IT Engagements, Inc. · 1 week ago
Bioinformatician (Level II)
South San Francisco, CA
Contract
Hybrid
Senior Level
5+ years expIT Engagements, Inc. is a global staff augmentation firm seeking a highly skilled Bioinformatician (Level II) to lead the development and optimization of bioinformatics pipelines and analyze NGS datasets. The role requires collaboration with cross-functional research teams and proficiency in Python or R.
Business IntelligenceInformation TechnologyRecruitingSoftware Engineering
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 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
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
Company
IT Engagements, Inc.
IT Engagement is your central hub for all your SAP needs and specializing in strategic solutions for the pharmaceutical, biotechnology, device and related industries.
11-50 employees
Funding
Current Stage
Early StageCompany data provided by crunchbase