| 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 | 704 | 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 | 173 | 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 | 87 | 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 | 57 | 2022 |
| 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 | 55 | 2021 |
| 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 | 52 | 2018 |
| 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 | 41 | 2013 |
| The Human Phenotype Ontology in 2024: phenotypes around the world MA Gargano, N Matentzoglu, B Coleman, EB Addo-Lartey, ... Nucleic Acids Research, gkad1005, 2023 | 38* | 2023 |
| 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 | 38 | 2018 |
| Democratising Knowledge Representation with BioCypher S Lobentanzer, P Aloy, J Baumbach, B Bohar, K Danhauser, T Doğan, ... Nature Biotechnology, 2023 | 33 | 2023 |
| 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 | 30 | 2020 |
| 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 | 30 | 2019 |
| 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 | 28 | 2019 |
| 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 | 27 | 2022 |
| 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 | 27 | 2021 |
| Automated assembly of molecular mechanisms at scale from text mining and curated databases JA Bachman, BM Gyori, PK Sorger Molecular Systems Biology, e11325, 2023 | 26 | 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 | 25 | 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 | 24 | 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 | 22 | 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 | 21 | 2019 |
John A. BachmanFellow in Therapeutic Sciences, Harvard Medical SchoolVerified email at fas.harvard.edu
