78 senior computational scientist jobs at 41 companies in Massachusetts
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Senior/Principal Scientist, Computational Biology
Boston or United States
$150k-$225k/yr OnsiteFull Time
3+ YOEPhD in Computational Biology or related field; 3+ years of genomic/transcriptomic data analysis; strong Python (scanpy/anndata) skills; quantitative expertise; biology-focused interpretation.
Python, scanpy, anndata, single-cell tooling
2w
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Scientist II/Senior Scientist, Computational Biophysics
Cambridge or London or San Francisco
$141k-$218k/yr OnsiteFull Time
PhD or equivalent experience in computational biophysics/chemistry, deep hands-on MD and free-energy expertise, experience with OpenMM/OpenFE, ability to define and validate biophysics workflows for drug discovery.
OpenMM, OpenFE, LLM
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Pathology Computational Scientist
Boston, Massachusetts, United States
$94k-$137k/yr OnsiteFull Time
Mass General Brigham: Provides integrated medical care, research, and clinical training services.
Experience in microbiome bioinformatics and machine learning, advanced deep learning skills, Python and PyTorch experience preferred, Git and SLURM familiarity, ability to manage large biomedical datasets and contribute to publications/grants.
Python, PyTorch, Git, SLURM
1w
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Founding Computational Scientist, Proteomics
Cambridge, Massachusetts, United States
OnsiteFull Time
PhD or equivalent depth; large-scale bottom-up proteomics; quantitative statistics; containerized workflows; Python, Git/GitHub, and reproducible pipeline development. AWS and experimental fluency valued.
Evosep LC, Orbitrap Astral Zoom, Spectronaut, DIA-NN, FragPipe, MSFragger, AlphaDIA, MaxQuant, Skyline, Nextflow, WDL, Snakemake, Python, Git, GitHub, AWS, Claude Code, Codex, LIMS, ProteomeXchange, PRIDE, MassIVE, GEO, SRA
1mo
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Senior Scientist, Computational Biology - Contract
Somerville, Massachusetts, United States
$74-$80/hr OnsiteContract
5+ YOEPhD (5+ yrs) or MS (10+ yrs) or BS (12+ yrs); broad genome editing and off-target discovery knowledge; NGS data and QC; developing and troubleshooting NGS pipelines in cloud; Nextflow/Dagster; AWS, version control, and software development best practices.
Nextflow, Dagster, AWS, NGS, CI/CD, AI agents
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Computational Scientist, Origin & Evolution of Life
Cambridge or London
OnsiteFull Time
PhD and publication record in computational biology/chemistry/systems biology/chemical engineering or adjacent field; demonstrated independent research and cross-disciplinary breadth; ability to drive publication-quality research.
AI, ML, QM/MD
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Senior Scientist - Principal Scientist, Computational Chemistry
Boston, Massachusetts, United States
OnsiteFull Time
1+ YOEPhD in Computational Chemistry or related field; 1-3+ years biotech/pharma experience; strong physics-based and ML modeling; excellent communication; design-experience with medicinal chemistry; structure-based drug discovery innovation.
Schrodinger suite, OpenEye, MOE, Python, RDKit, scikit-learn, numpy, pandas, pytorch
2mo
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Senior Scientist, Computational Biotherapeutics Engineering
Cambridge, Massachusetts, United States
$94k-$156k/yr HybridFull Time
0+ YOEPhD or Master’s with relevant years; experience with AI/ML for protein design; Python and ML libraries; large biological datasets.
Python, NumPy, SciPy, scikit-learn, PyTorch
6d
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Computational Scientist I - Digital Pathology Image Analysis
Cambridge, Massachusetts, United States
$88k-$124k/yr OnsiteFull Time
4+ YOEMaster’s or Ph.D. in a quantitative life sciences discipline; 4+ years’ relevant experience for Master’s candidates; expertise in digital pathology, QuPath, image analysis, Python, R, or Groovy.
QuPath, Groovy, Python, R, PyTorch, TensorFlow, Indica Labs HALO, HALO AI, Visiopharm, AWS, Google Cloud Platform, Docker
2w
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Principal Scientist, Computational Protein Design
Cambridge, Massachusetts, United States
$143k-$257k/yr HybridFull Time
5+ YOEPhD and 5+ years post-graduate experience in computational protein design with de novo binder generation, ML-guided design, experimental integration, leadership, and strong publication record.
AlphaFold, AlphaFold-Multimer, Rosetta, PyRosetta, RFdiffusion, ProteinMPNN, Python
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Principal Computational Scientist - Discovery Biology N & I (Billerica MA)
Billerica, Massachusetts, United States
$140k-$210k/yr OnsiteFull Time
10+ YOEPhD in a quantitative or life science discipline with substantial computational biology specialization, significant postdoctoral or industry experience, pharma or biotech drug discovery experience, and strong Python or R skills.
Python, R, CRISPR, RNAi, Perturb-seq, Cell Painting, machine learning, AI, systems biology, network analysis, gene regulatory networks, knowledge graphs, single-cell omics, spatial omics
2w
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Principal Computational Scientist - Discovery Biology N & I (Billerica MA)
Billerica, Massachusetts, United States
$140k-$210k/yr OnsiteFull Time
10+ YOEPhD in a quantitative or life science field with computational biology specialization, significant postdoctoral or industry drug discovery experience, and expertise in functional genomics, multi-omics, Python or R, and predictive modeling.
Python, R, CRISPR, RNAi, Perturb-seq, Cell Painting, machine learning
1mo
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Principal Computational Scientist - Discovery Biology N & I (Billerica MA)
Billerica, Massachusetts, United States
$140k-$210k/yr OnsiteFull Time
4+ YOEPhD in a quantitative or life-science discipline, significant postdoctoral or industry experience (pharma/biotech), expertise in computational biology/functional genomics, human genetics and multi-omics integration, strong programming in Python and/or R, and excellent communication.
Python, R
1mo
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Principal Scientist, Computational Biology
Cambridge, Massachusetts, United States
$167k-$202k/yr OnsiteFull Time
5+ YOEPhD in a quantitative field with 5+ years post‑graduate experience; advanced R or Python; experience with multi‑omics, single‑cell, spatial, and perturbation datasets; machine learning/statistical methods; strong communication.
R, Python, Claude
4w
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Principal Scientist/Sr. Principal Scientist, Computational Chemistry & Molecular Design
Boston, Massachusetts, United States
$185k-$240k/yr HybridFull Time
10+ YOEPhD or equivalent experience in computational chemistry or related field; 10+ years' drug discovery experience for Principal (12+ for Senior Principal); expertise in structure- and ligand-based design, molecular dynamics, free energy methods, ML-driven design; strong communication.
Schr\u0000dinger, MOE, OpenEye, Python, Claude Code, Codex
1d
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Senior Applied Research Scientist – Computational Geometry and Meshing
California or Massachusetts or Westford or New York or Pennsylvania or Washington
$192k-$357k/yr RemoteFull Time
5+ YOEPhD or equivalent experience and 5+ years in computational engineering; expertise in geometry, meshing, discretization, CAD/CAE algorithms, C++, Python, topology, numerical robustness, and solver requirements.
C++, Python, Parasolid, ACIS, Open Cascade, CATIA, NX, Creo, SOLIDWORKS, STEP, IGES, B-Rep, NURBS, Omniverse, OpenUSD, Warp
1w
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Applied Scientist - Computational Modeling, OMHS SCS
Boston or Westboro or North Reading
$136k-$184k/yr OnsiteFull Time
Advanced degree in a quantitative field; strong foundation in applied math, statistics, and ML; proficiency in Python/Java/C++; experience with deep learning frameworks and scientific Python stack.
Python, Java, C++, PyTorch, TensorFlow, NumPy, SciPy, scikit-learn, pandas
2mo
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Senior Scientist I, Data Science
Cambridge, Massachusetts, United States
$130k-$170k/yr OnsiteFull Time
3+ YOEPhD in computational biology or related field; 3+ years of experience analyzing multifaceted biological datasets; experience with CAR-T/RNA therapeutics; strong Python/R skills; able to lead cross-functional work.
Python, R, Nextflow, Snakemake, Git
4d
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Senior Quantum Scientist
Boulder or College Park or California or Massachusetts or Tennessee or Washington or Italy or Korea or Sweden or Switzerland or Canada or United Kingdom
$127k-$182k/yr HybridFull Time
PhD in physics or related discipline; experimental AMO or quantum computing expertise; quantum control, qubit calibration or benchmarking experience; strong programming, data analysis, and scientific communication skills.
4w
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Bioinformatics Senior Scientist-Biology
Cambridge, Massachusetts, United States
OnsiteFull Time
4+ YOEPhD in bioinformatics/computational biology/genomics with postdoc experience (or MS+8yrs). 4+ years industry/translational experience, multi-omics analysis, pipeline development, reproducible workflows, ML/AI exposure, strong communication.
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