Bioinformatics Software Developer for Microbiome Research

Stanford Center for Genomics & Personalized Medicine
Job Location
Palo Alto, CA 94304

Excellent 401K and medical benefits. Funds for conferences and classes.


Starts out as 1 year term but will be extended.

Job Description

 The Stanford Center for Genomics and Personalized Medicine ( and the Bhatt lab of Stanford Genetics and Hematology (, situated in the heart of SF Bay Area, have an excellent opportunity available for a motivated Bioinformatics Software Developer. This is a key position with the Stanford Genomics Core team that will support a new microbiome initiative with Bhatt lab.

In this position, you will be an integral part of a highly dedicated, multidisciplinary team of biologists, geneticists and physician scientists. You will work with high profile academicians, preeminent medical teams, petabytes of data and world-class computational resources while supporting a group of researchers (graduate students, post-doctoral fellows and physicians) who are dedicated to improving human health through genomics and bioinformatics. You are expected to be a strong analyst, an independent researcher, and an excellent communicator. Your work in designing and implementing state-of-the-art bioinformatics pipelines for microbiome analysis is expected to result in the publication of high profile papers and the execution of clinical trials that directly impact human health.

The ideal person for this position is a computational genomics ninja who is passionate about developing best-practice bioinformatics methods and tools. The successful candidate will have deep knowledge of scientific method development, pipeline/software development, experience with massive scale data analysis, and a strong grasp in high performance computing. The ideal candidate will have a strong desire to learn new methods and technologies and adapt to fast pace changes. The main focus for this position involves development of NGS analysis pipeline development and data analysis.

Example responsibilities:

  • Orient new students and visiting scholars to the computational environment at Stanford
  • Polish and scale up developmental analyses from researchers in the lab
  • Provide statistical, algorithmic and other methodological expertise to improve science done by lab members and collaborators
  • Provide support for published tools, administer git repositories
  • Design and implement analytical pipelines to solve biomedical mysteries
  • Organize an annual hackathon! 




  • Four-year degree in Computer Science, Biology, Computational Physics/Biology, Bioinformatics or related field and one five years of related experience.
  • Extensive experience with next-generation sequencing data.
  • Excellent verbal and written communication skills.
  • Proven experience working in a Linux cluster environment.
  • Proven ability to develop large-scale scientific software. This includes requirements and specification development, and deployment. 
  • Expert proficiency in git/github, issue trackers, and SCRUMs.
  • Expert programming skills in Java/Python. Familiarity with C++ and Perl are useful.
  • Strong background in one or more of: machine learning, statistical methods, distributed computing, algorithm development.
  • Strong background in one or more of: DNA-Seq, RNA-Seq, ChIP-Seq. Microbiome or metagenomic analysis.
  • Strong background in relational and/or no-SQL databases.
  • A selection of code examples will be requested.


  • Advanced degree in Computer Science, Computational Physics/Biology, Bioinformatics or related.
  • Knowledge of research in metagenomic analysis.
  • Experience working in academic environments.

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