Benjamin Gyori
Sy And Laurie Sternberg Interdisciplinary Associate Professor
Boston, Massachusetts, United States
Summary
👤
Senior🎓
Top SchoolBenjamin Gyori is an interdisciplinary computational biologist and AI researcher with 11+ years of experience building systems that turn scientific literature into executable biological models. He leads the Gyori Lab and previously directed the Machine-assisted Modeling & Analysis group at Harvard Medical School, where he created INDRA—a tool that assembles biochemical mechanisms from text into models and powerfully underpins applications from self-updating disease models to human–machine dialogue. A DARPA Young Faculty Award and Director’s Fellowship recipient, he currently runs DARPA-funded work in the ASKEM program and holds faculty roles bridging computer science and bioengineering at Northeastern. Benjamin combines deep software engineering roots with PhD-level systems biology expertise, emphasizing knowledge assembly, text mining, and human–AI collaboration to make cellular behavior computationally tractable. An often-overlooked strength is his fluency in translating literature-scale knowledge into reusable, domain-general software artifacts that accelerate both research and practical modeling.
11 years of coding experience
7 years of employment as a software developer
Bachelor of Science (B.Sc.), Computer Engineering, Bachelor of Science (B.Sc.), Computer Engineering at Budapesti Mûszaki és Gazdaságtudományi Egyetem / Technical University of BudapestDoctor of Philosophy (PhD), Computational Biology, Doctor of Philosophy (PhD), Computational Biology at National University of Singapore
Github Skills (200)
semantic-web10
encoding10
uri10
systems-biology10
nlp10
bioconda10
serializer10
pysb10
assembly10
hierarchical10
sqlalchemy10
proteins10
package-management10
python10
functional-genomics10
Programming languages (16)
Github contributions (5)
bgyori/Sbgnviz-Collaborative-Editor
Mar 2017 - Jan 2019
Contributions:32 pushes, 9 branches in 1 year 10 months
indralab/indra_deps_docker
Oct 2017 - Aug 2021
Docker image to build latest REACH and Kappa.
Contributions:3 PRs, 38 pushes, 4 branches in 3 years 10 months
kappadocker-imagedockerreach
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