Research Scientist II, Systems Biology

Takeda Pharmaceutical
Reading, Massachusetts, US
Sep 10, 2021
Sep 15, 2021
Employment Type
Full time
Salary Type
By clicking the "Apply" button, I understand that my employment application process with Takeda will commence and that the information I provide in my application will be processed in line with Takeda's Privacy Notice and Terms of Use. I further attest that all information I submit in my employment application is true to the best of my knowledge.

Job Description

Are you looking for a patient-focused company that will inspire you and support your career? If so, be empowered to take charge of your future at Takeda. Join us as a Systems Biology Scientist in the Gastroenterology Drug Discovery Unit in our Cambridge office.


We have an exciting opportunity for a Systems Biology Scientist to join a multi-disciplinary group that hunts for novel drug targets, elucidates molecular and cellular mechanisms of action, and evaluates the efficacy of new drug candidates.

We are looking for:
  • A creative computational biologist to join the Gastroenterology Drug Discovery Unit (GI-DDU) and play an important role in our mission to provide innovative therapies for gastrointestinal diseases including inflammatory bowel disease, liver and motility disorders.
  • The candidate will apply state-of-the-art computational approaches to analyze multi-omic and genome-wide, bulk, and single-cell readouts (scRNA-Seq, snucRNA-Seq, CyTOF), proteomics, metabolomics, and spatial datasets.
  • This person will be an integral part of the drug discovery process to deliver on our goals in the larger GI-DDU composed of a matrixed group and have wide visibility within the organization and among our academic and biotech partners.

  • Formulate and lead a data analytics strategy for the gastroenterology internal and external collaborations.
  • Apply computational methods to analyze, integrate, visualize and interpret data resulting from multi-omic and genome-wide analyses, with a focus on single-cell readouts (scRNA-Seq, snucRNA-Seq, CyTOF), proteomics, metabolomics, and spatial datasets.
  • Leverage high dimensional datasets from preclinical and clinical studies to identify novel drug targets, stratify patients, inform biomarker studies.
  • Actively develop and manage data analyses with our external partnerships (both biotechs and key academic groups) to ensure that milestones, deliverables are met in terms of timelines and expectations of data quality.
  • Perform systems and multi-modal data integration to summarize data-driven or hypothesis-driven analyses to support mechanism of action, identification of molecular predictors, and achieve translational medicine goals.
  • Prepare and present comprehensive technical and scientific reports for internal meetings with participants of all levels of the organization, and external audiences.
  • Establish a collaborative role within a matrixed and biology-oriented team and influence the experimental design, assays needed, data generation, analysis, integration, and interpretation.
  • Work collaboratively with computational/data science colleagues at the Takeda Data Sciences Institute, Computational Biology, Drug Discovery Sciences, and the translational medicine groups who are key collaborators of the GI Drug Discovery Unit.
  • Participate in due diligence of external opportunities when needed.


Technical/Functional (Line) Expertise
  • Strong scientific understanding of molecular biology, Next Generation Sequencing technologies, and single-cell -omics.
  • Able to develop in-silico data strategy and creative methods for integration of multi-omic and genome-wide data.
  • Demonstrated experience with large-scale omics and high-throughput data analysis, network analysis, and meta-analyses.
  • Experience in computational method implementation and algorithm generation.
  • Able to evaluate/develop computational methods based on project needs.

  • Ability to work in a team and influence team to make data-driven decisions
  • Initiates new method development, communicates data gaps and project resource needs. Suggests experimental approaches and data generation to inform translational studies.

Decision-making and Autonomy
  • Independently manages own workload
  • Scientifically independent
  • Independent, self-starting, supportive of team-based research, and able to work effectively in a matrix organization.
  • Ability to investigate and come up with innovative solutions to difficult problems.
  • Independently keep abreast of current literature in systems, NGS, and computational biology for drug development.
  • Proven track record of driving a significant scientific or technological project to success.
  • Experience in designing and conducting computational analysis strategies to meet program objectives; able to provide input on timelines and resource needs.

  • Conducts scientific presentations to internal and external audiences
  • Excellent communication, presentation, and interpersonal skills.

  • Receives high-level instructions on all work, determines methods on new assignments, works closely with manager, may manage junior staff
  • Determines methods on new assignments; perform literature search as needed to propose innovative solutions

  • PhD degree in Systems Biology, Molecular Biology, Bioinformatics or Computational Biology 2+ years experience
  • Experience with single-cell and spatial transcriptomics or spatial high content imaging data, and standard genomic analyses workflows.
  • Knowledge of and experience with machine learning.
  • Familiar with public domain biological data sources and programmatic interfaces (API).
  • Fluency in at least one programming language (e.g., R, Python) commonly used for statistical and computational -omics analysis.
  • Solid knowledge of Unix/Linux, command-line interfaces, and fluency in some common scripting and/or programming language.
  • Familiarity with parallel computing, relational databases (e.g., SQL), and cloud computing or distributed computing (Amazon Web Services).

  • 401(k) with company match and Annual Retirement Contribution Plan
  • Tuition reimbursement
  • Company match of charitable contributions
  • Health & Wellness programs including onsite flu shots and health screenings
  • Generous time off for vacation and the option to purchase additional vacation days
  • Community Outreach Programs

This job posting excludes CO applicants.

Empowering Our People to Shine

Discover more at

No Phone Calls or Recruiters Please.


EEO Statement

Takeda is proud in its commitment to creating a diverse workforce and providing equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, parental status, national origin, age, disability, citizenship status, genetic information or characteristics, marital status, status as a Vietnam era veteran, special disabled veteran, or other protected veteran in accordance with applicable federal, state and local laws, and any other characteristic protected by law.


Boston, MA

Worker Type


Worker Sub-Type


Time Type

Full time