Bioinformatics Software Developer

Stanford University, School of Medicine - Department of Genetics
Job Location: 
Palo Alto, CA
$80k/yr and up

Full medical, dental, vision + worklife

Job Description: 

The Stanford Center for Genomics and Personalized Medicine (SCGPM), situated in the heart of SF Bay Area, has an excellent opportunity available for a motivated Bioinformatics Software Developer. This is a key position with Center’s Big Data Genomics Core team that will support a new CIRM initiative, Center of Excellence in Stem Cell Genomics initiative.

Stanford University has been awarded $40 million from the California Institute for Regenerative Medicine to work with several partners to create a center that will focus on applying genomics approaches and technologies to stem cell science. The Center of Excellence in Stem Cell Genomics will be led by Co-directors Michael Snyder, chair of genetics at Stanford and Director of SCGPM, and Joseph Ecker, a professor in the plant biology lab at Salk. Stanford and its collaborators will use the CIRM funding to create the Center of Excellence in Stem Cell Genomics, which will apply genomics in developing better ways to use stem cells in research and treatment, and enhance understanding about diseases like cancer, diabetes, heart disease, and mental health. For a list of CIRM grants given to Stanford PIs, please visit

In this position, you will be an integral part of a highly dedicated core team that works with dozens of high profile academicians, petabytes of data, thousands of computational cores, dozens of Industry leaders while supporting hundreds of researchers. You are expected to be analytically strong, an independent researcher, respectful to your collaborators and strong in your communication skills.

The ideal person for this position is a computational genomics ninja who is passionate about developing best-practice scientific 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. What is perhaps most important is your 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.



Four-year degree in Computer Science, Biology, Computational Physics/Biology, Bioinformatics or related field and 2-3 years of related experience.

- Deep 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, regression,and deployment. Expect proficiency ingit/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.
- Strong background in one or more of: Relational and no-SQL databases, UI development.


- Advanced degree in Computer Science, Computational Physics/Biology, Bioinformatics or related.
- Knowledge of research in stem cells genomics.
- Experience working in academic environments.

Contact Information: 

Interested candidates must apply directly to:

About Our Organization: 

An underlying theme in the Stanford University Department of Genetics is that genetics is not merely a set of tools but a coherent and fruitful way of thinking about biology and medicine. To this end, we emphasize a a spectrum of approaches based on molecules, organisms, populations, and genomes. We provide training through laboratory rotations, dissertation research, seminar series, didactic and interactive coursework, and an annual three-day retreat of nearly 200 students, faculty, postdoctoral fellows, and research staff. The mission of the Department includes education and teaching as well as research; graduates from our program pursue careers in many different venues including research in academic or industrial settings, health care, health policy, and education. We are especially committed to increasing diversity within the program, and to the training of individuals from traditionally underrepresented minority groups to apply.