Bioinformatics Scientist II

Foundation Medicine; Boston (MA); Hybrid; USD 130,000 - 162,000; Full time

Benefits offered by this job

Discretionary annual bonus

Benefits

Job summary

Foundation Medicine in Boston, MA, is seeking a Bioinformatics Scientist II to develop and support clinical trial biomarker strategy and companion diagnostics. You will apply bioinformatics and cancer biology expertise to contribute to biomarker rule development, analytical methods, and scalable clinical reporting.

The role involves interdisciplinary collaboration, data mining for novel biomarker development, and mentoring Scientist I teammates in a fast-paced environment with HIPAA

Qualifications

• Master's degree required; 2+ years in industry or academia.
• Proficiency with scripting for data analysis using Python, R, or similar.

Responsibilities

• Develop and support biomarker strategy for clinical trials and CDx.
• Lead biomarker scoping and analytical validation across studies.
• Mentor junior team members and contribute to regulatory discussions.

Skills

Python

R

Education

Master's in Biochemistry/Bioinformatics/Computational Biology/CS

PhD (preferred) in Biochemistry/Bioinformatics/Computational Biology/CS

Job description

About the Job:

The Bioinformatics Scientist II develops and supports clinical trial and companion diagnostics (CDx) biomarker strategy through advanced analytical and scientific contributions. This role applies bioinformatics and cancer biology expertise to contribute to biomarker rule development, analytical methods, and workflow components that support consistent, scalable clinical reporting.

The incumbent provides scientific, technical, and directional contributions for designated projects on an interdisciplinary team focused on making a clinical impact through advanced analysis at large scale. The Bioinformatics Scientist II is also responsible for supporting novel biomarker and companion diagnostics development by mining and analyzing various types of data generated during the product development and validation process.

Key Responsibilities:

• Partners within an interdisciplinary team of Bioinformatics Scientists, Biostatisticians, Laboratory Scientists, Regulatory experts, and other teams to support the development and implementation of biomarker strategy for clinical trials and CDx
• Contributes to biomarker implementation by supporting rule development and technical execution across studies
• Leads biomarker scoping for individual studies by evaluating feasibility of biomarker definitions, performing data analyses to inform decisions, and providing technical input in partner-facing scoping discussions
• Identifies opportunities to improve existing biomarker workflows and documentation, and provides technical input to enhance quality and efficiency
• Contributes to development, refinement, and consistent application of biomarker guidance across studies
• Contributes scientific input to biomarker strategy discussions and evaluates feasibility across studies
• Develops and executes analytical and validation approaches for biomarker analyses
• Executes analytical work in support of product development, including method development, feasibility assessment, and evaluation of biomarker applicability
• Provides technical input to biopharma partner-specific discussions related to biomarker analyses and implementation
• Provides technical input to regulatory documentation and participates in regulatory discussions related to biomarker analyses
• Contributes to biomarker inquiry support by independently resolving standard inquiries, performing analyses, and assisting with triage and documentation of incoming questions
• Contributes to and improves shared tools and datasets, ensuring they are accurate, reusable, and well-document
• Mentors Scientist I team members and supports team coordination and documentation needs
• Presents scientific and technical data to colleagues in a clear and cohesive manner
• Other duties as assigned
• Comply with FMI's attendance policies

Qualifications:

Basic Qualifications:

• Master's degree in Biochemistry, Bioinformatics, Computational Biology, Computer Science or similar discipline
• 2+ years of relevant industry or academic experience
• Proficiency with scripting for data analysis using Python, R, or similar

Preferred Qualifications:

• PhD degree in Biochemistry, Bioinformatics, Computational Biology, Computer Science or similar discipline
• 3+ years of industry experience
• Strong scientific understanding of molecular biology and genomics
• Experience in cancer research, including a working understanding of computational approaches for cancer genome analysis
• Knowledge of predictive biomarkers for cancer therapy
• Knowledge of clinical trial and CDx biomarker strategy, processes, and requirements
• Knowledge and experience with Next-Generation Sequencing (NGS)
• Strong analytical skills with experience in genomic data analysis
• Demonstrated ability to work independently and contribute to team projects
• Ability to work in a multidisciplinary, fast-paced, dynamic, and results-oriented environment
• Understanding of HIPAA and the importance of patient data privacy
• Commitment to reflect FMI's values: Integrity, Courage, and Passion

The expected salary range for this position based on the primary location of Boston, MA is $129,840 - $162,300 per 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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