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Benjamin M. Gyori, Ph.D.
Benjamin M. Gyori, Ph.D.
Associate Professor, Northeastern University
Verified email at northeastern.edu - Homepage
Title
Cited by
Cited by
Year
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
6572014
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
1562017
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
782021
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
502018
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
422013
A Simple Standard for Sharing Ontological Mappings (SSSOM)
N Matentzoglu, JP Balhoff, SM Bello, C Bizon, M Brush, TJ Callahan, ...
Database 2022, baac035, 2022
412022
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
412021
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
362018
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
282020
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
272019
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
262019
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
232021
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
192019
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
182022
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
18*2022
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
172022
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
172022
Automated assembly of molecular mechanisms at scale from text mining and curated databases
JA Bachman, BM Gyori, PK Sorger
Molecular Systems Biology, e11325, 2023
162023
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
162022
Approximate probabilistic verification of hybrid systems
BM Gyori, B Liu, S Paul, R Ramanathan, PS Thiagarajan
International Workshop on Hybrid Systems Biology, 96-116, 2015
142015
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