Bioinformatics Associate II

We are seeking a highly skilled and motivated Bioinformatics Associate II with 5-10 years of hands-on experience and a Master’s 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 and has deep experience with NGS workflows and thrives in a fast-paced research environment. This is a 6-month contract position based in South San Francisco, CA. The schedule is 1 day onsite required and 4 days remote. 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. Qualifications • 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. • 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. Pay • $52.24-$65.30/hr Why Choose R&D Partners? As an employee, you have access to a comprehensive benefits package including: • Medical insurance – PPO, HMO & HSA • Dental & Vision insurance • 401k plan • Employee Assistance Program • Long-term disability • Weekly payroll • Expense reimbursement • Online timecard approval R&D Partners is a global functional service provider and strategic staffing resource specializing in scientific, clinical research & engineering. We provide job opportunities within major pharmaceutical, biopharmaceutical, biotechnology, and medical device companies. R&D Partners is an equal-opportunity employer.