Matthew Bernstein
Principal Computational Scientist
Boston, Massachusetts, United States
Summary
👤
Senior🎓
Top SchoolMatthew Bernstein is a Principal Computational Scientist with 12 years of experience turning high-dimensional genomics and bioimaging data into actionable insights for human health. He builds end-to-end computational and machine learning solutions for spatial transcriptomics, single-cell assays, and multimodal clinical biomarker discovery, having led core algorithm and generative-model development at startups and translational biotech. Currently at Somite AI (Cellular Intelligence), he focuses on deciphering cell signaling patterns that govern differentiation, drawing on prior work converting terabyte-scale imaging into spatial gene expression at Stellaromics. His background blends a PhD in Computer Science with hands-on production experience across ML model design, scalable data pipelines, and cross-assay integration (flow cytometry, NanoString, IHC, multiplex IF). Colleagues rely on him for rigorous benchmarking strategies—he has built simulators of raw imaging data to validate complex pipelines—and for bridging computational research with clinical trial biomarker needs. Based in Boston, he brings a rare mix of deep technical depth and translational focus that accelerates discovery in spatial and single-cell biology.
12 years of coding experience
9 years of employment as a software developer
Doctor of Philosophy (Ph.D.) Computer Sciences, Doctor of Philosophy (Ph.D.) Computer Sciences at University of Wisconsin-MadisonBachelor of Science (BS) Computer Science, Bachelor of Science (BS) Computer Science at University of Notre Dame
Github Skills (72)
python10
transcriptomics10
gene-expression10
computational-biology10
ontologies10
single-cell-analysis10
rna-seq10
complexheatmap10
data-science10
classification10
scanpy10
scales10
hierarchical10
machine-learning10
jekyll10
Programming languages (8)
Github contributions (5)
deweylab/cell-type-classification-paper
Apr 2019 - Jul 2020
Contributions:13 commits, 9 pushes, 1 branch in 1 year 2 months
deweylab/MetaSRA-pipeline
Nov 2016 - Mar 2021
MetaSRA: normalized sample-specific metadata for the Sequence Read Archive
Contributions:2 releases, 94 commits, 87 pushes in 4 years 4 months
normalizedsequencemetadataarchive
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