Bioinformatics Scientist 2

Illumina • San Diego, CA

1d

About The Position

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. Overview: Since 2001, the cost of DNA sequencing has dropped more than 100,000-fold, from $100,000,000 USD per human genome to less than $600 USD today. This is resulting in the explosive growth of genomics data, which we are combining with machine learning for data-driven agriculture, cancer treatment, reproductive health, and other life-changing applications. The Bioinformatics group contributes to the development of new customer-facing bioinformatics solutions. The team is responsible for defining and creating applications and pipelines that facilitate a seamless user experience, integrating best-in-class community tools, as well as developing new methods and algorithms, and deploying them both locally and on Illumina’s cloud computing environment. The ideal candidate will be able to work in a cross functional team, translating the challenges faced by the group into bioinformatics solutions. The position requires a strong background in bioinformatics with an interest in expanding software engineering, architecture, and cloud-based computing skills.

Requirements

• Advanced knowledge of software engineering and computational biology, with demonstrated hands-on experience analyzing proteomics data and Illumina-generated datasets.
• Strong experience developing and maintaining bioinformatics pipelines using Python, Nextflow/Groovy, Bash, and Unix/Linux environments, following modern software development practices (Git, testing, documentation).
• Practical experience working with NGS data formats and tools (e.g., BCL Convert, SAMtools, STAR, Velvet) and applying statistical methods using tools such as R, DESeq2, limma, or equivalent frameworks.
• Broad technical expertise across proteomics, RNA-seq, and DNA sequencing data, including the ability to integrate and interpret multi-omics datasets.
• Solid understanding and application of statistics, machine learning, and algorithmic approaches for biological data analysis.
• Demonstrated ability to independently execute new tasks and workflows, and to train or mentor others on advanced software tools, analytical methods, or laboratory-adjacent computational workflows.
• Strong written and verbal communication skills, with the ability to clearly present analytical results, technical trade-offs, and project progress to cross-functional stakeholders.
• All listed requirements are deemed as essential functions to this position; however, business conditions may require reasonable accommodations for additional task and responsibilities.

Responsibilities

• Independently designs, develops, and executes computational and analytical workflows for proteomics and next-generation sequencing data; interprets results from own and others’ work and evaluates impact on project milestones and deliverables. Proposes alternative analytical or software strategies as needed and may contribute to invention disclosures.
• Applies best-practice software engineering methods—including version control, testing, documentation, and continuous integration—to analyze large-scale biological datasets in a fast-paced product development environment.
• Designs, implements, and maintains scalable bioinformatics pipelines using workflow frameworks such as Nextflow, integrating tools for data conversion, alignment, quantification, and statistical analysis, and deploying pipelines in local, HPC, and cloud computing environments.
• Collaborates closely with wet lab scientists and cross-functional stakeholders to gather requirements, troubleshoot assays, define quality metrics, and translate experimental needs into robust computational solutions.
• Plans and owns projects within their technical area of expertise, including scope, timelines, and deliverables, and may provide technical direction to other scientists and engineers contributing to pipeline development or data analysis.
• Establishes standards and best practices for experimental design, data processing, statistical analysis, and data visualization, defining technical requirements for products or small projects with attention to robustness, scalability, reproducibility, and cost.
• Identifies technical risks within bioinformatics pipelines, data quality, or computational infrastructure, and provides recommendations for risk mitigation, validation, and benchmarking.

Benefits

• 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.

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level