Job Description

Essential skills: Senior Bioinformatics Scientist | RNAseq | Snakemake | Nextflow | Python | Genomics | High-throughput sequencing | Cloud pipelines | Data visualization | San Francisco | Full-Time

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

• 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.

This Senior Bioinformatics Scientist role focuses on building and optimizing scalable, production-grade bioinformatics workflows to accelerate scientific research. Collaborate with a skilled, multidisciplinary team to develop robust pipelines, transform complex sequencing data into clear insights, and help drive innovation in a mission-driven environment.

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