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Bioinformatics Associate II

South San Francisco, CA 94080

Posted: 01/05/2026 Employment Type: Contract Industry: Research and Discovery Job Number: 12473 Pay Rate: $31.00 - $65.00 Remote Friendly: Onsite

Job Description

Our client is a leading biotechnology company that discovers, develops, manufactures and commercializes medicines to treat patients with serious or life-threatening medical conditions. They are among the world's leading biotech companies, with multiple products on the market and a promising development pipeline.

Position Overview:

We are seeking a highly skilled and motivated Bioinformatician (Level II) with 5-10 years of hands-on experience and a Masters degree in Bioinformatics, Computational Biology, Genomics, Computer Science, or a related quantitative field.
This individual will lead the development and optimization of bioinformatics pipelines, analyze NGS datasets, and collaborate closely with cross-functional research teams. The ideal candidate is highly proficient in Python or R, has deep experience with NGS workflows, and thrives in a fast-paced research environment.

Key Responsibilities:
  • Bioinformatics Pipeline Development Develop, automate, and maintain robust pipelines for RNA-seq, WGS/WES, scRNA-seq, or other sequencing datasets.
  • Optimize workflows for reproducibility, scalability, and performance across HPC or cloud environments.

NGS Data Analysis:
  • Perform advanced computational analyses including:
  • Variant calling
  • Differential gene expression
  • Transcriptomic and epigenomic analysis
  • Pathway/enrichment analysis
  • Genomic annotation
  • Conduct QC for FASTQ, BAM/CRAM, VCF, and related formats.
    Programming & Scripting:
    • Write efficient, reproducible, and well-documented code in Python or R.
    • Build custom tools for data integration, transformation, and visualization.

    Tool & Algorithm Implementation:
    • Implement, evaluate, and adapt existing bioinformatics tools and algorithms.
    • Integrate open-source resources to support project objectives.

    Cross-Functional Collaboration:
    • Work closely with wet-lab scientists to interpret data, troubleshoot issues, and align computational analyses with experimental design.
    • Communicate complex findings clearly to technical and non-technical audiences.

    Troubleshooting & Optimization:
    • Diagnose pipeline failures, data issues, and computational inefficiencies.
    • Ensure data integrity, workflow reproducibility, and methodological rigor.

    Documentation & Reporting:
    • Prepare clear reports, visualizations, and presentations summarizing analysis outcomes.
    • Maintain precise documentation of workflows, code, and datasets.

    Continuous Learning:
    • Stay current with bioinformatics tools, NGS technologies, and computational methods.

    • Job Requirements

    Required Qualifications:
    • Masters degree is required (Bioinformatics, Computational Biology, Genomics, Computer Science, or related quantitative field).
    • 5-10 years of hands-on experience working in bioinformatics or computational genomics.
    • Demonstrated proficiency in Python or R (candidate must specify their primary language)
    • Extensive experience analyzing NGS datasets and implementing standard workflows
    • Proficiency with key tools, including: STAR, BWA, Bowtie2, GATK, Samtools, bcftools DESeq2, EdgeR, Seurat, Scanpy
    • Experience with public genomic databases (NCBI, Ensembl, UCSC, GTEx, TCGA).
    • Strong understanding of statistics, experimental design, and computational biology principles.
    • Proficiency using Git/GitHub for version control.
    • Excellent communication, problem-solving, and organizational skills.

    Preferred Qualifications:
    • Experience with workflow management systems (Nextflow, Snakemake, WDL/Cromwell).
    • Background in cloud computing (AWS, GCP, Azure) and containerization (Docker, Singularity).
    • Previous work with HPC clusters.
    • Experience with specialized sequencing applications such as:
    • Single-cell assays (scRNA-seq / ATAC-seq)
    • Long-read sequencing (PacBio, ONT)
    • Epigenomics assays

    Meet Your Recruiter

    Lexie Pierce
    Senior Recruiter

    As a Compass recruiter, Lexie brings in 15 years of experience in leadership and employee growth and development. She's incredibly passionate about helping candidates find and accept new opportunities, ultimately leading her to start her recruiting career in the life science industry. Her favorite part about connecting with Compass candidates and clients is witnessing the excitement the candidates exude and making an impact on their lives.

     

    Outside of the office, Lexie enjoys going to the farmers' market on Saturdays with her son so she can find the best produce to use in her family dinners. She enjoys cooking, reading, knitting, restoring furniture, and spending time with her family and friends. Lexie is also passionate about supporting organizations that are looking to educate the community about Congenital Heart Defects (CHD).

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