Scientist II

Overview

The Knowledge Systems Group (KSG) builds systems for precision oncology at Dana-Farber, including MatchMiner for clinical trial matching and the cBioPortal for exploration of cancer clinico-genomic data.

These systems draw on standard analytical outputs as well as supplemental genomic, transcriptomic and clinical biomarkers generated by KSG. This role focuses on generating those supplemental biomarkers, contributing the genomics, transcriptomics and bioinformatics expertise to support it.

In this role, you will work with DFCI faculty to understand their requests and translate those into clear specifications that the engineering team can build. The Scientist II works directly with oncologists, pathologists, and researchers to prioritize biomarker selection, establish requirements, select computational methods, develop quality control metrics, prototype data visualization and delivery mechanisms, and transform these scientific decisions into technical specifications which engineers can readily implement. Much of the current work centers on genomic and transcriptomic profiling data: targeted cancer gene panel, whole exome DNA (WES), and RNA sequencing. Those data get turned into clinical biomarkers for trial matching and captured in cBioPortal for research exploration.

This is a multi-omics literate role that faces outward. The Scientist II has to be fluent enough in cancer genomics and transcriptomics to earn a researcher's trust, and comfortable enough with software to keep several concurrent builds organized and on track.

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute is a leader in life changing breakthroughs in cancer research and patient care. We are united in our mission of conquering cancer, HIV/AIDS, and related diseases. We strive to create an inclusive, diverse, and equitable environment where we provide compassionate and comprehensive care to patients of all backgrounds, and design programs to promote public health particularly among high-risk and underserved populations. We conduct groundbreaking research that advances treatment, we educate tomorrow's physician/researchers, and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

-Biomarker definition and prioritization. Identify the clinical biomarkers DFCI faculty need, and decide how each is computed, interpreted, and displayed.

-Genomics analysis and quality. Work hands-on with WES and RNAseq data, write bioinformatics pipelines, validate biomarker outputs, and keep current with the relevant cancer genomics methods and literature.

-Clinical biomarker reporting. Work with KSG's genomics team to surface clinical biomarkers derived from NGS molecular profiling for use in clinical trial matching.

-Genomics data in cBioPortal. Work with KSG’s cBioPortal team to capture the relevant clinical biomarkers and genomic data, especially RNAseq-derived results.

-Scientific direction for the engineering team. Provide engineers well-defined software and bioinformatics workflow specifications, review the approach for scientific correctness, keep the scope honest, and mentor junior team members.

-Faculty and researcher partnership. Meet with oncologists, pathologists, and researchers; capture requirements; keep requests organized; and be able to assert when the data will not support a request.

-Data quality and reproducibility. Keep biomarker definitions documented, versioned, and reproducible so results can be trusted and rebuilt.

Knowledge, skills, and abilities

-Cancer-omics depth (required). Hands on familiarity with cancer genomics and transcriptomics data (targeted gene panels, WES, and RNA sequencing) and a thorough understanding of the biology and analysis associated with those assays.

-Researcher facing judgment (required). Comfortable taking requirements directly from researchers and clinicians, and capable of discerning and asserting what the data supports.

-Software fluency and direction setting (required). Enough exposure to software projects to set scientific direction with engineers, review approach and scope, and keep a build on track.

-Scientific and product judgment. Able to define a biomarker or data element, decide how it should be reported and visualized, and prioritize across competing clinical and research requests.

-Highly organized. Keeps multiple requests, definitions, and deliverables moving without dropping threads.

-Technical leadership and mentoring. Comfortable guiding a small group of engineers on the science: setting direction, reviewing work, and providing the team opportunities to learn and grow in their understanding.

-Communication. Explain genomic and transcriptomic methods and their limitations to both technical and clinical audiences.

-Strong interpersonal skills. Able to work effectively as part of a team, and with individuals spanning clinical, research and technical roles.

Minimum job qualifications

-Education: PhD in genomics, computational biology, bioinformatics, or a related field required.

-Cancer genomics experience (required): Demonstrated hands-on experience with cancer-omics data and direct work with genomics/transcriptomic researchers or clinicians.

-Software project experience (required): Some experience with software projects and coordinating with engineers, enough to set scientific direction and keep a build on scope.

- 6 to 9 years of relevant experience post undergraduate (1 to 2 years post advanced degree), with progressively increasing scope and complexity.

At Dana-Farber Cancer Institute, we work every day to create an innovative, caring, and inclusive environment where every patient, family, and staff member feels they belong. As relentless as we are in our mission to reduce the burden of cancer for all, we are committed to having faculty and staff who offer multifaceted experiences. Cancer knows no boundaries and when it comes to hiring the most dedicated and compassionate professionals, neither do we. If working in this kind of organization inspires you, we encourage you to apply.

Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other characteristics protected by law.

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Pay Transparency Statement

The hiring range is based on market pay structures, with individual salaries determined by factors such as business needs, market conditions, internal equity, and based on the candidate’s relevant experience, skills and qualifications.

For union positions, the pay range is determined by the Collective Bargaining Agreement (CBA).

$85,000.00 - $104,650.00