St Jude Children's Research Hospital
Bioinformatics Research Scientist (Immunology & TCR Repertoire) - Jeremy Chase C
St Jude Children's Research Hospital, Memphis, Tennessee, us, 37544
Job Description
The Bioinformatics Research Scientist is responsible for designing, developing, improving, modifying, and operating data analysis pipelines. The role manages projects and coordinates other efforts related to analysis and infrastructure as directed.
Jeremy Chase Crawford's lab is seeking a highly skilled bioinformatician to lead the computational analysis of next-generation immune repertoire sequencing data. This position works 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 develop 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 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 audits.
Merge wetlab and computational data sources (LIMS, spreadsheets, devices, bioinformatic pipelines, etc.) to create up-to-date reports in PowerBI.
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 related field.
Experience in at least one programming language (Python preferred) and a 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 (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 environment management using Conda/Mamba to ensure reproducible 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 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 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 state and municipal pay transparency laws, St. Jude is including a reasonable estimate of the compensation range for this role. The current salary range is $86,320 – $154,960 per year for the Bioinformatics Research Scientist (Immunology & TCR Repertoire) – Jeremy Chase Crawford Lab.
Equal Opportunity Employer St. Jude is an Equal Opportunity Employer.
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 will result in no fee being paid if the candidate is hired.
#J-18808-Ljbffr
Jeremy Chase Crawford's lab is seeking a highly skilled bioinformatician to lead the computational analysis of next-generation immune repertoire sequencing data. This position works 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 develop 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 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 audits.
Merge wetlab and computational data sources (LIMS, spreadsheets, devices, bioinformatic pipelines, etc.) to create up-to-date reports in PowerBI.
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 related field.
Experience in at least one programming language (Python preferred) and a 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 (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 environment management using Conda/Mamba to ensure reproducible 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 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 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 state and municipal pay transparency laws, St. Jude is including a reasonable estimate of the compensation range for this role. The current salary range is $86,320 – $154,960 per year for the Bioinformatics Research Scientist (Immunology & TCR Repertoire) – Jeremy Chase Crawford Lab.
Equal Opportunity Employer St. Jude is an Equal Opportunity Employer.
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 will result in no fee being paid if the candidate is hired.
#J-18808-Ljbffr