Genomic Scientist- Pipeline Development

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

Position Summary

Research Informatics supports basic, translational, and clinical pediatric research by delivering cutting-edge digital tools, high-performance computing (HPC), and advanced data science expertise. We bring together PhD-level bioinformaticians, genomic scientists, software engineers, and HPC specialists to collaborate with physician-scientists on work ranging from CryoEM to translational genomics.

As a Genomic Data Scientist, you will drive pipeline engineering and high-dimensional multi-omics analysis across pediatric rare disease initiatives. Working under general scientific direction, you will serve as a key technical and analytical contributor to genomics projects, architecting automated, reproducible workflow systems (e.g., Nextflow, WDL, Snakemake) to process and interpret RNA-seq, methylation, long-read, and whole genome/exome (WGS/WES) data.

Key Responsibilities

• Pipeline Engineering & Workflow Automation: Design, build, optimize, and maintain scalable, reproducible bioinformatics pipelines and automated variant interpretation workflows for research and clinical-grade multi-omics data.
• Hypothesis-Driven Data Analysis: Deploy automated analytical workflows to execute rigorous exploratory and inferential data processing on high-dimensional genomic datasets using advanced statistics, machine learning, and quantitative modeling.
• HPC & Infrastructure Optimization: Containerize computational tools (Docker/Singularity), implement version control (Git), and optimize code performance for efficient execution across High-Performance Computing (HPC) clusters.
• Biological Discovery & Project Execution: Partner with physician-scientists to translate raw multi-omics data into biological insights, managing computational project milestones and troubleshooting pipeline bottlenecks with minimal supervision.
• Documentation & Scientific Communication: Thoroughly document computational pipelines and code bases, contribute to peer-reviewed scientific publications, and present analytical methods at internal and external research forums.

Minimum Qualifications

Education

• Bachelor's degree; PhD in Genetics, Genomics, Computational Biology, Bioinformatics, or a related quantitative field highly preferred.

Experience

• A minimum of one year of position-specific experience might potentially include experience acquired through MSc or Ph.D. studies.
• Demonstrated experience building, maintaining, and automating bioinformatics pipelines using workflow orchestration engines (e.g., Nextflow, WDL, Snakemake).
• Strong programming proficiency in Python, R, and Bash in Linux/Unix High-Performance Computing (HPC) environments, including experience with containerization (Docker/Singularity) and version control (Git).
• Computational experience analyzing multi-omic datasets (WGS/WES, RNA sequencing, methylation, or long-read platforms).
• Experience with human genetics research, variant annotation tools, and familiarity with clinical NGS testing frameworks or ACMG interpretation guidelines in a research setting.
• Demonstrated ability to manage pipeline development tasks independently under general guidance, troubleshoot technical software issues, and collaborate effectively with multidisciplinary research teams.

The posted pay range is Boston Children's reasonable and good-faith expectation for this pay at the time of posting.

Any base pay offer provided depends on skills, experience, education, certifications, and a variety of other job-related factors. Base pay is one part of a comprehensive benefits package that includes 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 certain License and Certification Reimbursement, cell phone plan discounts and discounted rates on T-passes.

Experience the benefits of passion and teamwork.

• 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 certain License and Certification Reimbursement
• cell phone plan discounts
• discounted rates on T-passes