Senior Bioinformatics Scientist
Location: San Francisco, CA
Employment Type: Full-Time
Department: Engineering
Overview
We are proud to be partnering with an industry-leading biotechnology innovator whose mission is to accelerate global research through powerful, next-generation DNA sequencing and analysis tools. Their technology supports thousands of scientists - from fast-growing startups to academic labs - helping advance critical discoveries and improve health outcomes worldwide.
As a Senior Bioinformatics Scientist, you will bring deep technical expertise and a creative mindset to design, build, and optimize high-throughput bioinformatics workflows. Working in close collaboration with scientists, engineers, and product teams, you will help shape the future of bioinformatics infrastructure, enabling faster and smarter science.
Responsibilities
Develop, maintain, and optimize state-of-the-art sequence analysis workflows capable of processing thousands of samples per day
Integrate and evaluate new bioinformatics tools to improve accuracy, speed, and scalability of pipelines
Troubleshoot and resolve complex challenges related to sequencing data, including biological artifacts and platform-specific edge cases
Translate raw bioinformatics outputs into actionable, clear, and user-friendly reports, visualizations, and interactive tools
Mentor and support junior team members while continuously growing your own technical skill set
Collaborate cross-functionally to develop and deliver new product features
Write clean, maintainable, production-ready code
Contribute to a culture of innovation, curiosity, and scientific excellence
Requirements
Education & Experience:
PhD in a biological science or related discipline
8+ years of experience developing production-scale bioinformatics pipelines
Technical Skills:
Deep experience in bulk and single-cell RNAseq analysis, including differential expression workflows
Proven expertise in developing Snakemake or Nextflow pipelines deployed in local and/or cloud environments
Solid understanding of molecular biology and sequencing technologies (Illumina, Oxford Nanopore)
Proficiency in Python (including numpy, pandas, biopython, Jupyter) and Conda environments
Familiarity with Docker/Singularity, Git, and Linux shell scripting
Strong knowledge of core sequence analysis concepts (alignment, assembly, QC)
Experience with large-scale genomic data processing and public genomic repositories
Ability to develop intuitive web-based reporting or visualization tools (e.g., R Shiny, Streamlit)
Clean, maintainable, production-grade coding practices
Preferred Qualifications:
Experience developing performant software in a compiled language (C++, Rust, etc.)
Interest in advanced data visualization and intuitive UX
1+ year of experience in a molecular biology wet-lab environment
Demonstrated ability to develop novel bioinformatics algorithms
Benefits
Competitive salary
Employee stock options
4 weeks paid time off + 10 paid holidays
Comprehensive health, dental, and vision insurance
401(k) with company matching
Life insurance, mental health support, health advocacy services
Gym membership reimbursement
Why Apply?
Contribute directly to accelerating world-changing biotech research
Work in a collaborative, inclusive, mission-driven team
Leverage cutting-edge tools and methodologies in a high-impact environment
We encourage applications from diverse and creative thinkers who thrive in collaborative, inclusive teams. If you'd like to learn more, please apply today or reach out in confidence to discuss further
