Scientist II, Systems Biology - Takeda Pharmaceutical

At Takeda, we are a forward-looking, world-class R&D organization that unlocks innovation and delivers transformative therapies to patients. By focusing R&D efforts on three therapeutic areas and other targeted investments, we push the boundaries of what is possible in order to bring life-changing therapies to patients worldwide.

Certified as a Global Top Employer, Takeda offers stimulating careers, encourages innovation, and strives for excellence in everything we do. We foster an inclusive, collaborative workplace, in which our teams are united by an unwavering commitment to deliver Better Health and a Brighter Future to people around the world.

Are you looking for a patient-focused, innovation-driven company that will inspire you and empower you to shine? Join us as a Scientist II, Systems Biology in our Cambridge, MA location.

Objective / Purpose:

• Be part of a computational team focused on utilizing computational and systems biology approaches to analyze multi-omics data supporting Takeda drug discovery and development projects.
• Utilize advanced bioinformatics, computational and AI/ML techniques to analyze multi–omics and multi-modal data, identifying novel drug targets and biomarkers, and elucidating molecular and cellular mechanisms of action in Gastroenterology and Inflammation portfolio. 
• Evaluate the efficacy of potential target candidates through the application of state-of-the-art computational approaches, working closely with biologists, computational genetics, data science, quantitative statistics, engineering groups, translational medicine, and biomarker teams. 
• Report to the Computational Biology Group leader and collaborate with key stakeholders to drive innovative therapies for inflammatory bowel disease, chronic liver disorders, and chronic inflammatory indications in dermatology and rheumatology

Accountabilities:

• Serve as a subject matter expert in projects requiring genomic and high-dimensional data analyses. 
• Use high dimensional datasets including multi-omics datasets, from preclinical and clinical studies to identify and execute biomarker studies, patient stratification, and identify novel drug targets/biomarkers. 
• Perform multi-omics and multi-modal data integration to identify molecular predictors, inform pathway/target mechanism of action, and achieve translational medicine goals. 
• Design and apply computational methods to analyze, integrate, visualize, and interpret bulk and single cell readouts (scRNA-Seq, snRNA-Seq, CyTOF), proteomics, metabolomics, epigenomics, and spatial tissue profiling datasets. 
• Present scientific reports in internal meetings in all settings and with participants of all levels of the organization, as well as for external audiences. 
• Proactively identify complex obstacles, recommend and implement solutions using a diverse set of resources. 
• Work collaboratively with data and quantitative scientists and data engineering groups to enhance our computational infrastructure, build on innovative C&SB solutions and intuitive multi-omics interface. 

Technical/Functional (Line) Expertise (Breadth and depth of knowledge, application and complexity of technical knowledge)

• Strong knowledge of molecular biology and genomics.
• Biological knowledge in one or more areas of inflammation and fibrosis (IBD, chronic liver disorders, chronic inflammatory indications in dermatology and rheumatology)
• Demonstrated experience in large scale multi-omics (e.g. bulk or single-cell, spatial sequencing, proteomics, epigenetics, and more), multi-modal data integration, network analysis, and meta-analyses.
• Strong machine learning experience is preferred.
• Statistical analysis experience with working knowledge of regression analysis, multivariate data analysis, and linear/nonlinear mixed effects modeling is preferred.
• Demonstrated ability to integrate and analyze multimodal biomedical data.
• Background and work experience in graph-neural networks, deep learning, multimodal fusion, transformer models, transfer learning, contrastive learning.
• Experience in developing clinical knowledge graphs and working with NLP and retrieval-augmented generation pipelines.
• Experience with multimodal/foundational model development including but not limited to clinical data, single-cell, and genomics.
• Ability to independently solve scientific problems using multiple, state-of-the-art technologies and approaches.
• Experience with computational method evaluation, development, and implementation.
• Solid knowledge of Unix/Linux, command line interfaces, and fluency in some common scripting and/or programming language (e.g., R, Python, Perl, Java, C / C++) used for statistical and computational multi-omics analysis.
• Experience with high performance computing, relational databases (e.g., SQL), and cloud computing or distributed computing (Amazon Web Services).

Education & Competencies

• PhD degree in Systems Biology, Bioinformatics or Computational Biology with 2+ years relevant experience, or MS with 8+ years relevant experience, or BS with 10+ years relevant experience.
• Previous industry experience is preferred and a strong background in applying computational and systems biology, including multi-omics data analyses, to research, translational and clinical programs with demonstrated ability to meet program objectives and timelines.
• Strong organizational and effective communication skills.

This position is currently classified as “hybrid” by Takeda’s Hybrid and Remote Work policy

The estimated salary range reflects an anticipated range for this position. The actual base salary offered may depend on a variety of factors, including the qualifications of the individual applicant for the position, years of relevant experience, specific and unique skills, level of education attained, certifications or other professional licenses held, and the location in which the applicant lives and/or from which they will be performing the job. The actual base salary offered will be in accordance with state or local minimum wage requirements for the job location. 

U.S. based employees may be eligible for short-term and/ or long-term incentives. U.S. based employees may be eligible to participate in medical, dental, vision insurance, a 401(k) plan and company match, short-term and long-term disability coverage, basic life insurance, a tuition reimbursement program, paid volunteer time off, company holidays, and well-being benefits, among others. U.S. based employees are also eligible to receive, per calendar year, up to 80 hours of sick time, and new hires are eligible to accrue up to 120 hours of paid vacation.