Bioinformatics Associate II

Job Title: Bioinformatics Associate II/ Bioinformatician (Level II)
Job Location: South San Francisco, CA
Job Duration: 06 Months

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

Experience Level: 5–10 years hands-on experience required
Education Requirement: Master’s degree required

Position Overview:
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, 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

Pay: $55.00 - $65.00 per hour

Benefits:

• 401(k) matching

Ability to Commute:

• South San Francisco, CA 94080 (Required)

Work Location: In person

Salary : $55 - $65