John A. Bachman
John A. Bachman
Fellow in Therapeutic Sciences, Harvard Medical School
Verified email at - Homepage
Cited by
Cited by
Programming biological models in Python using PySB
CF Lopez, JL Muhlich, JA Bachman, PK Sorger
Molecular systems biology 9 (1), 646, 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
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
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
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
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
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
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
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
New approaches to modeling complex biochemistry
JA Bachman, P Sorger
Nature methods 8 (2), 130-131, 2011
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
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
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
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
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
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
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
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
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
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
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