Staff Bioinformatics Scientist

Illumina; San Diego, Northern (CA, KY); Hybrid; USD 156,000 - 233,000; Full time

Benefits offered by this job

Genomics sequencing access

Family planning

Health/dental/vision benefits

Retirement benefits

Paid time off

Job summary

Illumina is seeking a Staff Bioinformatics Scientist to join the methods development team, focusing on secondary analysis algorithms for DRAGEN. You will design and implement production-grade C/C++ software for structural variant detection and graph-based methods, collaborating across QC, FPGA, SW, and clinical genomics teams.

You should have a strong CS and genomics background, with experience in NGS, multi-threading, and AI-assisted prototyping, and you will contribute to a fast-paced,

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 developing next generation sequencing data analysis methods.
• Extensive experience in an object-oriented programming language; C++ preferred.
• Strong background in computer science algorithms relevant to bioinformatics.
• Ability to efficiently leverage AI-assisted tools in development to rapidly iterate and prototype ideas.
• Strong communication skills and ability to describe complex analyses to audiences with diverse backgrounds.
• Ability to contribute independently and collaboratively, take ownership of assigned tasks, and excel in a fast-paced environment.
• Experience using version control systems such as Git.
• Knowledge or background in NGS-based methods for assembly, structural variant detection, and cancer-related applications would be especially well suited to this role.

Responsibilities

• Design, prototype, and implement innovative computational or statistical algorithms to extract meaningful biological signal from sequencing assays.
• Implement algorithms in production-grade C/C++ software.
• Collaborate deeply with interdisciplinary teams (QC/QA test teams, FPGA teams, SW teams, clinical genomics teams).
• Engage with external scientific teams to build product credibility and define emerging requirements.
• Clearly communicate technical methods and findings across internal teams with diverse expertise.

Skills

C++

Algorithms

Bioinformatics

Multi-threading

AI-assisted tools

Communication

Git

NGS data analysis

Education

PhD

Master's degree

Bachelor's degree

Tools

Git

CI/CD

NGS data analysis tools

Python

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.## Our team specializes in developing a fast and accurate platform called DRAGEN for the secondary analysis of NGS genomic data. The platform covers a wide range of pipelines spanning germline and somatic analysis (WGS and targeted; tumor/normal and tumor-only), DNA and RNA workflows, and variant classes including small variants, CNVs, and structural variants. We are looking for a highly driven and talented Staff Bioinformatics Scientist to join our methods development team to work on secondary analysis algorithms. The ideal candidate will have a strong background in computer science, algorithms, statistics, or digital signal processing in addition to expertise in genomics and next generation sequencing. The candidate should be a proven team player and will contribute to the production software codebase. This role will focus on software development for structural variant detection, pangenome references, graph-based algorithms, and NGS assembly methods. **Responsibilities:*** Design, prototype, and implement innovative computational or statistical algorithms to extract meaningful biological signal from sequencing assays.* Implement algorithms in production-grade C/C++ software.* Collaborate deeply with interdisciplinary teams (QC/QA test teams, FPGA teams, SW teams, clinical genomics teams).* Engage with external scientific teams to build product credibility and define emerging requirements.* Clearly communicate technical methods and findings across internal teams with diverse expertise. Listed responsibilities are an essential but not exhaustive list of the usual duties associated with the position. Changes to individual responsibilities may occur due to business needs. **Required Skills and Experience:*** 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 developing next generation sequencing data analysis methods.* Extensive experience in an object-oriented programming language; C++ preferred.* Strong background in computer science algorithms relevant to bioinformatics.* Ability to efficiently leverage AI-assisted tools in development to rapidly iterate and prototype ideas.* Strong communication skills and ability to describe complex analyses to audiences with diverse backgrounds.* Ability to contribute independently and collaboratively, take ownership of assigned tasks, and excel in a fast-paced environment.* Experience using version control systems such as Git.* Knowledge or background in NGS-based methods for assembly, structural variant detection, and cancer-related applications would be especially well suited to this role.* Willingness to learn and grow with an exceptionally talented group of scientists and engineers! **Desired Skills and Experience:*** Experience with multi-threading and memory management techniques.* Knowledge and experience with probability and statistics or machine learning.* Knowledge and experience with a wide range of bioinformatics tools.* Familiarity with professional software development practices (testing, CI/CD, debugging, source control).* Demonstrated success in collaborating in a team environment and delivering high-quality software products using agile development methodologies.### The estimated base salary range for the Staff Bioinformatics Scientist 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.