Genomic Data Scientist: Pipeline & Multi-Omics Engineering

Boston Children's Hospital; Boston (MA); On-site; USD 110,000 - 150,000; Full time

Benefits offered by this job

flexible schedules

affordable health

vision and dental insurance

child care and student loan subsidies

generous levels of time off

403(b) Retirement Savings plan

Pension

Tuition and license/certification Reim

cell phone plan discounts

discounted rates on T-passes

Job summary

Boston Children's Hospital is seeking a Genomic Data Scientist to lead pipeline engineering and multi-omics analysis for pediatric research. You will architect automated workflow systems (Nextflow, WDL, Snakemake) to process RNA-seq, methylation, long-read, and WGS/WES data, collaborating with physician-scientists on rare disease initiatives.

You will apply advanced statistics, machine learning, and quantitative modeling to drive biological insights, optimize HPC pipelines, and contribute to

Qualifications

• Bachelor's degree; PhD in Genetics, Genomics, Computational Biology, Bioinformatics, or related field highly preferred.
• At least one year of experience; MSc/PhD studies count toward this.
• Experience building/maintaining automated bioinformatics pipelines with Nextflow, WDL or Snakemake.
• Strong programming in Python, R, Bash in Linux/HPC environments; containerization and Git.
• Experience analyzing multi-omic datasets (WGS/WES, RNA-seq, methylation, long-read).
• Familiarity with human genetics research, variant annotation tools, ACMG guidance in research.
• Ability to manage pipeline development independently and troubleshoot with teams.

Responsibilities

• Pipeline Engineering & Workflow Automation: design, build, optimize scalable bioinformatics pipelines.
• Hypothesis-Driven Data Analysis: deploy automated analyses on high-dimensional genomic data using statistics and ML.
• HPC & Infrastructure Optimization: containerize tools, use Git, optimize performance on HPC clusters.
• Biological Discovery & Project Execution: translate data into insights, manage milestones and bottlenecks.
• Documentation & Scientific Communication: document pipelines and contribute to publications.

Education

Bachelor's degree

PhD preferred in Genetics/Genomics/Computational Biology/Bioinformatics

Tools

Nextflow

Snakemake

Docker

Singularity

Git

WDL

Python

Job description

Boston Children's Hospital is seeking a Genomic Data Scientist to lead pipeline engineering and multi-omics analysis for pediatric research. You will architect automated workflow systems (Nextflow, WDL, Snakemake) to process RNA-seq, methylation, long-read, and WGS/WES data, collaborating with physician-scientists on rare disease initiatives.

You will apply advanced statistics, machine learning, and quantitative modeling to drive biological insights, optimize HPC pipelines, and contribute to