BEPC Inc. - Business Excellence Professional Consulting · 2 days ago
Bioinformatics Associate II
South San Francisco, CA
Contract
Hybrid
Senior Level
$60.85/hr - $64.85/hr
5+ years expBEPC Inc. is a 100% employee-owned company providing consulting and staffing solutions across various industries. They are seeking a highly motivated Bioinformatician (Level II) to support the development and optimization of bioinformatics pipelines and analyze NGS datasets while collaborating with cross-functional research teams.
BiotechnologyConsulting
Hiring Manager
Jessica Vazquez
Responsibilities
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
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
Write efficient, reproducible, and well-documented code in Python or R
Build custom tools for data integration, transformation, and visualization
Implement, evaluate, and adapt existing bioinformatics tools and algorithms
Integrate open-source resources to support project objectives
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
Diagnose pipeline failures, data issues, and computational inefficiencies
Ensure data integrity, workflow reproducibility, and methodological rigor
Prepare clear reports, visualizations, and presentations summarizing analysis outcomes
Maintain precise documentation of workflows, code, and datasets
Stay current with bioinformatics tools, NGS technologies, and computational methods
Qualification
Required
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
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
Benefits
Medical
Dental
Vision
Life insurance
Company
BEPC Inc. - Business Excellence Professional Consulting
BEPC Incorporated provides Technical Engineering and Information Technology Project Management services to Fortune 500 companies in the industries: Life Science, Engineering, Manufacturing, Information Technologies, Advanced Technologies, Automotive, and Construction.
201-500 employees
H1B Sponsorship
BEPC Inc. - Business Excellence Professional Consulting has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (1)
2023 (3)
2020 (3)
Funding
Current Stage
Growth StageLeadership Team
Oscar Casillas
President and CEO
Andrew Casillas
Human Resources Partner
Company data provided by crunchbase