Scientist II, Bioinformatics

Location: Santa Fe, NM, United States of America

Annual base pay: $52,000–$130,000

Company

Global provider of clinical research services, commercial insights, and healthcare intelligence for the life sciences and healthcare industries.

What you will do

• Operate Sanger sequencing pipelines for assembly, trimming, quality control, variant calling, and curated sequence delivery.
• Run NGS workflows across Illumina, PacBio, and Oxford Nanopore platforms for antibody discovery, including paired-chain assembly, clonotyping, repertoire annotation, and longitudinal analysis.
• Manage sequencing-analysis requests, define deliverables, set timelines, and track work in progress.
• Perform NGS sample preparation, library quality control, plate and sample tracking, Sanger submissions, and coordination with sequencing cores or vendors.
• Develop, maintain, debug, and document scripts, visualizations, reports, dashboards, and pipelines using AI coding assistants with review for correctness.
• Run production workflows on AWS, HPC, or parallel compute; maintain documentation in Benchling and version-controlled repositories.

Requirements

• PhD in bioinformatics, computational biology, computer science, molecular biology, immunology, biochemistry, or a related discipline; a fresh PhD is acceptable, or an MSc with 2+ years of relevant experience.
• Hands-on sequencing data analysis experience involving Sanger and/or NGS, with experience operating Sanger and at least one NGS platform.
• Wet-lab experience in molecular biology and/or NGS sample preparation.
• Working knowledge of AWS S3 and EC2, with readiness to develop skills in HPC, parallel computing, and workflow frameworks such as Nextflow or Snakemake.
• Knowledge of antibody discovery, antibody sequencing fundamentals, library design, display campaigns, and sequencing-based readouts.
• Strong communication, prioritization, quality-control, collaboration, and SOP-compliance skills.

Nice to have

• Experience with R, Streamlit, Dash, Plotly, FastAPI, PyTorch, scikit-learn, AlphaFold, or RoseTTAFold.
• Experience with the Benchling SDK or APIs, laboratory information systems, AWS Batch, or ParallelCluster.

Culture & Benefits

• Benefits programs support employees and their families across physical, mental, emotional, financial, and social well-being.
• Equal opportunity employment and an integrity-focused hiring process.
• Potential additional incentive plans, bonuses, and health and welfare benefits may be available depending on the position.