Computational Biologist I

Foundation Medicine; Boston (MA); Hybrid; USD 113,000 - 133,000; Full time

Benefits offered by this job

Annual bonus

Comprehensive benefits

Hybrid work model

Job summary

Foundation Medicine in Boston, MA is seeking a Computational Biologist I to join our oncology bioinformatics team. You will help develop novel signatures and genomic biomarkers using large-scale datasets and contribute to high-impact abstracts, presentations, and manuscripts.

You will also help design data architectures, pipelines, and cloud-based storage, ensuring data quality while collaborating with R&D, Medical, Commercial, and Regulatory teams to translate findings into clinical context.

Qualifications

• Bachelor’s degree in related field and 6+ years of research experience in life sciences, or Master’s with 2+ years, or PhD with no experience.
• Proficiency in Unix-like OS and programming languages (Python, R, SQL) and cloud experience (AWS).
• Experience with public datasets (TCGA, Genomic Data Commons) and bioinformatics analyses.

Responsibilities

• Develop and evaluate potential signatures and biomarkers using large-scale datasets.
• Apply statistical analyses and analyze genomic data on HPC clusters.

Skills

Python

R

SQL

Unix

AWS

Git

Public datasets

Statistical methods

Bioinformatics

Scientific writing

Education

Bachelor's degree in related field

Master's degree in related field

PhD in a life sciences/related field

Tools

HPC clusters

Genomic Data Commons

TCGA data portals

Job description

About the Job

The Computational Biologist I contributes to the early innovation of novel bioinformatics methods and genomic signatures in oncology. Leveraging Foundation Medicine’s FoundationCORE dataset of 800,000+ samples and the Flatiron Health-Foundation Medicine joint Clinico-Genomic Database of 100,000+ samples with annotated clinical outcomes, this role explores novel patterns in cancer biology. The position plays a key role in conducting original research, generating insights, and preparing high-impact scientific abstracts, presentations, and peer-reviewed manuscripts. The work drives foundational understanding that supports clinical diagnostics and translational research in oncology.

In addition to research, this role develops sub-specialization in the data architecture supporting the team’s efforts, including pipeline workflow development, cloud-based data storage, and maintaining data quality and integrity.

Key Responsibilities

• Develop and evaluate potential signatures and biomarkers using large-scale datasets; investigate genomic mechanisms underlying oncogenesis.


• Apply statistical analyses, analyze genomic data via HPC clusters, and improve assay performance.


• Organize, visualize, and interpret data in a high-throughput, data-intensive environment.


• Collaborate with internal cross-functional teams — including R&D, Medical, Commercial, Biopharma, and Regulatory — and engage with external collaborators to support enterprise goals.


• Work closely with molecular biologists, computational scientists, and regulatory teams to inform the feasibility and planning of translational next-generation sequencing (NGS) assays.


• Maintain awareness of current bioinformatics methods and diagnostic oncology literature.


• Prepare and present results in internal meetings and contribute to scientific literature.


• Design and refine bioinformatics algorithms, workflows, and analysis pipelines; manage cloud-based data infrastructure and ensure data quality.


• Build, maintain, and enhance internal data workflows and computational pipelines; implement and uphold best practices in data architecture and cloud-based data systems


• Other duties as assigned.

Qualifications

Basic Qualifications

• Bachelor’s degree in related field and 6+ years of research experience preferred in the life sciences industry; OR,


• Master’s and 2+ year of research experience preferred in the life sciences industry; OR,


• PhD and no experience

Preferred Qualifications

• 1+ years of industry or post-doctoral research experience in cancer biology, bioinformatics, or a related field using NGS data


• Proficiency in Unix or Unix-like operating systems; proficiency in one or more programming languages such as Python, R, SQL, or similar scientific computing languages; familiarity with other programming or scripting languages


• Familiarity with cloud computing platforms (e.g. AWS)


• Experience using version control tools (e.g. Git)


• Experience working with public datasets (e.g., TCGA, cBioPortal, Genomic Data Commons)


• Competence in basic statistical methods and applications in bioinformatics


• Fundamental understanding of molecular biology and NGS principles (e.g., DNA-seq, library prep, target enrichment)


• Effective collaboration and communication skills, including scientific writing and presenting data to multidisciplinary teams


• Understanding of HIPAA and the importance of patient data privacy


• Commitment to reflect FMI's values of Integrity, Courage, and Passion

The expected salary range for this position based on the primary location of Boston, MA is $112,560 - $133,000per year. The salary range is commensurate with Foundation Medicines compensation practice and considers factors including, but not limited to, education, training, experience, external market conditions, criticality of role, and internal equity. A discretionary annual bonus may be available based on individual and Company performance. This position also qualifies for Foundation Medicine's benefits.

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