Bioinformatics Associate II

BEPC is actively looking for Bioinformatics Associate II, in South San Francisco, CA area!

W2 Contract – 6 months with possible extensions!

Benefits include medical, dental, vision, and life insurance

Pay Rate: $60.85 - $64.85 /hour - Determined based on experience (Paid weekly)

Work Model: Hybrid – South San Francisco (1 day onsite / 4 days remote)

Required knowledge: Programming language (Python or R)

Note: This is a W2 only role — C2C, C2H will not be considered

BEPC is seeking a highly motivated Bioinformatician (Level II) to join our client’s site in South San Francisco, CA. This role will support the development and optimization of bioinformatics pipelines, analysis of NGS datasets, and close collaboration with cross-functional research teams.

The ideal candidate has 5–10 years of hands-on experience, a Master’s degree in Bioinformatics, Computational Biology, Genomics, Computer Science, or a related quantitative field, is highly proficient in Python or R, has deep experience with NGS workflows, and thrives in a fast-paced research environment.

Summary of Duties and 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 metho.

Qualifications:

• Master’s degree 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.

About BEPC

BEPC Inc., founded in 2007, is a 100% employee-owned company providing top-tier consulting and staffing solutions across industries like technology, engineering, manufacturing, and project management. At BEPC, we are driven by innovation and a commitment to excellence. We take pride in fostering a collaborative and innovative environment where our team members thrive. With competitive benefits, including medical, dental, vision, and life insurance, BEPC is dedicated to supporting our employees' personal and professional growth.

Apply Now!

Qualified candidates are encouraged to apply by submitting an up-to-date resume that highlights how your experience aligns with the role. Please include specific examples that demonstrate your qualifications. We look forward to connecting with you!