85 computational research scientist jobs at 44 companies in Boston, MA
3d
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Research Scientist, Computational Enzymology
Cambridge or London
OnsiteFull Time
Expertise in enzymatic reaction modeling with QM/MM and free-energy methods; strong knowledge of enzyme catalysis, kinetics, cofactors, method selection, limitations, and computational cost.
QM/MM, MD, ML
2mo
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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
1mo
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Computational Scientist I - Scalable Services
Burlington, Massachusetts, United States
$88k-$124k/yr OnsiteFull Time
0+ YOEPhD required in computer science, mathematics, bioinformatics, physics or related; strong computational and data analysis skills; excellent communication; experience developing software; 0+ years experience.
3mo
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Computational Scientist, Protein Engineering
Boston, Massachusetts, United States
$118k-$138k/yr OnsiteFull Time
4+ YOEPhD and/or 4+ years in computational biology, bioinformatics, protein engineering, or related field; strong Python, data pipelines, Unix, and antibody engineering experience; experience with MPRA/NGS data; collaboration skills.
Python, Unix, Git, NGS data analysis
2w
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Research Scientist, Computational Condensed Matter Physics
Cambridge, Massachusetts, United States
$176k-$304k/yr OnsiteFull Time
PhD-level expertise in computational condensed matter physics or equivalent experience; strong electronic structure and atomistic simulation knowledge; Python programming; experience integrating computation with experiment.
Python
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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Scientist, Computational Biology
Cambridge, Massachusetts, United States
$115k-$165k/yr OnsiteFull Time
2+ YOEPhD in computational biology or related field, 2+ years industry experience, strong mass-spec proteomics and multi-omics analysis, proficiency in R or Python, statistical and ML expertise, NGS experience.
R, Python, NGS, transformers, Greenhouse
5d
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Principal Research Scientist
Bedford, New Hampshire, United States
$176k-$282k/yr OnsiteFull Time
10+ YOEPhD in computer science or related field, 10+ years of experience, cybersecurity research and software development expertise, proposal and customer engagement experience, and ability to obtain Top Secret/SCI clearance.
DARPA, IARPA, ARL, AFRL
6d
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Principal Research Scientist
Bedford, New Hampshire, United States
$176k-$282k/yr OnsiteFull Time
10+ YOEPhD in computer science or related field, 10+ years of experience, cybersecurity research and development expertise, proposal and technical marketing experience, project leadership, US citizenship, and ability to obtain Top Secret/SCI clearance.
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
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
2mo
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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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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
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 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
2mo
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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
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
1mo
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Research Scientist, Spatial AI & Perception
Waltham, Massachusetts, United States
$177k-$225k/yr OnsiteFull Time
PhD (or equivalent research experience) in robotics/computer vision/ML; experience building and deploying SLAM, visual odometry or 3D reconstruction systems; strong math, C++ and Python skills.
C++, Python, PyTorch, JAX
1d
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Research Senior Scientist, Cheminformatics
Boston or Cambridge
$137k-$215k/yr OnsiteFull Time
2+ YOEPhD in computational chemistry, cheminformatics, computer science, or related field; 2+ years in pharma or biotech; agentic AI, MLOps, chemical databases, scalable workflows, programming, RDKit, and DMTA expertise.
Python, R, C, C++, RDKit, MLOps, CI/CD, model registries, version control, cloud storage, vector search
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