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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
7202014
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
1762017
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
902021
A Simple Standard for Sharing Ontological Mappings (SSSOM)
N Matentzoglu, JP Balhoff, SM Bello, C Bizon, M Brush, TJ Callahan, ...
Database 2022, baac035, 2022
662022
The Human Phenotype Ontology in 2024: phenotypes around the world
MA Gargano, N Matentzoglu, B Coleman, EB Addo-Lartey, ...
Nucleic Acids Research, gkad1005, 2023
60*2023
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
572021
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
532018
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
412013
Democratising Knowledge Representation with BioCypher
S Lobentanzer, P Aloy, J Baumbach, B Bohar, K Danhauser, T Doğan, ...
Nature Biotechnology, 2023
392023
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
382018
Automated assembly of molecular mechanisms at scale from text mining and curated databases
JA Bachman, BM Gyori, PK Sorger
Molecular Systems Biology, e11325, 2023
322023
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
312020
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
312019
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
302019
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
292022
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
292021
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
282022
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
272022
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
232022
Unifying the Identification of Biomedical Entities with the Bioregistry
CT Hoyt, M Balk, TJ Callahan, D Domingo-Fernandez, MA Haendel, ...
Scientifc Data 9 (714), 2022
222022
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Articles 1–20