BioInformatics Associate

Only local San Francisco Bay Area candidates! No 3rd party agencies! No Visa Sponsorhips available. 

We are seeking a highly skilled and motivated Bioinformatician (Level 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, 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.

Required 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.

● 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, Google Cloud Platform, 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