Benjamin M. Gyori, Ph.D.
Benjamin M. Gyori, Ph.D.
Associate Professor, Northeastern University
Verified email at - Homepage
Cited by
Cited by
OpenComet: an automated tool for comet assay image analysis
BM Gyori, G Venkatachalam, PS Thiagarajan, D Hsu, MV Clement
Redox biology 2, 457-465, 2014
From word models to executable models of signaling networks using automated assembly
BM Gyori, JA Bachman, K Subramanian, JL Muhlich, L Galescu, ...
Molecular Systems Biology 13 (11), -, 2017
COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
M Ostaszewski, A Niarakis, A Mazein, I Kuperstein, R Phair, ...
Molecular Systems Biology 17 (10), e10387, 2021
A Simple Standard for Sharing Ontological Mappings (SSSOM)
N Matentzoglu, JP Balhoff, SM Bello, C Bizon, M Brush, TJ Callahan, ...
Database 2022, baac035, 2022
Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases
S Sampattavanich, B Steiert, BA Kramer, BM Gyori, JG Albeck, PK Sorger
Cell Systems 6 (6), 664-678, 2018
GeneWalk identifies relevant gene functions for a biological context using network representation learning
R Ietswaart, BM Gyori, JA Bachman, PK Sorger, LS Churchman
Genome Biology 22 (55), 2021
Statistical model checking based calibration and analysis of bio-pathway models
SK Palaniappan, BM Gyori, B Liu, D Hsu, PS Thiagarajan
International Conference on Computational Methods in Systems Biology, 120-134, 2013
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining
JA Bachman, BM Gyori, P Sorger
BMC Bioinformatics 19 (248), 2018
Robustness and parameter geography in post-translational modification systems
KM Nam, BM Gyori, SV Amethyst, DJ Bates, J Gunawardena
PLoS Computational Biology 16 (5), e1007573, 2020
Eidos, INDRA, & Delphi: From Free Text to Executable Causal Models
R Sharp, A Pyarelal, BM Gyori, K Alcock, E Laparra, ...
Proceedings of the 2019 Conference of the North American Chapter of the …, 2019
Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language
C Hoyt, D Domingo-Fernandez, R Aldisi, L Xu, K Kolpeja, S Spalek, ...
Database 2019, baz068, 2019
A resource for exploring the understudied human kinome for research and therapeutic opportunities
N Moret, C Liu, BM Gyori, JA Bachman, A Steppi, C Hug, R Taujale, ...
BioRxiv, 2020.04. 02.022277, 2021
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes
LM Doherty, CE Mills, SA Boswell, X Liu, CT Hoyt, BM Gyori, SJ Buhrlage, ...
eLife 11 (e72879), 2022
Automated assembly of molecular mechanisms at scale from text mining and curated databases
JA Bachman, BM Gyori, PK Sorger
Molecular Systems Biology, e11325, 2023
A roadmap for the functional annotation of protein families: a community perspective
V de Crécy-Lagard, R Amorin de Hegedus, C Arighi, J Babor, A Bateman, ...
Database 2022, 2022
Democratising Knowledge Representation with BioCypher
S Lobentanzer, P Aloy, J Baumbach, B Bohar, K Danhauser, T Doğan, ...
Nature Biotechnology, 2023
ChemicalX: A Deep Learning Library for Drug Pair Scoring
B Rozemberczki, CT Hoyt, A Gogleva, P Grabowski, K Karis, A Lamov, ...
Proceedings of the 28th ACM SIGKDD International Conference on Knowledge …, 2022
INDRA-IPM: interactive pathway modeling using natural language with automated assembly
PV Todorov, BM Gyori, JA Bachman, PK Sorger
Bioinformatics 35 (21), 4501–4503, 2019
Assembling a phosphoproteomic knowledge base using ProtMapper to normalize phosphosite information from databases and text mining
JA Bachman, PK Sorger, BM Gyori
bioRxiv, 822668, 2022
STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs
H Balabin, CT Hoyt, C Birkenbihl, BM Gyori, JA Bachman, AT Kodamullil, ...
Bioinformatics 38 (6), 1648–1656, 2022
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