Featured RNA-Seq Job – Staff Bioinformatics Scientist, RNA-Seq

Position Summary:

Our engineering team specializes in developing a fast and accurate FPGA-accelerated platform called DRAGEN, for the secondary analysis of NGS genomic data.

The platform covers a wide range of pipelines, WGS and targeted (enriched/amplicon) germline, WGS and targeted somatic (T/N and tumor-only), DNA/RNA, small variants, CNV and structural variants.

For this position, we are looking for a candidate with strong experience on secondary analysis RNAseq pipelines and lead a team of bioinformatic scientists.

The Staff Bioinformatics Scientist will have a strong quantitative background in statistical methods to lead a team focused on the development of novel algorithms for genome interpretation, starting from RNASeq datasets.

Our team develops DNA/RNA analysis solutions for use by researchers and clinicians worldwide, which provide sample-to-answer pipelines with high reliability, speed, and completeness of results. The applications are many, from rare and undiagnosed inherited diseases, to population-scale genetics, to cancer.

Key objectives would include:

  • Algorithm design of analysis methods for bulk RNASeq pipelines (Whole transcriptome or targeted), RNAseq alignment, RNA quantification and differential gene expression, gene fusion, RNA variant calling.
  • Algorithm design of analysis methods for single cell RNA
  • Experience with product development and product software, validation and regression tests, software release management.

The ideal candidate will be able to contribute both to the algorithm design based on statistics background, and contribute to the software code base, based on proficient C/C++ programming skills.


  • Bulk RNA and single cell RNA Algorithm development – Design, prototype and implement computational algorithms for analysis of secondary pipelines for bulk RNASeq and single cell RNA datasets.
  • Data analysis – apply best practice statistical/computational methods to analyze large-scale biological data, such as RNASeq read alignments, gene quantification and expression, single cell RNA cluster visualization, etc… in a fast-paced product development environment.
  • Product development – Implement algorithms in production-grade C/C++ software. Collaborate deeply with inter-disciplinary teams (QC/QA test teams, FPGA teams, SW teams, clinical genomics teams) as the platform has many different end-users with different requirements and applications to ensure a smooth, end-to-end workflow with external organizations.

Required Skills and Experience:

  • PhD in Bioinformatics, Computational Biology, Biostatistics, Computer Science
  • Expert knowledge on current bioinformatics/genomics RNASeq methods for NGS secondary analysis pipelines bulk RNASeq and single cell RNASeq applications.
  • Deep knowledge on NGS RNASeq assay development
  • Expert in C/C++/C#, and/or Python, R, high performance computing
  • Strong experience in statistics, data analysis and pipeline development
  • Ability to contribute independently and collaboratively, and to excel in a fast-paced environment
  • Superior written and verbal communication skills

Desired Skills and Experience:

  • Experience with secondary analysis of human whole-transcriptome sequencing data.
  • Experience with using version control systems such as git
  • Experience with cloud computing, parallel computing, and big data.


  • 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 experience; or equivalent experience.

When you join the high-performing team at Illumina, your work takes on new meaning. Our growth, our positive culture, and the impact our products are having in the world ignite a passion that drives our people forward. And together, we accomplish beyond expectations.


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