Bioinformatics Scientist

Job Location
San Diego, CA 92121
Highly Competitive
Job Description

Our team specializes in developing tools and workflows to analyze somatic mutations found in tumor and normal tissue samples. One of the many challenges in this area involve analyzing archived FFPE samples that often present problematic sequence artifacts. We devise methods to counteract these sources of error and to continually expand the limits of detection for our tools.

Our team is actively developing variant annotation tools that are both more accurate than existing tools, but also orders of magnitude faster. We aspire to bridge the gap between variant discovery and providing actionable information for research and clinical use.

We are seeking an exceptional individual to join our team in developing analysis tools that will be used by researchers and clinicians worldwide. These tools will be incorporated in Illumina’s expanding oncology portfolio and used in high visibility projects such as the 100,000 Genomes Project.


  • Creation of novel sequence analysis workflows (i.e. read alignment, variant calling, and variant annotation) to support both research and clinical products.
  • Design, prototype, and implement computational algorithms that utilize both statistical and machine learning approaches.
  • Software optimization at the design, algorithm, and source code level.
  • Identify opportunities to improve the bioinformatics user experience and implement solutions.
  • Collaborate with internal project teams and with external organizations.
  • Contribute to the bioinformatics open source community.


  • Strong background in developing software with multiple languages and multiple platforms. Experience with C#, C++, Java, and Go is highly advantageous.
  • Personal initiative and ability to work effectively as part of a team.
  • Familiarity with applying statistical approaches to algorithm development.
  • Superior written and verbal communication skills.
  • Basic knowledge of genomics, genetics, and sequencing technologies.


  • Familiarity with agile software development processes (e.g. scrum).
  • Hands-on experience with sequence analysis tools such as samtools and GATK.
  • Experience with sequencing data analysis.
  • Experience with cloud computing, parallel computing, and big data.
  • Familiarity with genomic annotation databases (e.g. RefSeq, Ensembl, dbSNP, DGV, dbVAR, ClinVar, COSMIC, and ExAC).
  • Experience with using version control systems such as git and TFS.


  • Master’s degree or PhD in bioinformatics, biology, engineering, physical sciences, computer science, mathematics, statistics, or equivalent.
How to Apply

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About Our Organization

Headquartered in San Diego, California, Illumina (NASDAQ: ILMN), is a leading developer, manufacturer, and marketer of next generation life science tools and integrated systems for large-scale analysis of genetic variation and biological function. These systems are enabling studies that were not even imaginable just a few years ago, and moving us closer to the realization of personalized medicine. With the innovative advances in our sequencing technologies, we are rapidly impacting the clinical market in areas such as reproductive health and oncology. The expanding Illumina oncology portfolio of next- generation sequencing NGS and microarray technologies is revolutionizing cancer genomics research. Our customers include a broad range of academic, government, pharmaceutical, biotechnology, and other leading institutions around the globe.

lllumina has experienced phenomenal growth from $10 million in revenues in 2002 to over $1.4 billion in 2013. Forbes named Illumina #1 on the 2009 list of 25 Fastest-Growing Technology Companies in the United States, the second time over a three year period that Forbes ranked Illumina #1 on its list of rapidly growing technology companies. Illumina was also named #1 smartest company in the world as part of MIT’s 2014 Technology Review.  As of August 2014, the company had a $24 billion market capitalization.

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