Bioinformatics Research Scientist (Immunology & TCR Repertoire) - Jeremy Chase Crawford Lab

The Bioinformatics Research Scientist is responsible for designing, developing, improving, modifying, and operating data analysis pipelines. Manages projects and coordinates other efforts related to analysis and infrastructure as directed.

The lab of Jeremy Chase Crawford is seeking a highly skilled bioinformatician to lead the computational analysis of next-generation immune repertoire sequencing data. This position will work at the cross-section of immunology and computational biology to decipher T-cell specificity in the context of vaccine responses (e.g., SARS-CoV-2) and pediatric immune development.

The successful candidate will be responsible for developing robust automated pipelines for novel assays—specifically TIRTLseq and 5’RACE—to track clonal expansion, infer HLA genotypes, and map TCRs to their cognate epitopes.

Key Responsibilities

• Pipeline Development & Automation:
  • Develop and maintain robust pipelines to automate the parsing, quality control, and characterization of human sequencing data.
  • Create automated reporting tools to characterize clonal expansion across longitudinal samples and assess sensitivity differences between assay platforms.

• Advanced TCR Repertoire Analysis:
  • Perform paired chain (alpha/beta) analysis to infer patient HLA genotypes and "de-orphan" single-chain TCRs from earlier time points.
  • Utilize network analysis approaches to infer the epitopes recognized by expanding TCR clones.

• Database Management:
  • Create and maintain databases to track subject and sample metadata, ensuring data integrity for any possible audits.
  • Merge wetlab and computational data sources (LIMS, Spreadsheets, devices, bioinformatic pipelines etc.) to create up-to-date reports in PoweBI.
  • Design and optimize a static and iteratively updated TCR/epitope matching database to predict antigen specificity.
  • Evaluate data for quality assurance and mine relevant bioinformatics databases to support wet-lab validation.

• Collaboration & Communication:
  • Work closely with wet-lab scientists to design experiments (e.g., defining sample exclusion criteria based on expansion evidence) and interpret complex immunological data.
  • Assist in the evaluation of products and solutions pertaining to St. Jude's technology needs (e.g., cloud computing integration).

Minimum Qualifications

• For Senior Bioinformatics Analyst:
  • Bachelor's degree with 2+ years of relevant post-degree work experience (or Master's degree with 0-2 years experience) in Bioinformatics, Computational Biology, or a related field.
  • Experience in at least one programming language (Python preferred) and statistical package (R).

• For Bioinformatics Research Scientist:
  • Bachelor's degree with 4+ years experience, Master's with 2+ years, or PhD with no work experience.
  • Demonstrated ability to independently perform advanced statistical analysis and algorithm implementation.

Preferred Skills for this Project

• TCR Specificity: Experience with immune repertoire tools (e.g., MiXCR, VDJtools, TCRdist) and handling paired-chain sequencing data.

• Structural Biology/Inference: Familiarity with HLA inference algorithms and epitope prediction models.

• Cloud & HPC: Experience interacting with High-Performance Computing clusters (LSF) and strong experience with environment management using Conda/Mamba to ensure reproducible analysis pipelines.

• Database and Reporting: Experience working with relational databases (MSSQL/MySql/PostgreSQL) and reporting tools (PowerBI/Tableau).

Minimum Education and/or Training:

• Bachelor's degree in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry) or related field.
• Master's degree or PhD preferred.

Minimum Experience:

• Minimum Requirement: Bachelor's degree with 6+ years of relevant post-degree work in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry).
• Experience Exception: Master's degree with 4+ years of relevant post-degree experience (OR) PhD with no experience.
• Experience in at least one programming or scripting language and at least one statistical package, with R preferred.

Compensation

In recognition of certain U.S. state and municipal pay transparency laws, St. Jude is including a reasonable estimate of the compensation range for this role. This is an estimate offered in good faith and a specific salary offer takes into account factors that are considered in making compensation decisions including but not limited to skill sets, experience and training, licensure and certifications, and other business and organizational needs. It is not typical for an individual to be hired at or near the top of the salary range and compensation decisions are dependent on the facts and circumstances of each case. A reasonable estimate of the current salary range is $86,320 - $154,960 per year for the role of Bioinformatics Research Scientist (Immunology & TCR Repertoire) - Jeremy Chase Crawford Lab.

Explore our exceptional benefits!

No Search Firms

St. Jude Children's Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form and/or method without a valid written search agreement in place and approved by HR will result in no fee being paid in the event the candidate is hired by St. Jude.