• Palo Alto, CA, USA
  • Full Time

The Palo Alto Veterans Institute for Research (PAVIR) is seeking a Senior Bioinformatics Scientist who will support research in the Genetic Medicine Program at the newly established research center - Epidemiology Research and Information Center for Genomics.

The Senior Bioinformatics Scientist will take the lead in developing tools, pipelines, and platforms based on cutting-edge informatics and cloud technologies to support the center's task in analyzing and interpreting large and high-quality human genetic data. These analyses will primarily be on DNA-seq data generated from large human cohorts (100s to 1000s to 10,000s), but may span different experiment types (RNA-Seq, Methyl-Seq, SNP-array), data modalities (sequencing to clinical claims data) and external datasets (ENCODE, GTEx). These cohorts are focused on complex diseases, and the Senior Bioinformatic Scientist will utilize his/her expertise in informatics and big data computation to develop scalable and interactive tools on public cloud environments, including those for accurate detection of DNA/RNA variants, quantification of biomolecules, pathway analysis, and machine learning techniques, to help discover unique biological and medical insights geared towards precision health and medicine.

This is a regular, full time (40 hrs/wk), exempt (salary-paid) position. Benefits:

  • Medical Insurance
  • Vision Insurance
  • Dental Insurance
  • Vacation
  • Sick Pay
  • 13 paid Holidays
  • Life Insurance - paid by PAVIR
  • Long-term Disability Insurance - paid by PAVIR
  • Short-term Disability Insurance - paid by PAVIR
  • Flexible Spending Account
  • 401(k) Retirement Plan with Company Match and Profit Share
  • Employee Assistance Program
  • Commuter Benefit

PAVIR is a nonprofit foundation affiliated with the Veterans Affairs Palo Alto Health Care System (VAPAHCS). As a condition of employment, all PAVIR employees are required to have an approved appointment with VAPAHCS and complete a background check before they can commence work.


  • Develop methods and pipelines on the public cloud platforms for big data genomics, including accurate detection of DNA/RNA variants (SNVs, INDELs, and SVs) and quantification of biomolecules (RNAseq, proteome);
  • Write and run programs in languages including python and R; Benchmark driven developments are a routine;
  • Analyze and interpret omics data (WGS, WES, RNAseq, proteome, methylation) for biological and medical discoveries;
  • Use tools such as GWAS, pathway analysis, network analysis, and machine learning to aid the discovery processes;
  • Write papers describing studies, methodologies and results for publication in quality peer reviewed journals;
  • Present findings at scientific meetings;
  • Stay abreast with best practices (e.g. large consortium Data Coordination Centers like ENCODE and HMP), as well as cutting-edge data analysis methods from recent publications;
  • Create and maintain documentation for study set-up, directories, quality assurance monitoring and programs;
  • Train and coach others (such as research assistants, data analysts, etc.), which may include to direct and advise personnel in proposal writing;
  • Recommend measures to improve methods, performance, and quality of research.


Education: M.Sc. in computer science, bioinformatics, genetics, or a related field.

Work Experience:


  • 5 years or more of related research experience;
  • Hands-on experience working with very large data sets;
  • Experience in at least one relevant programming language (Python, R, Java, etc.).

Knowledge / Skills / Abilities:

  • Broad knowledge of NGS analysis tools and methods; enough experience to quickly and judiciously evaluate new methods and tools;
  • Extensive experience with a few pipelines, their underlying statistics and algorithms, and troubleshooting problems;
  • At ease in a Linux environment;
  • Excellent verbal and written communication skills;
  • Ability to deliver excellent results while working independently and being a team player;
  • Ability to comply with VA rules and regulations.

Environmental Conditions / Physical Demands:

Physical: Sitting in front of a computer for long periods of time, repetitive movement, etc.

Environmental: Exposure to office equipment and office environment.

PAVIR engages in nonprofit medical research and works with sponsors and the Veterans Affairs Palo Alto Health Care System (VAPAHCS) in administering funds for conducting research to find new and improved ways to combat human disease and help people with disabilities. Please refer to our website for additional information: 

PAVIR is pleased to be an Equal Opportunity Employer. Minorities, Women, Veterans, and Individuals with a Disability are encouraged to apply. We welcome and encourage diversity in the workplace regardless of race, color, religion, age, gender, sexual orientation, national origin, disability status, protected veteran status, or any other characteristic protected by law. If you need special assistance or an accommodation to apply for a posted position, please contact our Human Resources department at

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