link provided below. Benefits Who we are At Roche, more than 100,000 people across 100 countries are pushing back the frontiers of healthcare. Working together, we’ve become one of the world’s leading research-focused healthcare groups. Our success is built on innovation, curiosity and diversity. Unless entitled to a reasonable accommodation under applicable law, employees are required to be fully vaccinated against COVID-19 in accordance with customer requirements, the company’s health and safety obligations and/or applicable law or guidelines. Roche is an equal opportunity employer and strictly prohibits unlawful discrimination based upon an individual’s race, color, religion, gender, sexual orientation, gender identity/expression, national origin/ancestry, age, mental/physical disability, medical condition, marital status, veteran status, or any other characteristic protected by law. If you have a disability and need an accommodation in connection with the on-line application process, please email us at

Senior Manager, Bioinformatics (Remote - US)


What if the work you did every day could impact the lives of people you know? Or all of humanity? At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the world. Our efforts enable life-changing discoveries that are transforming human health through the early detection and diagnosis of diseases and new treatment options for... patients. Working at Illumina means being part of something bigger than yourself. Every person, in every role, has the opportunity to make a difference. Surrounded by extraordinary people, inspiring leaders, and world changing projects, you will do more and become more than you ever thought possible. Why Us We are a multi-disciplinary and multinational team working on innovative technologies and algorithms that support genomics researchers making the discoveries that change the world. Our algorithms will be part of DRAGEN, Illumina’s software platform to analyze high-throughput sequencing data. In tight collaboration with Illumina’s R&D team, this group is focused on novel genomics applications: algorithms, bio-marker development and emerging genomics and multi-omics applications. Why You Like you, we know the importance of your role and offer you a collaborative and supportive environment in which you are actively encouraged to develop your skills and knowledge. If you want to make a difference, Illumina's mission is to improve human health by unlocking the power of the genome - if that inspires you, let's talk. If you are excited as we are about new genomics applications, are not afraid of complex equations, and have a track record of exceptional coding ability, this is the role for you. This position will inspire you to push boundaries and in a culture fueled by innovation, collaboration, and openness. If you want a brilliant, fast-paced, mission-driven environment, then Illumina is the place for you. To be successful as a Senior Manager, Bioinformatics, you will need a proven track record of accomplishments in bioinformatics with a particular focus on algorithm development, biomarkers and oncology. A consummate scientific background in at least one or all of Genomics, Statistics, Machine Learning, and/or High-Performance Computing will be key to your success. This role may be performed in our San Diego headquarters or remotely within the United States. The position requires a significant amount of work within the Pacific time zone hours. The Role The Senior Manager Bioinformatics will drive the development of innovative genomics solutions: support treatment decisions based the cancer’s molecular profile, early detection, and monitoring of malignancies. The primary function of this position will be to drive algorithm development, prototype software implementations, and execution of feasibility studies to demonstrate that our assays and algorithms meet the biomarker needs of pharma partners. The candidate will lead a team of PhD level bioinformatics scientists and will interface with cross functional teams within and outside of Illumina. Responsibilities: • Lead a team of bioinformatics scientists in innovative software and algorithm development for oncology NGS applications. • In collaboration with our experimental teams, design and analysis of experiments to support novel biomarkers using existing or new Illumina oncology assays. • Provide technical and strategic guidance to the team. • Deeply collaborate with SMEs cross-functionally within Illumina • Lead cross functional assay and algorithm R&D teams with minimal oversight. • Works closely with scientific, assay, engineering, software and commercial teams to develop, and validate new products. • Manage oncology algorithm roadmap for industry leading analysis platform. Requirements: • PhD in bioinformatics, physics, or math or related field with 4+ years of regulated industry experience in clinical algorithm development (IVD, LDT, and/or CDx). • Expert knowledge of existing bioinformatics NGS algorithms and methodology. • Proven ability to develop innovative bioinformatics algorithms. • Fluency in statistics, common bioinformatics methods, and NGS data analysis. • Ability to set technical goals for product roadmaps. • Ability to lead technical collaborations and make technical sound decisions. • Ability to think innovatively toward solving problems effectively and efficiently. • Adept interpersonal skills to contribute to cross functional project teams and work with stakeholders. • Experience with project management and good documentation practices. #LI-REMOTE #LI-HYBRID The estimated base salary range for the Senior Manager, Bioinformatics (Remote - US) role based in the United States of America is: $163,900 - $245,900. Should the level or location of the role change during the hiring process, the applicable salary range may be updated accordingly. Compensation decisions are dependent on several factors including, but not limited to, an individual’s qualifications, location where the role is to be performed, internal equity, and alignment with market data. Additionally, all employees are eligible for one of our variable cash programs (bonus or commission) and eligible roles may receive equity as part of the compensation package. We offer a wide range of benefits as innovative as our work, including access to genomics sequencing, family planning, health/dental/vision, retirement benefits, and paid time off. At Illumina, we strive to foster a diverse and inclusive workplace by cultivating an environment in which everyone contributes to our mission. Built on a strong foundation, Illumina has always been rooted in openness, collaboration, and seeking alternative views and perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and demonstrate our collective commitment to diversity and inclusion in the communities we live and work. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. If you require accommodation to complete the application or interview process, please contact To learn more, visit:

Bioinformatics Engineer/Scientist 3

San Francisco, CA

Invitae (NYSE: NVTA) is a leading medical genetics company trusted by millions of patients and their providers to deliver timely genetic information using digital technology. We aim to provide accurate and actionable answers to strengthen medical decision-making for individuals and their families. Invitae's genetics experts apply a rigorous approach to data and research, serving as the foundation... of their mission to bring comprehensive genetic information into mainstream medicine to improve healthcare for billions of people. Bioinformatics Engineer/Scientist 3Remote in U.S.A Invitae is a biotechnology company passionate about providing tools and services for clinical research applications of genomics. Our mission is to unlock the power of precision medicine in improving patient care by providing a technology platform to advance genomics and facilitate collaborative research. Invitae is seeking Bioinformaticians to join our team. This role will be centered around crafting workflows, tools and algorithms to complement assay/product development. The ideal candidate should be able to perceive a problem clearly and dissect it into components which can be resolved programmatically. Having a comprehensive grasp of genomics and next generation sequencing will be key to succeeding in this role. This person should be independent, well organized and collaborative with clear communication skills. In addition, the ability to frequently switch between tasks will be helpful. As necessary, but not as a primary role, the candidate will assist the Clinical team in ad-hoc analysis and research required to meet regulatory requirements. You will be responsible for scaling our pipelines as we work toward our goal of providing low-cost genetic answers to billions of people. Responsibilities:• Develop high-performance bioinformatics workflows that can accurately and reliably analyze large volumes of Next Generation Sequencing data using Nextflow in a system agnostic manner • Collaborate in a cross-disciplinary team by building, deploying, and maintaining software solutions compatible with distributed and/or containerized systems • Designing APIs using industry best practices to streamline communication between various Invitae platforms • Develop best practices for processing of NGS data including optimization of parameters, resource utilization, and consensus approaches across various NGS applications • Drive genetics technology development in a cross-disciplinary setting by critically analyzing and deriving insights from experimental data (including NGS, arrays, and novel technologies) using open source NGS tools and building custom tools when needed • Develop reproducible analysis for research and development purposes • Review, understand, and stay in compliance with Invitae HIPAA Security policies and procedures Qualifications:• MS with 3+ years experience or PhD in Bioinformatics or Computational Biology Fluent in Python, R, • nix, and SQL like DB technology for data analysis • Working knowledge of pipeline workflow engines: Nextflow, Snakemake • Working knowledge of standard bioinformatic tools used in NGS pipelines • Strong knowledge of Genomics and Molecular Biology • Solid understanding of Illumina sequencing technologies and metrics • Formal statistics background is a plus • Formal software development experience (preferred) • Understanding of Cloud Computing (preferred) Please apply even if you don’t meet all of the “What you bring” requirements noted. It’s rare that someone checks every single item, it’s ok, we encourage you to apply anyways. Join us! 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 to request accommodation. At Invitae, we value diversity and provide equal employment opportunities (EEO) to all employees and applicants without regard to race, color, religion, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status. We will consider for employment qualified applicants with criminal histories in a manner consistent with the requirements of the San Francisco Fair Chance Ordinance. We truly believe a diverse workplace is essential to our company's success and to better serve our diverse patients. Your input is especially valuable. We’d greatly appreciate it if you can take a quick moment to make your selection(s) below. Submissions will be anonymous. #LI-Remote This salary range is an estimate, and the actual salary may vary based on a wide range of factors, including your skills, qualifications, experience and location. This position is eligible for benefits including but not limited to medical, dental, vision, life insurance, disability coverage, flexible paid time off, Spring Health, Carrot Fertility, participation in a 401k with company match, ESPP, and many other additional voluntary benefits. Invitae also offers generous paid leave programs so you can spend time with your new child, recover from your own illness or care for a sick family member. USA National Pay Range $88,000—$137,500 USD Please apply even if you don’t meet all of the “What you bring” requirements noted. It’s rare that someone checks every single item, it’s ok, we encourage you to apply anyways. Join us! At Invitae, we value diversity and provide equal employment opportunities (EEO) to all employees and applicants without regard to race, color, religion, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status. We will consider for employment qualified applicants with criminal histories in a manner consistent with the requirements of the San Francisco Fair Chance Ordinance. We truly believe a diverse workplace is crucial to our company's success and to better serve our diverse patients. Your input is especially valuable. We’d greatly appreciate it if you can take a quick moment to make your selection(s) below. Submissions will be anonymous. You can find a detailed explanation of our privacy practices here



The University of Southern California (USC), founded in 1880, is located in the heart of downtown Los Angeles and is the largest private employer in the City of Los Angeles. USC is consistently ranked among the nation’s most prestigious universities, and the USC Leonard Davis School of Gerontology features one of the world’s best degree and research programs in gerontology. The USC Leonard Davis... School has an international reputation as a hub of aging research and with additional strong programs throughout the university leads the way in defining and advancing the field of gerontology. An exciting opportunity has been created for an enterprising Bioinformatician to join the USC-Buck Nathan Shock Center (NSC) Genomic Translation Across Species Core (GTASC) within the Leonard Davis School of Gerontology’s Bioinformatics Core at the University of Southern California (USC). The mission of the Gerontology Bioinformatics Core (GBC) is to facilitate the development of data analytic procedures to enable the translation of big data into research findings. The Bioinformatics Core has growth opportunities with funded research projects that integrate multiple disciplines, including aging biology, geroscience, lifespan, and developmental psychology, genetics, demography, and public health. In particular, we have a strong focus on using genomic data derived from diverse human cohorts to validate findings in model organisms to better understand the architecture of complex traits related to aging-related diseases and longevity. For more information about the GBC ( or the Davis School of Gerontology (, click on the included links Responsible for creating and running analytical pipelines to answer research questions on funded projects. Serves as an integral part of the research team. Works closely with faculty and research leads to develop and implement coding approaches. Educates and cross-trains graduate students, staff, or post-docs in external collaborating groups. Makes independent decisions on analysis approaches, free from immediate direction, within scope of responsibilities. The GTASC focuses on testing hypotheses in humans that were generated from research conducted in model organisms to aid in identifying processes that influence health and lifespan. We do this using genomic data (genetic, epigenetic, gene expression) collected as part of large population-based studies. The bioinformatician would be responsible for creating and running analytical pipelines to answer research questions that are instrumental in accelerating the pace of translational genomics relevant to human aging. The bioinformatician will be an integral part of the research team and work closely with the core leaders to develop, implement, and document these pipelines. Demonstrated knowledge of programming and/or scripting languages (i.e., R, SAS, python) is required for this position. The ideal candidate will be a person who has demonstrated skills in genomics data analysis (e.g., GWAS, EWAS, TWAS, etc.), using high-performance computing clusters, managing large data files, documenting methods used for bioinformatic analyses, applying statistical methods for work with high dimensional data. High attention to detail, good organization, and communication skills are essential. The successful candidate will perform quality control, data management, and analysis of data using biosocial, behavioral, health, environmental, and genetic/epigenomic measures; assist with annotation of findings; prepare data for reports and manuscripts, and grant applications; stay abreast of new technology and analytic techniques; and present research activities within the group and with collaborators. The bioinformatician will have the authority to make independent decisions on matters of significance, free from immediate direction, within the scope of their responsibilities. Flexible working environment. Posting will remain open until a suitable candidate is identified. Key Accountabilities • Evaluate and assess epigenome- and genome-wide data in large population studies of older adults (e.g. Health and Retirement Study, English Longitudinal Study of Ageing). Independently analyze and interpret data analyses from quality control to regression models. This includes developing/implementing quality control protocols, generating epigenetic or genetic measures (epigenetic age, polygenic scores, etc), and conducting analyses (e.g. EWAS, GWAS, SKAT, etc). Annotate findings. • Consult with collaborators to clarify, improve and evaluate research projects. Manage data acquisition, storage, and sharing tasks, such as data use agreements and interfacing with data repositories (e.g. dbGaP, NIAGADS, and GEO). • Perform regular maintenance of datasets including merging refreshment files, restructuring and recoding variables, and checking for errors (while providing feedback to analysts during this process). Create and maintain clear and organized workflow documentation for internal and external review. Chronicle data management and analysis steps and annotate program files to ensure full transparency and reproducibility as part of a public analysis pipeline (interface with Github, etc.) to accompany manuscripts. • Perform code review for other analysts as part of the team, including working with other team members to fix errors and discuss differences in scientific opinion. Assist in the supervision of students/staff/postdocs, including guiding and managing tasks. Conduct literature reviews on aging, genomic, and bioinformatic topics. Write data, analysis, and results sections for working papers, reports, grants, and manuscripts. Collaborate in the development of data presentations for conferences and workshops. The GBC fosters a work environment that is inclusive as well as diverse, where ideas and perspectives are valued. We are building a team where individuals can thrive, contribute to cutting-edge research related to health with aging, and collaboratively elevate translational science. We welcome applicants from all backgrounds and do not discriminate based on race, color, religion, sex, sexual orientation, gender identity or expression, national origin, age, disability, veteran status, marital status, or an individual’s status in any group or class protected by applicable federal, state, or local law. Required Qualifications • Master’s degree in a recognized field of science or learning which is directly related to the duties of the position, including, but not limited to, biostatistics, quantitative social science, molecular genetics, statistical genetics, translational genomics, or bioinformatics. • Two or more years of experience in at least two domains characteristic of the bioinformatics, including at least one biological/biomedical science and one quantitative/informatics/computing science, with an aptitude for others. • Experience analyzing large and complex biological and/or -omics datasets using reproducible analysis approaches (e.g. analysis pipelines). • Data management and statistical modeling programming experience in R or other –omic analysis software using command line programming such as Linux/Unix. • Highly motivated to learn and implement novel quality control and analyses techniques for genomic data. • Ability to multi-task in order to facilitate several research projects at different stages of completion. • Experience with record-keeping for documentation of analyses and analysis pipelines. • Good communication on technical and non-technical aspects of data analysis, tasks, and timelines. • Must be able to work independently and as part of a research team. • Familiarity with statistical genetic and social science research methods. Preferred Qualifications • Familiarity with statistical genetic and social science research methods. • Experience with genomic analysis of large health or social science studies. • Programming experience with R Markdown, Python, and R shiny apps. • Experience with standard bioinformatics software tools and packages e.g. Bioconductor. • Experience analyzing large and complex biological and/or -omics datasets using reproducible analysis approaches (e.g. analysis pipelines). Work Locations This position will be on-site at the University of Southern California, Leonard Davis School of Gerontology, with flexible scheduling and remote opportunities made available within our overall school policies. If relocation is required, we will allow for reasonable time and flexibility to make necessary arrangements. Additional Information The University of Southern California offers a competitive benefits package including medical, dental, vision, life insurance, accidental death, and dismemberment insurance, and short and long term disability insurance. The annual base salary range for this position is $80,000-$96,000. When extending an offer of employment, the University of Southern California considers factors such as (but not limited to) the scope and responsibilities of the position, the candidate’s work experience, education/training, key skills, internal peer equity, federal, state and local laws, contractual stipulations, grant funding, as well as external market and organizational considerations. REQUIRED DOCUMENTS: In order for your application to be considered, a cover letter and resume must be attached. Minimum Education: Master's degree Minimum Experience: 2 years Minimum Skills: Experience analyzing large and complex biological/-omics datasets using reproducible analysis approaches (e.g., analysis pipelines). Demonstrated knowledge of programming/scripting languages (e.g., R, SAS, python). Programming experience in data management and statistical modeling (e.g., R or other –omic analysis software, using command line programming). Demonstrated skills in genomics data analysis (e.g., GWAS, EWAS, TWAS, etc.); experience using high performance computing clusters, managing large data files, documenting methods used for analytical procedures, and applying statistical methods for working with repeated measures data (e.g., from large-scale, population-based datasets). Highly motivated to learn and implement novel quality control and analyses techniques. Ability to multi-task. Experience with analysis pipeline record-keeping. Strong organizational and communication skills. High level of attention-to-detail. Ability to work independently and as part of a research team. Familiarity with statistical genetic and social science research methods. Preferred Skills: Experience with genomic analysis of large health or social science studies. Programming experience with R Markdown, Python, and R shiny apps. Experience with standard bioinformatics software tools and packages (e.g., Bioconductor). Experience analyzing large and complex biological/-omics datasets using reproducible analysis approaches (e.g., analysis pipelines

Bioinformatics Scientist

Stanford, CA

The Department of Dermatology at Stanford School of Medicine, is seeking a Bioinformatics Scientist to develop software and conduct bioinformatics and statistical analysis to facilitate biomedical research. The candidate will work with a team of bioinformatics scientists and basic science researchers, postdoctoral researchers, and graduate students to design data analysis plans, implement these... plans through bioinformatics programming, present results orally to investigators and publish findings. The candidate will also be responsible to help develop and maintain bioinformatics software platforms. This position will be based at the Stanford Medical campus and provides hybrid flexibility, subject to operational need. The labs perform cutting-edge research using high-throughput techniques to understand stem cell function, development, cancer, and other biological processes, with a focus on epigenomics. Technologies currently in use include next generation sequencing platforms, spatial genomics, mass spectrometry, custom tiling arrays, and functional genomics screens. Previous experience with analysis of high throughput data and large datasets from NGS platforms using established software is strongly desired. In addition, applicants are required to have familiarity with scripting languages (Python, R, or other languages) to create custom data analysis pipelines, to mine databases and test directed hypotheses with internal data. Applicants will be expected to have experience with relational database management systems and to integrate large volumes of data generated from multiple sources. Previous experience with Unix-like environment is required, high performance computing familiarity is needed and some familiarity with cloud computing can also be helpful. Software development skills and some background in biology are also desired. We are looking for a person with good ability to communicate information to both technical and non-technical audiences, and work in cross functional teams. Duties include: • Assess user needs and requirements. • Design and develop applications that may involve sophisticated data manipulation. • Maintain and update existing programs. • Troubleshoot and solve technical problems. • Create programs to meet reporting and analysis needs. • Design and implement user and operations training programs. • Document changes in software for end users. • Follow team software development methodology. • Serve as technical resource with respect to applications. • - Other duties may also be assigned DESIRED QUALIFICATIONS: • Bachelor’s in Bioinformatics, Statistics, Computer Science or related field, and three years of relevant experience • Master’s in Bioinformatics, Statistics, Computer Science or related field, and one year of relevant experience • Proficient in R and Python, and a statistical analysis software e.g., SAS or SPSS • Experience with NGS analysis and bioinformatics pipelines e.g., RNA-seq, ATAC-seq and etc. • Experience with relational databases, data integration and statistical analysis • Familiarity with software development practices and version control systems e.g., GitHub • Experience with Unix-like and HPC environments, and some familiarity with cloud computing • Good ability to communicate information to both technical and non-technical audiences EDUCATION & EXPERIENCE (REQUIRED): Bachelor's degree and three years of relevant experience, or a combination of education and relevant experience. KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED): • Current knowledge of latest software and design standards. • Ability to define and solve logical problems for technical applications. • Knowledge of and ability to select, adapt, and effectively use a variety of programming methods. • Ability to recognize and recommend needed changes in user and/or operations procedures. • Basic knowledge of software engineering principles. • Strong knowledge of at least one programming language. CERTIFICATIONS & LICENSES: None PHYSICAL REQUIREMENTS*: • Constantly perform desk-based computer tasks. • Frequently sit, grasp lightly/fine manipulation. • Occasionally stand/walk, writing by hand. • Rarely use a telephone, lift/carry/push/pull objects that weigh up to 10 pounds • - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job. WORKING CONDITIONS: May work extended hours, evening and weekends. WORK STANDARDS (from JDL) • 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, 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

Bioinformatics Programmer - 121793


Payroll Title: BIOINFORMATICS PROGR 2 Department: CELLULAR & MOLECULAR MEDICINE Hiring Pay Scale... $75,850 - $92,000 / Year Worksite: La Jolla Appointment Type: Career Appointment Percent: 100% Union: Uncovered Total Openings: 1 Work Schedule: Days, 8 hrs/day, Monday - Friday #121793 Bioinformatics Programmer Extended Deadline: Tue 3/28/2023 Apply Now UC San Diego values equity, diversity, and inclusion. If you are interested in being part of our team, possess the needed licensure and certifications, and feel that you have most of the qualifications and/or transferable skills for a job opening, we strongly encourage you to apply. For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus and influenza before they will be allowed on campus or in a facility or office. For more information visit: Flu Vaccine Mandate / COVID Vaccine Policy UCSD Layoff from Career Appointment: Apply by 03/01/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 03/10/2023. Eligible Special Selection clients should contact their Disability Counselor for assistance. DESCRIPTION The mission of the collaborative effort between the Bintu lab and the UCSD Center for Epigenomics is to develop a quantitative and molecular framework to study the function and regulation of the human genome, with the ultimate goal to understand the molecular basis of neurodegenerative diseases. The epigenome plays a central role in regulating the functional output of the genome during development. Changes in the epigenome that result from exposure to stress, pathogenic conditions, and aging can determine the patterns of gene expression and predispose an individual to diseases. Epigenome research promises to significantly improve our understanding of the factors that drive human development and disease. The Bintu lab and the UCSD Center for Epigenomics works with researchers on the UCSD campus and beyond to foster the application of epigenomic concepts and technologies to clinical, translational, and basic research. Under the co-mentoring of Assistant Professor Bogdan Bintu and the Associate Director of Spatial Genomics Quan Zhu, the incumbent will help in running, customizing, and optimizing data analyses pipelines for spatial transcriptomics/genomics experiments. The incumbent will help to evaluate data quality and gain biological insights, as well as assist to prepare results for oral presentation, scientific publications, and grant applications. Furthermore, the incumbent will be trained in maintaining the advanced Fluorescence In Situ Hybridization (FISH)-based imaging technologies to conduct high throughput, spatially resolved single cell analysis of transcriptomics and chromatin structure. CT - Uses professional bioinformatics concepts. Applies computational procedures to resolve a variety of analysis and research issues. Works on assignments of moderate scope where analysis of data requires a review of a variety of factors. Assists in additional analyses as needed to achieve research objectives. MINIMUM QUALIFICATIONS • Bachelor's degree in biological science, computational / programming, or related area and / or equivalent experience / training. • Two (2+) or more years of relevant experience. • Working knowledge of bioinformatics methods and data structures. • Thorough knowledge of applications programming and web development. • Working knowledge of databases. • Working project management skills. Excellent organizational, problem solving, and analytical skills, and attention to detail. • Working knowledge of modern biology and applicable field of research. • Effective interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization. • Ability to communicate technical information in a clear and concise manner. • Thorough knowledge of application and data security concepts. • Working knowledge in genomics, biostatistics, molecular biology, and/or genetics. • Ability to work in a dynamic "startup" atmosphere. • Knowledge of analyzing next generation sequencing data. Experience with single cell genomics data like single cell RNA-seq, single cell ATAC-seq or single cell DNA methylation data is a plus. • Prior experience in statistics and programming languages such as Python, Perl, and R. Proficiency with relational databases and programming languages used in the development of web-based MIS systems is a plus plus (e.g. SQL Server, HTML). SPECIAL CONDITIONS • Job offer is contingent upon satisfactory clearance based on Background Check results. • Occasional holidays, weekends, evenings, nights, and on-call may be required. Pay Transparency Act Annual Full Pay Range: $59,700 - $124,300 (will be prorated if the appointment percentage is less than 100%) Hourly Equivalent: $28.59 - $59.53 Factors in determining the appropriate compensation for a role include experience, skills, knowledge, abilities, education, licensure and certifications, and other business and organizational needs. The Hiring Pay Scale referenced in the job posting is the budgeted salary or hourly range that the University reasonably expects to pay for this position. The Annual Full Pay Range may be broader than what the University anticipates to pay for this position, based on internal equity, budget, and collective bargaining agreements (when applicable). Apply Now Job offer is contingent on successful engagement in the UC COVID-19 Vaccination program (fully vaccinated with documented proof or approved exception/deferral). If applicable, life-support certifications (BLS, NRP, ACLS, etc.) must include hands-on practice and in-person skills assessment; online-only certification is not acceptable. UC San Diego Health Sciences is comprised of our School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The Herbert Wertheim School of Public Health and Human Longevity Science, and our Student Health and Well-Being Department. We have long been at the forefront of translational - or "bench-to-bedside" - research, transforming patient care through discovery and innovation leading to new drugs and technologies. Translational research is carried out every day in the hundreds of clinical trials of promising new therapies offered through UC San Diego Health, and in the drive of our researchers and clinician-scientists who are committed to having a significant impact on patient care. We invite you to join our team! Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached. To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community. UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see: UC San Diego is a smoke and tobacco free environment. Please visit for more information. UC San Diego Health maintains a marijuana and drug free environment. Employees may be subject to drug screening

Data Manager - Bioinformatics Analyst (Naval Health Center)

San Diego, CA

GDIT's Military Health team is seeking a Data Manager - Bioinformatics Analyst in support of the Naval Health Research Center (NHRC) Infectious Disease Field Surveillance and Laboratory Research Services. As the Navy hub for the Armed Forces Health Surveillance Center the NHRC Operational Infectious Diseases Directorate conducts on-going, laboratory-based surveillance of US military populations... in unique environments to quantify and study the etiology of infectious illnesses. This position will provide support services for operational infectious disease surveillance, accredited clinical laboratory testing, diagnostic evaluations, clinical research support and scientific research services. HOW YOU WILL MAKE AN IMPACT • The Bioinformatics Analyst is responsible for providing collaborative bioinformatics support to the investigators at the Naval Health Research Center (NHRC). • Support to NHRC’s COVID-19 surveillance efforts via the analysis of complex data sets. • Analysis and interpretation of high-throughput biomedical data generated by diverse platforms with emphasis on next-generation sequencing • Contribute to a team effort in designing, developing and deploying robust workflows, as well as custom scripts, to support the analysis of high-throughput data • Responsible for the organization and management of large genomic datasets, and the integration of data from multiple sources • Mining publicly available biological data to generate novel hypotheses or insights • Presenting analysis results, in a clear and concise manner, to an audience not familiar with bioinformatics WHAT YOU’LL NEED TO SUCCEED • Education: Bachelors Degree in biomedical science/bioinformatics/math/statistics/computer-related field • Required Experience: 2 years related experience • Required Technical Skills: Experience with bioinformatics tools and databases • Experience managing large genomic data sets including integration with data available from public sources • Proficiency in at least two of the following programming languages: Perl, Python, R, Java and C/C++ • Record of scientific achievements including journal publications or presentations • Preferred Skills: Experience in analysis of next generation sequencing (NGS) data (including quality metrics, mapping, variant calling, quantitation of gene expression and biological interpretation) • Experience in analysis of large genomic data sets including integration with data available from multiple sources • Hands-on experience in data processing and analyzing sequencing and expression and other array data including quality and biological assessment are also essential • Ability to understand and analyze data from complex experimental designs • Experience in at least two of the following areas: metagenomics, ChIPSeq, RNASeq, ExomeSeq, DHS-Seq, microarray analysis • Familiarity with public databases: NCBI, Ensembl, TCGA, cBioPortal, Broad FireHose • Location: Onsite in San Diego • Security Clearance Level: Ability to obtain a favorable NACLC T3 security investigation prior to start date. • US Citizenship Required: Must be a US citizen WHAT GDIT CAN OFFER YOU: • Challenging work that makes a real impact on the world around you • Internal mobility team dedicated to helping you own your career • 401K with company match • Diverse, highly collaborative teams • Professional development, education assistance, certification and training opportunities #MILITARYHEALTHGDITJOBS #GDITFedHealthJobs #GDITPublicHealthJobs #GDITLabScienceJobs #GDITClinicalResearchJobs

Research Bioinformatician II - Knott Lab - Center for...

Los Angeles, CA

The Knott Laboratory at Cedars-Sinai Medical Center is seeking to hire a highly motivated computational scientist to fill the position of Research Bioinformatician II! The Knott laboratory is searching for a computational scientist with strong software engineering skills. We prefer this person have a background in single cell RNA sequencing or image analysis, or have experience studying the... spatial distribution of objects and their influence over one another. This research bioinformatician will lead the analysis of novel single cell sequencing and spatial data for a multidisciplinary team that is studying how cancer cells metastasize to distant organs away from the primary tumor site. To learn more, please visit: Knott Research Lab | Cedars-Sinai. The Research Bioinformatician II (RBII) performs general bioinformatics analysis and software support for projects involving in omics, and interacts with investigators to identify research problems, find appropriate software tools and recognize national biological databases and online resources for omic data. The RBII will also work with bioinformatics faculties to determine future bioinformatics needs, and helps to develop tools and pipelines as necessary to keep pace with rapid advances in sequencing technology. The RBII will demonstrate continuous self-improvement, make effective contributions to the section, and adhere to CSHS compliance plan, code of conduct, and hospital and departmental policies and procedures. Primary Job Duties & Responsibilities: • Provides general bioinformatics analysis support for omic projects and mainly responsible for data analysis and software compilations including next generation sequence alignment, polymorphism identification, expression analysis, and visualization tools and browsers. • Summarizes data analyzes results in the form suitable as the basis for the first draft of written reports, and makes preliminary interpretations of the data. • Develop, test, and maintain modular software pipelines for genome sequencing, assembly, annotation, metagenomic analysis, and genotyping using high-throughput sequencing platforms including 454, Illumina, and Pacific Biosciences • Manages data including loading and querying data from database systems, downloading omic data from public repositories • Familiar with medical and biological terminologies, bioinformatics resources, and national biological databases, Ready to provide solutions for investigator’s problems through data mining and extraction • Identify, evaluate, and incorporate relevant algorithms and software pipelines by reviewing pertinent literatures in bioinformatics and computational biology • Assists or collaborates in the preparation of grant proposals, publications, and presentations involving omic data • Educate others about bioinformatics through mentoring and teaching colleagues, investigators, fellows, and graduate students. Education: • Master of Science Degree in Computer Science, Electric Engineering, Computational biology, or Bioinformatics, or Master of Science/ Engineering in relevant fields (e.g. Biology with strong quantitative training, biostatistics with a concentration in bioinformatics) is required. • Doctorate in Computer Science or a related computational field is preferred. Experience & Skills: • Three (3) years in a research environment. • Background and work knowledge in algorithms, scientific computing, and machine learning or statistics. • Previous experience with C/C++, Java, Perl, python, and the Unix (Linux) environment. • Experiences in manipulating, analyzing, and annotating very large genomic (e.g. NGS) data sets both in exploratory and pipelined fashions. Working Title: Research Bioinformatician II - Knott Lab - Center for Bioinformatics and Functional Genomics Department: BMS - Bioinfo & Func Genomics Business Entity: Academic / Research Job Category: Academic/Research Job Specialty: Bioinformatics Position Type: Full-time Shift Length: 8 hour shift Shift Type: Day Base Pay:$78,400.00 - $133,100.00

Senior Bioinformatics Engineer (On-Site / Hybrid) #2877

Menlo Park, CA

GRAIL is a healthcare company whose mission is to detect cancer early, when it can be cured. GRAIL is focused on alleviating the global burden of cancer by developing pioneering technology to detect and identify multiple deadly cancer types early. The company is using the power of next-generation sequencing, population-scale clinical studies, and state-of-the-art computer science and data science... to enhance the scientific understanding of cancer biology, and to develop its multi-cancer early detection blood test. GRAIL is headquartered in Menlo Park, CA with locations in Washington, D.C., North Carolina, and the United Kingdom. GRAIL, LLC is a wholly-owned subsidiary of Illumina, Inc. (NASDAQ:ILMN). For more information, please visit GRAIL is seeking a Senior Bioinformatics Engineer to join the Bioinformatics and Data Science team. In this role, you will work with Scientists, Bioinformaticians, and Statisticians to develop bioinformatics data processing pipelines and scientific software for processing and analyzing molecular data. This software will be at the core of critical scientific and product development activities including training machine learning classifiers, analyzing experimental results, and processing data as part of GRAIL's diagnostic tests. The ideal candidate will have a strong computer science background, with a passion for creating well-written, scalable, and robust software for sample processing pipelines in a regulated environment. Responsibilities • Coordinate with a cross-functional team to develop new software features, process study samples, support analysis objectives, and lock device software for new products. • Design and implement efficient and horizontally-scalable bioinformatics software, in support of research and product initiatives. • Maintain a high level of software reliability by adhering to and enforcing sound engineering principles, including thorough testing. • Follow the formal development and release procedures needed to convince others of this reliability, meeting the high standards expected of regulated diagnostic devices. • Take the initiative to rigorously investigate and fix issues that still fall through the cracks; and pioneer new initiatives that make this come up less often. Qualifications • Engineering, Bioinformatics, Math, or related Master's degree with 5+ years of experience or Ph.D. with 3+ years of experience in a relevant position. • Expert knowledge in designing, building, and testing scientific software and data analysis pipelines. • Professional software engineering experience, including extensive experience in at least one system-level programming language like Go, Java, or C++. • Previous experience working in and developing infrastructure for cloud environments. • Moderate familiarity with developing bioinformatics pipelines with a workflow engine, like Reflow or NextFlow. • Experience with cross-functional collaborations while ensuring data quality and commitment to analysis reproducibility. • Strong communicator who can discuss complex technical concepts with cross-functional collaborators and capture solutions in technical documentation. Bonus • Working knowledge of common bioinformatic tools for processing next-generation sequencing data. • Experience developing software for regulated products. The estimated, full-time, annual base pay scale for this position is $150,000 - $176,000. Actual base pay will consider skills, experience, and location. Based on the role, colleagues may be eligible to participate in an annual bonus plan tied to company and individual performance, or an incentive plan. We also offer a long-term incentive plan to align company and colleague success over time. In addition, GRAIL offers a progressive benefit package, including flexible time-off, a 401k with a company match, and alongside our medical, dental, vision plans, carefully selected mindfulness offerings. GRAIL is an Equal Employment Office and Affirmative Action Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability or any other legally protected status. We will reasonably accommodate all individuals with disabilities so that they can participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation. GRAIL maintains a drug-free workplace. Following extensive monitoring, consideration of business implications, and advice from internal and external experts, GRAIL US has made the decision to require that all U.S. employees be “Fully Vaccinated” with the COVID-19 vaccine. “Fully Vaccinated” is defined as two weeks after both doses of a two-dose vaccine (e.g. Pfizer or Moderna) or two weeks since a single-dose vaccine (e.g. Johnson & Johnson) has been administered. Absent a qualifying exemption, all GRAIL US employees are to comply with this requirement, including providing documentation of such vaccination status, as a condition of employment. Anyone unable to be vaccinated, either because of a sincerely held religious belief or a medical condition or disability that prevents them from being vaccinated, can request a reasonable accommodation for consideration by GRAIL

Bioinformatics Analyst


Bioinformatics Analyst Interested in building a career in life sciences? An exciting mid-size Pharmaceutical company on the west coast is looking for talented Bioinformatics Analyst! The opportunity is a fully remote, 6 to 12 month contract-to-extend with benefits. There is an Oncology emphasis but all therapeutic backgrounds are encouraged to apply... The Bioinformatics Analyst will be responsible for: · Leading computational biology and data analysis efforts · Partnering with team members to develop robust data analysis pipelines · Communicating strategies and progress to cross-functional management · Integrating and interpreting heterogenous & noisy datasets from ongoing clinical trials The Bioinformatics Analyst should have the following qualifications: · Master's Degree in scientific discipline · Proficiency with R & Python with working knowledge of AWS · Experience with PowerBI, Tableau, or Splunk · 5+ years experience in the Life Sciences Benefits: · Opportunity for growth at an exciting Pharmaceutical company · Fully remote · Competitive pay rate If you are interested in the Bioinformatics Analyst role, then please don’t wait to apply. Please note this role is only offered on a W2 basis through EPM Scientific

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