About the Job

The Senior Computational Biologist defines and analyzes alterations in tumor DNA and RNA detected by NGS-based molecular assays and improves and optimizes existing methods. This individual contributes scientific and technical expertise to an interdisciplinary team focused on making a clinical impact through advanced analysis at large scale. The Senior Computational Biologist is responsible for supporting novel biomarker and companion diagnostics development by mining and analyzing various types of data generated along the product development and validation process.

This is a regulated position and additional information may be available from QA on the qualifications for this role pertaining to regulatory guidelines.

We are seeking a talented and highly motivated Senior Computational Biologist to define and analyze alterations in tumor DNA and RNA detected by NGS-based molecular assays and to improve and optimize existing methods. This highly skilled individual will contribute scientific and technical expertise to an interdisciplinary team focused on making a clinical impact through advanced analysis at large scale. The Senior Computational Biologist will also be responsible for supporting novel biomarker and companion diagnostics development by mining and analyzing various types of data generated along the product development and validation process. The successful candidate will possess strong analytical skills, solid programming experience, and ability to consistently meet deadlines under pressure. You would join a team responsible for the biomarker development and biomarker analysis that powers every test at Foundation Medicine. You would contribute to many of the projects we undertake, and those efforts will have direct impact on patient care.

Key Responsibilities

• Lead efforts to improve the consistency of how biomarker rules are defined and formatted including:

·   Define the process of intaking/organizing new biomarkers and manage the process moving forward;

·   Provide biomarker definitions and rules;

·   Work with other functional teams to implement new biomarkers in our pipeline;

·   Gather biomarker requirements from partners and perform gap analyses supported by the other functional teams;

·   Maintain an accounting of all biomarker rules (definition, partner/program, description of implementation);

·   Solicit feedback and communicate biomarker definitions/rules and biomarker analysis results within FMI and to external stakeholders.

• Accountable for management of biomarker rules:

·   Propose definitions and obtain feedback from relevant functional groups;

·   Manage regularly scheduled cross-functional meetings to ensure that development work is completed on time as needed and that biomarker rules are correctly integrated for biomarker reporting.

• Support Pharma partnering work:

·   Attend partner meetings to gather biomarker requirements and communicate rules/technical details to partners;

·   Perform gap analyses to determine if development work is required;

·   Function as a subject matter expert on basic analysis pipeline, curation, and biomarker discussions.

• Provide key contributions to the clinical and analytical studies in the program, including but not limited to protocol development, testing and execution, and biomarker analysis

• Contribute to the planning and delivery of key analytical components of regulatory submissions, including but not limited to Q-subs, PMAs, and sPMAs.

• Provide strategic contributions in addressing issues related to biomarker analysis and biomarker harmonization.

• Represent the Biomarker team in key regulatory meetings.

• Contribute to the development of new methods and algorithms to identify and characterize alterations in tumor DNA and RNA derived from clinical cancer specimens.

• Enhance existing methods, improving their assay capabilities as well as their technical robustness.

• Monitor and evaluate analytical aspects of new and emerging technologies.

• Present scientific and technical data to colleagues in a clear and concise manner.

• Work independently and prepare timetables, deliverables, and project schedules.

• Other duties as assigned.

Qualifications

Basic Qualifications

• Master’s Degree in Computational Biology, Bioinformatics, Biochemistry, Molecular Biology, Biochemistry, Genetics, Cancer Genomics, or a related field with a significant quantitative base

• 3+ years of relevant industry experience

• Fluency in one or several scripting languages, e.g. Python

Preferred Qualifications

• Ph.D. in Biochemistry, Bioinformatics, Computational Biology, Computer Science

• Experience with bioinformatics tools and databases (e.g., NCBI, UCSC Genome Browser, IGV)

• Experience in cancer research, including a working understanding of computational approaches for cancer genome analysis

• Experience contributing to a complex production analytical system

• Demonstrated record of successful independent work and contributions to team projects

• Knowledge and experience with Next-Generation Sequencing (NGS)

• Strong scientific understanding of molecular biology, cancer genetics and genomics

• Extensive knowledge of predictive biomarkers for cancer therapy

• Ability to work well under pressure while maintaining a professional demeanor

• Ability to work independently in a multidisciplinary, fast-paced, dynamic, and results-oriented environment

• Ability to present data to a multidisciplinary audience in a clear and cohesive manner

• Excellent teamwork, time management, and organizational skills

• High level of attention to detail with a focus on quality

• Understanding of HIPAA and importance of privacy of patient data

• Commitment to FMI values: patients, innovation, collaboration, and passion