John A. Bachman
John A. Bachman
Fellow in Therapeutic Sciences, Harvard Medical School
Verified email at fas.harvard.edu - Homepage
Title
Cited by
Cited by
Year
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
2042013
Programming biological models in Python using PySB
CF Lopez, JL Muhlich, JA Bachman, PK Sorger
Molecular systems biology 9 (1), 646, 2013
2042013
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
942017
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
872017
New approaches to modeling complex biochemistry
JA Bachman, P Sorger
Nature methods 8 (2), 130-131, 2011
452011
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
362012
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
202019
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), 1-14, 2018
172018
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
122019
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
102020
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
102019
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, 2019
102019
Exploring the understudied human kinome for research and therapeutic opportunities
N Moret, C Liu, BM Gyori, JA Bachman, A Steppi, R Taujale, LC Huang, ...
bioRxiv, 2020
82020
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
82019
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), 1-35, 2021
72021
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
M Ostaszewski, A Niarakis, A Mazein, I Kuperstein, R Phair, ...
bioRxiv, 2020
72020
Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature
A Steppi, BM Gyori, JA Bachman
Journal of open source software 5 (45), 2020
22020
From knowledge to models: Automated modeling in systems and synthetic biology
BM Gyori, JA Bachman
Current Opinion in Systems Biology, 100362, 2021
12021
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
12021
Capturing scientific knowledge in computable form
JV Wong, M Franz, MC Siper, D Fong, F Durupinar, C Dallago, A Luna, ...
bioRxiv, 2021
12021
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Articles 1–20