Bioinformatics Developer, Research

Stanford University
Job Location: 
Palo Alto, CA

Medical, 401k, Vacations

Job Description: 

The Stanford Department of Genetics is looking for an outstanding bioinformatics software developer to join the bioinformatics group responsible for development of infrastructure to aid large scale analysis of sequence data. Successful candidate will be adept at established and newly emerging analysis techniques. The individual must be able to quickly grasp the objectives of research projects, and assemble solutions from a range of technologies, standards and approaches.

Your primary responsibilities will be to:
• Evaluate commercial and public bioinformatics software. Integrate existing software and develop new tools to build automated analysis pipelines, using a combination of scripting languages and high-level languages.
• Take software developed by Stanford researchers and create production oriented versions of these software. Practice strong coding principles to deliver production oriented software. Responsibility includes converting user requirements into design, implementation, testing, maintaining, documenting and distributing these software packages.
• Add to usability and ease of user experience by creating QA metrics, graphics and visualization. Help researchers with training, running analysis and troubleshoot.
• Maintain expertise in analysis of sequence data using a variety of bioinformatics software tools on our HPC cluster and Amazon AWS.

You must be self-motivated, independent and flexible with good communication skills. You will have the chance to participate in cutting-edge science in a dynamic, small-team environment.


Required Qualifications:
• B.S. in Computational Biology or similar with 3+ years of related experience.
• Expertise with bioinformatics analysis (e.g. alignment, variant calling) and bioinformatics software (e.g. GATK, TopHat, Galaxy, CLCBio). Experience with variant and other biological databases is a strong plus.
• Experience developing on Linux platforms and in distributed programming environment.
• Strong experience with an OO language such as C++, C# or Java and one or more scripting languages (Python, Perl, shell). Strong software development skills. Typical programming is expected to be in Python and Java.
• Strong communication skills needed to interact with a large cross-section of researchers, PIs and students. Position will require training other researchers on bioinformatics analysis.
• Proven ability to learn quickly and adapt to new projects and work in a fast paced environment.

Desired Qualifications:
• Advanced degree in Computer Science, Bioinformatics, Computational Biology, Statistics, Applied Mathematics or related field
• 5+ years of experience in bioinformatics software development or analysis.
• Experience with multiple sequencing platforms and multiple applications. Experience in genetic data interpretation is a strong plus.
• Team leadership experience.

Contact Information: 
About Our Organization: 

The current revolution in genomics makes it possible not only to determine our entire DNA sequence but also to begin to understand how our specific genome sequence can inform our health. Someday both genetic and molecular profiling will become powerful and routine tools for predicting disease risk and monitoring and treating a wide range of pathologies. At Stanford, we are developing collaborative intellectual and technological resources that promote genomic research and analysis. This includes large basic science projects such as ENCODE that decipher the human genome, clinical research projects such as the sequencing of cancer genomes and individuals with inherited diseases as well as human population genomics for complex biomedical traits.

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