Bioinformatician (Level II)

Greetings from IT Engagements

IT Engagements is a global staff augmentation firm providing a wide-range of talent on-demand and total workforce solutions. We have an immediate opening for the below position with one of our premium clients.

Role: Bioinformatician (Level II) (Contract W2 Role)

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

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 ollaborate 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
  
  

Supplier Instructions (Mandatory)

All Submissions Must Include

• Candidate’s primary programming language (Python or R) at the top of the resume.
• No job-to-job resumes; resumes must show tangible accomplishments and clear tenure.
• Specific NGS pipelines, data types, and tools the candidate has directly used.
• Candidate confirmation that they can commit to 1 day onsite weekly.