Staff Bioinformatics Scientist - DNA/RNA Secondary Analysis Algorithms

Illumina; San Diego (CA); On-site; USD 156,000 - 233,000; Full time

Benefits offered by this job

Bonus program

Equity eligibility

Health/dental/vision benefits

Paid time off

Employee resource groups

Job summary

Illumina in San Diego is seeking a Staff Bioinformatics Scientist with deep expertise in transcriptomics, computational biology, and bioinformatics software development to advance DRAGEN analysis solutions. You will lead the development of novel algorithms and production‑quality software for RNA, multiomic sequencing, and AI‑enabled workflows.

The role requires a PhD or extensive experience, strong programming (C++, Python), leadership, and collaboration across cross‑functional teams.

Qualifications

• Degree in Bioinformatics, Computational Biology, Computer Science, Statistics, Biology, or related discipline or equivalent experience.
• Significant experience developing DNA/RNA bioinformatics algorithms and production software for NGS applications.
• Strong background in genomics, transcriptomics and biological data analysis.

Responsibilities

• Lead development of novel algorithms and analytical methods for RNA and multiomic sequencing applications.
• Design, evaluate, and implement scalable bioinformatics algorithms for bulk RNA-seq, single-cell sequencing, and multiomic assays.
• Apply ML/AI methods and foundation models to accelerate method development, validation, and product innovation.
• Develop production-quality software with cross-functional teams including engineers and product teams.
• Lead technical projects, define requirements, influence product direction, and drive innovation.

Skills

C++

Python

Genomics

Leadership

Education

Degree in Bioinformatics

Advanced degree preferred

Tools

Cloud computing

NGS pipelines

Job description

What if the work you did every day could impact the lives of people you know? Or all of humanity? At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the world. Our efforts enable life‑changing discoveries that are transforming human health through the early detection and diagnosis of diseases and new treatment options for patients. Working at Illumina means being part of something bigger than yourself. Every person, in every role, has the opportunity to make a difference. Surrounded by extraordinary people, inspiring leaders, and world changing projects, you will do more and become more than you ever thought possible.

The DRAGEN Bioinformatics team develops industry‑leading secondary analysis solutions for DNA and RNA NGS applications used by researchers and clinicians worldwide. Our team builds high‑performance, scalable algorithms and software for transcriptomics, oncology, population genomics, and multiomic analysis. We leverage advanced computational methods, machine learning, artificial intelligence, foundation models, and cloud technologies to transform genomic data into actionable insights. We are seeking a Staff Bioinformatics Scientist with deep expertise in transcriptomics, computational biology, and bioinformatics software development to help advance the next generation of DRAGEN analysis solutions. The successful candidate will combine biological insight with strong algorithmic, statistical, and software engineering skills, and will provide technical leadership and product development experience across multiple product cycles.

Responsibilities

• Lead development of novel algorithms and analytical methods for RNA and multiomic sequencing applications.
• Design, evaluate, and implement scalable bioinformatics algorithms and methods for bulk RNA‑seq, single‑cell sequencing, CRISPR/Perturb‑seq analysis, ATAC‑seq, CROP‑seq, and emerging multiomic assays.
• Apply machine learning, AI‑based methods, foundation models, LLM‑enabled workflows, and biological foundation models to accelerate method development, validation, interpretation, and product innovation.
• Develop production‑quality software solutions in collaboration with bioinformatics scientists, software engineers, FPGA engineers, assay development teams, and product teams.
• Lead technical projects, define requirements, influence product direction, evaluate risks, and drive innovation across multiple product cycles.
• Mentor scientists and engineers and contribute to scientific and technical leadership within the organization.
• Evaluate emerging technologies and identify opportunities for new features, products, analytical capabilities, and intellectual property.

Required Qualifications

• Degree in Bioinformatics, Computational Biology, Computer Science, Statistics, Biology, or a related discipline, or equivalent industry experience.
• Significant experience developing DNA/RNA bioinformatics algorithms, analytical methods, and production software for NGS applications, such as genome alignment, transcript expression, calling fusions and splice variants in RNA, and calling small and large (structural, CNV) in DNA.
• Strong background in genomics, transcriptomics and biological data analysis.
• Proficiency in one or more programming languages such as C++, Python, or similar.
• Experience designing, validating, benchmarking, and interpreting computational methods for complex biological datasets.
• Demonstrated technical leadership and ability to independently drive complex projects from concept to product delivery.
• Strong communication and collaboration skills with the ability to influence cross‑functional teams and technical strategy.
• Track record of innovation through publications, patents, invention disclosures, open‑source contributions, or commercial product development.

Preferred Qualifications

• Typically requires a minimum of 8 years of related experience with a Bachelor’s degree; or 6 years and a Master’s degree; or a PhD with 3 years of experience; or equivalent experience.
• Experience with bulk RNA‑seq, gene expression analysis, alternative splicing, gene fusion detection, and RNA biomarker development.
• Experience applying machine learning, artificial intelligence, or modern data science techniques to biological data analysis, method development, or software validation.
• Experience with single‑cell genomics and transcriptomics workflows.
• Experience with CRISPR/Perturb‑seq analysis, CROP‑seq, ATAC‑seq, spatial transcriptomics, CROP‑seq, or other multiomic assays.
• Experience using AI‑assisted software development and scientific analysis tools to accelerate method development, testing, validation, or interpretation.
• Experience with cloud computing, distributed computing, or large‑scale genomic data processing.
• Knowledge of oncology, clinical genomics, population genomics, translational research, or biotechnology product development.

#LI-REMOTE

The estimated base salary range for the Staff Bioinformatics Scientist -- DNA/RNA Secondary Analysis Algorithms role based in the United States of America is: $155,600 - $233,400. Should the level or location of the role change during the hiring process, the applicable base pay range may be updated accordingly. The range reflects long‑term growth in the role; therefore, most candidates are hired between the minimum and middle of the range. Placement depends on experience, skills, location, and internal equity.

Additionally, all employees are eligible for one of our variable cash programs (bonus or commission) and eligible roles may receive equity as part of the compensation package.

We offer a wide range of benefits as innovative as our work, including access to genomics sequencing, family planning, health/dental/vision, retirement benefits, and paid time off.

We are a company deeply rooted in belonging, promoting an inclusive environment where employees feel valued and empowered to contribute to our mission. Built on a strong foundation, Illumina has always prioritized openness, collaboration, and seeking alternative perspectives to propel innovation in genomics.

We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race.

We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and offer opportunities to engage in social responsibility.

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.

Illumina conducts background checks on applicants for whom a conditional offer of employment has been made. Qualified applicants with arrest or conviction records will be considered for employment in accordance with applicable local, state, and federal laws. Background check results may potentially result in the withdrawal of a conditional offer of employment. The background check process and any decisions made as a result shall be made in accordance with all applicable local, state, and federal laws.

Illumina prohibits the use of generative artificial intelligence (AI) in the application and interview process. If you require accommodation to complete the application or interview process, please contact [e-mail].

To learn more, visit: https://www.dol.gov/ofccp/regs/compliance/posters/pdf/eeopost.pdf.

The position will be posted until a final candidate is selected or the requisition has a sufficient number of qualified applicants.

This role is not eligible for visa sponsorship.

The potential of genomics to change the world is unparalleled. At Illumina, we are leading the way. Our technology empowers researchers and clinicians globally to improve cancer treatments, change the course of diseases, protect the environment, and fight food insecurity.

We are made up of dedicated professionals, all‑in on creating a better world – and we need every skill set on our path to making genomics useful for all. Learn more about life at Illumina.