Bioinformatics Scientist 1

Job Location
5200 Illumina Way
San Diego, CA 92122
Job Description

Why is one person more likely to develop a disease—like cancer, diabetes or Parkinson’s—than someone else? Why would one person respond differently to treatment than another? What is the most effective treatment for each patient? Illumina’s technologies are helping researchers and clinicians around the world to answer these questions and others, on a scale not even possible a few years ago.

Our team specializes in developing algorithms and software for genomic data, from raw images through interpreted human genomes.  Challenges in this area include handling specific sample types or variant calling problems.  In addition, assembling methods into an end-to-end pipeline poses integration challenges.  We develop methods to address these challenges and provide a sample-to-answer pipeline with high reliability, speed, and completeness of results.

We are seeking an exceptional individual to join our team in developing DNA analysis solutions for use by researchers and clinicians worldwide.  This software will be a key part of new sequencing platforms. These methods will also be a key component of population-scale sequencing projects as well as a sample-to-actionable-answer workflow for rare and undiagnosed genetic disease


  • Construction and improvement of high-performance image analysis pipelines for new sequencing platforms

  • Creation and iterative enhancement of sequence analysis workflows (i.e. read alignment, variant calling, and variant annotation) to support both research and clinical products.

  • Design, prototype, and implementation of computational algorithms that utilize both statistical and machine learning approaches.

  • Software optimization at the design, algorithm, and source code level.

  • Deep collaboration with other teams to ensure a smooth, end-to-end workflow with external organizations.



  • Strong background in developing production-grade software. Experience with C#, C++ 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.



  • Experience with analysis of human whole-genome sequencing data.

  • Experience with image processing algorithms and techniques.

  • Familiarity with agile software development processes (e.g. Scrum).

  • Experience with using version control systems such as git.

  • Experience with cloud computing, parallel computing, and big data.


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

Illumina believes that everyone has the ability to make an impact, and we are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. If you have a disability or special need that requires accommodation, please contact us at 858-255-5081. To learn more, visit:

How to Apply

Please apply on our career site; here is the direct link:

We have multiple bioinformatics roles available, feel free to apply to more than one. You may also contact Britt Epperson, Senior Recruiter via LinkedIn. Thank you! 

About Our Organization

Do you want to make a difference? Illumina’s mission is to improve human health by unlocking the power of the genome. If that inspires you, let’s talk. We’ve built a culture fueled by innovation, collaboration and openness, and established ourselves as the global leader in DNA sequencing and array-based technologies. Our people and our technology change lives by driving advancements in life sciences, oncology, reproductive health, agriculture and other emerging markets. Life at Illumina is about working with teammates who are deeply passionate about what we do, because we know that our work has the power to improve lives.

We’re an established company with a track record of phenomenal growth. Just check out our investor events and presentations to learn about our financial accomplishments. Our growth isn’t just in financials, we’ve been busy hiring the best and the brightest. Perhaps that’s why MIT has ranked Illumina near the top of its World’s Smartest Companies each of the last three years. If you thrive in a brilliant, fast-paced, and mission-driven environment, Illumina is the place for you. Join the journey of a lifetime. Join Illumina.

The Nature Jobs blog reports that the University of Chicago is no longer requiring graduate school applicants to submit standardized test scores.

At Nature, the University of Alberta's Devang Mehta calls on PIs to engage in conversations about racism.

A National Academies of Sciences, Engineering, and Medicine report calls for changing metrics to make STEM graduate school more student-centered, according to Science.

Two postdocs and a PhD hosted a panel discussion at Memorial Sloan Kettering on career advancement in science and what researchers can expect when they leave the lab.