| Programming biological models in Python using PySB CF Lopez, JL Muhlich, JA Bachman, PK Sorger Molecular systems biology 9 (1), 646, 2013 | 270 | 2013 |
| BID preferentially activates BAK while BIM preferentially activates BAX, affecting chemotherapy response KA Sarosiek, X Chi, JA Bachman, JJ Sims, J Montero, L Patel, A Flanagan, ... Molecular cell 51 (6), 751-765, 2013 | 269 | 2013 |
| 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), 954, 2017 | 159 | 2017 |
| Fundamental trade-offs between information flow in single cells and cellular populations R Suderman, JA Bachman, A Smith, PK Sorger, EJ Deeds Proceedings of the National Academy of Sciences 114 (22), 5755-5760, 2017 | 126 | 2017 |
| COVID19 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 | 81 | 2021 |
| Synthetic lethal interaction of SHOC2 depletion with MEK inhibition in RAS-driven cancers R Sulahian, JJ Kwon, KH Walsh, E Pailler, TL Bosse, M Thaker, ... Cell reports 29 (1), 118-134. e8, 2019 | 71 | 2019 |
| Optimizing ring assembly reveals the strength of weak interactions EJ Deeds, JA Bachman, W Fontana Proceedings of the National Academy of Sciences 109 (7), 2348-2353, 2012 | 54 | 2012 |
| shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data K Shimada, JA Bachman, JL Muhlich, TJ Mitchison Elife 10, e57116, 2021 | 53 | 2021 |
| New approaches to modeling complex biochemistry JA Bachman, P Sorger Nature methods 8 (2), 130-131, 2011 | 47 | 2011 |
| 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, 1-35, 2021 | 46 | 2021 |
| FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining JA Bachman, BM Gyori, PK Sorger BMC bioinformatics 19, 1-14, 2018 | 37 | 2018 |
| Eidos, INDRA, & Delphi: from free text to executable causal models R Sharp, A Pyarelal, B Gyori, K Alcock, E Laparra, ... Proceedings of the 2019 conference of the north American chapter of the …, 2019 | 27 | 2019 |
| Re-curation and rational enrichment of knowledge graphs in Biological Expression Language CT Hoyt, D Domingo-Fernández, R Aldisi, L Xu, K Kolpeja, S Spalek, ... Database 2019, baz068, 2019 | 27 | 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, 2020 | 25 | 2020 |
| Community assessment of the predictability of cancer protein and phosphoprotein levels from genomics and transcriptomics M Yang, F Petralia, Z Li, H Li, W Ma, X Song, S Kim, H Lee, H Yu, B Lee, ... Cell systems 11 (2), 186-195. e9, 2020 | 22 | 2020 |
| Automated assembly of molecular mechanisms at scale from text mining and curated databases JA Bachman, BM Gyori, PK Sorger Molecular Systems Biology 19 (5), e11325, 2023 | 21 | 2023 |
| 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 | 19 | 2019 |
| STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs H Balabin, CT Hoyt, C Birkenbihl, BM Gyori, J Bachman, AT Kodamullil, ... Bioinformatics 38 (6), 1648-1656, 2022 | 16 | 2022 |
| Science Forum: Author-sourced capture of pathway knowledge in computable form using Biofactoid JV Wong, M Franz, MC Siper, D Fong, F Durupinar, C Dallago, A Luna, ... Elife 10, e68292, 2021 | 13 | 2021 |
| Assembling a phosphoproteomic knowledge base using ProtMapper to normalize phosphosite information from databases and text mining JA Bachman, BM Gyori, PK Sorger BioRxiv, 822668, 2019 | 13 | 2019 |
Peter K. SorgerHarvard Medical SchoolVerified email at hms.harvard.edu
