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R&D Partners · 1 week ago

Bioinformatics Associate II

South San Francisco, CA

Contract

Hybrid

Senior Level

$52.24/hr - $65.30/hr

5+ years exp

R&D Partners is a global functional service provider specializing in scientific, clinical research & engineering. They are seeking a highly skilled Bioinformatics Associate II to lead the development and optimization of bioinformatics pipelines and analyze NGS datasets while collaborating with cross-functional research teams.

Staffing Agency

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

BioinformaticsNGS analysisPythonRGit/GitHubStatisticsCloud computingWorkflow managementCommunication skillsProblem-solving skillsOrganizational skills

Required

Master's 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 required

Demonstrated proficiency in Python or R

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) preferred

Background in cloud computing (AWS, GCP, Azure) and containerization (Docker, Singularity) preferred

Previous work with HPC clusters preferred

Experience with specialized sequencing applications such as: Single-cell assays (scRNA-seq / ATAC-seq), Long-read sequencing (PacBio, ONT), Epigenomics assays preferred