Senior Computational Biologist

Senior Computational Biologist

Date Posted February 4, 2018
Job Type Regular
Hours Per Week 40
PAVIR Job ID TSA1705.18
Salary Range DOE


The Palo Alto Veterans Institute for Research (PAVIR) is seeking a Senior Computational Biologist position to support research in the Genetic Medicine Program at the newly established research center – Epidemiology Research and Information Center for Genomics.

The Senior Computational Biologist will take the lead in using cutting-edge HPC and cloud technologies to analyze and interpret 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 Computational Biologist will use a toolset of GWAS, pathway analysis, and machine learning techniques to discover unique biological and medical insights with ample opportunity to publish.

This is a regular, full time (40 hours/week), Exempt position.

As a condition of employment, all PAVIR employees are required to receive an approved WOC appointment with VAPAHCS and complete a background check.


  • Using a toolset of GWAS, pathway analysis, and machine learning techniques, analyze and interpret large human genetic data, including DNA-seq data generated from large human cohorts, RNA-Seq, Methyl-Seq, SNP-array, data modalities (sequencing to clinical claims data) and external datasets (ENCODE, GTEx);
  • Establish and refine the process for bioinformatics analysis and validation; Write and run programs in languages including python and R for streamlining the analysis procedures; Benchmark driven development is expected;
  • 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: Ph.D. in genetics, bioinformatics or a related field required.


  • Required:
    • Two 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: Office environment and equipment.

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 for Minorities, Females, Protected Veterans, and Qualified Individuals with a Disability. If you need special assistance or an accommodation to apply for a posted position, please contact – Human Resources department.


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