Lead Bioinformatics Scientist - Transcriptomics & Multiomics

Illumina; Coronado (CA); On-site; USD 171,000 - 256,000; Full time

Benefits offered by this job

Genomics sequencing access

Health/dental/vision insurance

Retirement benefits

Paid time off

Job summary

Illumina is seeking a Sr. Staff Bioinformatics Scientist to advance DRAGEN analysis solutions with deep expertise in transcriptomics, computational biology, and bioinformatics software development.

You will lead development of novel algorithms, design scalable workflows for RNA applications, and apply ML/AI methods to accelerate product innovation. The role requires a PhD with extensive experience in NGS bioinformatics, production software, and strong leadership to drive projects from concept to

Qualifications

• PhD in Bioinformatics, Computational Biology, Computer Science, Statistics, Biology, or related discipline, or equivalent industry experience.
• Significant experience developing bioinformatics algorithms, analytical methods, and production software for NGS applications.
• Strong background in transcriptomics, statistical modeling, and biological data analysis.
• Proficiency in programming languages such as C++, Python, or similar.
• Experience designing, validating, benchmarking, and interpreting computational methods for complex biological datasets.
• Experience applying machine learning, artificial intelligence, or modern data science techniques to biological data analysis, method development, or software validation.
• 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.

Responsibilities

• Lead development of novel algorithms and analytical methods for RNA and multiomic sequencing applications.
• Design, evaluate, and implement scalable bioinformatics workflows 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.

Skills

Transcriptomics

Bioinformatics

Algorithms

ML/AI

Leadership

C++

Python

Education

PhD in Bioinformatics or related field

Job description

Illumina is seeking a Sr. Staff Bioinformatics Scientist to advance DRAGEN analysis solutions with deep expertise in transcriptomics, computational biology, and bioinformatics software development.

You will lead development of novel algorithms, design scalable workflows for RNA applications, and apply ML/AI methods to accelerate product innovation. The role requires a PhD with extensive experience in NGS bioinformatics, production software, and strong leadership to drive projects from concept to