Computational Biologist - Spatial Multi-Omics (Cambridge, Massachusetts, US)

Biopharma Careers; Cambridge (MA); On-site; USD 106,000 - 160,000; Full time

Job summary

Bayer is seeking a Computational Biologist – Spatial Multi-Omics to join the Translational Sciences Cardiovascular Renal Team at the Kendall Sq, Cambridge, MA campus. You will build scalable pipelines for spatial multi-omics analyses and integrate diverse data types to enable target discovery and biomarker development.

The role emphasizes development of novel analysis methods, collaboration with scientists and clinicians, and ensuring reproducible, well-documented workflows suitable for internal

Qualifications

• PhD in Computational Biology, Bioinformatics, Systems Biology, Biostatistics, Computer Science, or related field; or MSc with substantial relevant experience.
• Hands-on experience analyzing mass spectrometry and transcriptomics spatial data, including QC, normalization, feature extraction, and statistical interpretation.
• Background in image analysis and spatial statistics (segmentation, registration, spatial point patterns, neighborhood analysis). Exposure to machine learning or deep learning for omics or imaging data.
• Familiarity with MS and spatial tools like MZmine, MaxQuant, Proteome Discoverer, Skyline, OpenMS, etc.; and spatial frameworks like Squidpy, Giotto, Seurat/Spatial, Napari, ImageJ/Fiji, CellProfiler, etc.
• Experience with pathway/network analysis (e.g., KEGG, Reactome, MetaboAnalyst, Cytoscape).
• Proficiency in Python and/or R; comfort with Linux/Unix environments, high-performance computing, and version control (Git).
• Demonstrated ability in high-dimensional data analysis, statistics, and reproducible pipeline development.
• Solid understanding of molecular biology, biochemistry, and metabolism to interpret results and design analyses.
• Strong communication skills; experience collaborating within interdisciplinary teams and presenting complex results to diverse audiences.

Responsibilities

• Build and maintain scalable pipelines for spatial and deep visual multi-omics analysis, including data ingestion, QC, normalization, batch correction, feature extraction, and annotation from mass-spectrometry and transcriptomics platforms.
• Integrate spatial metabolomics/proteomics with transcriptomics, genomics, and histopathology images to deliver multi-modal insights for target discovery, biomarker development, and mechanism-of-action studies.
• Evaluate, benchmark, and optimize tools and workflows; contribute to internal software (R/Python) and visualization frameworks to streamline spatial omics analytics.
• Perform spatially aware statistical analyses to identify regulated molecular markers across tissue regions, cell types, and phenotypes.
• Develop and apply algorithms for spatial segmentation, clustering, co-localization, neighborhood analysis, and spatial correlation; conduct pathway/network analyses.
• Collaborate with experimental biologists, pathologists, chemists, and clinicians to shape hypotheses, design studies, and translate findings into decisions for research programs.
• Document pipelines and analyses to ensure reproducibility, compliance, and knowledge transfer; prepare clear visualizations and narratives for internal reviews, publications, and external collaborations.
• Partner with data engineering/IT to manage large spatial datasets, define metadata standards, and implement versioning, governance, and access control best practices.

Skills

Mass spectrometry

Transcriptomics spatial data

Image analysis

Spatial statistics

Python

R

Git

High-performance computing

Education

PhD in Computational Biology

MSc with relevant experience

Tools

MZmine

MaxQuant

Proteome Discoverer

Skyline

OpenMS

Squidpy

Giotto

Seurat/Spatial

Napari

ImageJ/Fiji

CellProfiler

Job description

At Bayer we’re visionaries, driven to solve the world’s toughest challenges and striving for a world where 'Health for all Hunger for none’ is no longer a dream, but a real possibility. We’re doing it with energy, curiosity and sheer dedication, always learning from unique perspectives of those around us, expanding our thinking, growing our capabilities and redefining ‘impossible’. There are so many reasons to join us. If you’re hungry to build a varied and meaningful career in a community of brilliant and diverse minds to make a real difference, there’s only one choice.

Computational Biologist - Spatial Multi-Omics

Bayer has an opening for a Computational Biologist – Spatial Multi-Omics to join our Translational Sciences Cardiovascular Renal Team based at the Bayer Innovation Campus in the heart of Kendall Sq, Cambridge, MA.

We are seeking a highly skilled Bioinformatics Scientist to join our team, focusing on the development and maintenance of scalable pipelines for spatial and deep visual multi-omics analysis. The successful candidate will play a crucial role in integrating various omics data types to drive insights for target discovery, biomarker development, and mechanism-of-action studies.

YOUR TASKS AND RESPONSBILITIES

• Build and maintain scalable pipelines for spatial and deep visual multi-omics analysis, including data ingestion, QC, normalization, batch correction, feature extraction, and annotation from mass-spectrometry and transcriptomics platforms.
• Integrate spatial metabolomics/proteomics with transcriptomics, genomics, and histopathology images to deliver multi-modal insights for target discovery, biomarker development, and mechanism-of-action studies.
• Evaluate, benchmark, and optimize tools and workflows; contribute to internal software (R/Python) and visualization frameworks to streamline spatial omics analytics.
• Perform spatially aware statistical analyses to identify regulated molecular markers across tissue regions, cell types, and phenotypes.
• Develop and apply algorithms for spatial segmentation, clustering, co-localization, neighborhood analysis, and spatial correlation; conduct pathway/network analyses.
• Collaborate with experimental biologists, pathologists, chemists, and clinicians to shape hypotheses, design studies, and translate findings into decisions for research programs.
• Document pipelines and analyses to ensure reproducibility, compliance, and knowledge transfer; prepare clear visualizations and narratives for internal reviews, publications, and external collaborations.
• Partner with data engineering/IT to manage large spatial datasets, define metadata standards, and implement versioning, governance, and access control best practices.

WHO YOU ARE

Required qualifications:

• PhD in Computational Biology, Bioinformatics, Systems Biology, Biostatistics, Computer Science, or related field; or MSc with substantial relevant experience.
• Hands-on experience analyzing mass spectrometry and transcriptomics spatial data, including QC, normalization, feature extraction, and statistical interpretation.
• Background in image analysis and spatial statistics (segmentation, registration, spatial point patterns, neighborhood analysis). Exposure to machine learning or deep learning for omics or imaging data.
• Familiarity with MS and spatial tools like MZmine, MaxQuant, Proteome Discoverer, Skyline, OpenMS, etc.; and spatial frameworks like Squidpy, Giotto, Seurat/Spatial, Napari, ImageJ/Fiji, CellProfiler, etc.
• Experience with pathway/network analysis (e.g., KEGG, Reactome, MetaboAnalyst, Cytoscape).
• Proficiency in Python and/or R; comfort with Linux/Unix environments, high-performance computing, and version control (Git).
• Demonstrated ability in high-dimensional data analysis, statistics, and reproducible pipeline development.
• Solid understanding of molecular biology, biochemistry, and metabolism to interpret results and design analyses.
• Strong communication skills; experience collaborating within interdisciplinary teams and presenting complex results to diverse audiences.

Employees can expect to be paid a salary between $106,400.00 - $159,600.00. Additional compensation may include a bonus or commission (if relevant). Additional benefits include health care, vision, dental, retirement, PTO, sick leave, etc.

This salary range is merely an estimate and may vary based on an applicant’s location, market data/ranges, an applicant’s skills and prior relevant experience, certain degrees and certifications, and other relevant factors.

This posting will be available for application until at least 08/17/2026

Bayer is an Equal Opportunity Employer/Disabled/Veterans

Bayer is committed to providing access and reasonable accommodations in its application process for individuals with disabilities and encourages applicants with disabilities to request any needed accommodation(s) using the contact information below.

Equal Opportunity Employer Statement: Notice for U.S. Visitors: All information on this site is subject to compliance with local rule and regulations as they may vary from time to time and across different geographies, including, without limitation, U.S. Executive Orders.

Bayer is an E-Verify Employer.

Location: United States : Massachusetts : Cambridge

Division: Pharmaceuticals

Reference Code: 868556

Bayer does not accept unsolicited third party resumes.

Contact Us

Email: [e-mail]