Follow
Jonathan Monk
Jonathan Monk
Verified email at ucsd.edu
Title
Cited by
Cited by
Year
Constraint-based models predict metabolic and associated cellular functions
A Bordbar, JM Monk, ZA King, BO Palsson
Nature Reviews Genetics 15 (2), 107-120, 2014
9002014
Using genome-scale models to predict biological capabilities
EJ O’Brien, JM Monk, BO Palsson
Cell 161 (5), 971-987, 2015
6932015
Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network
YS Ang, SY Tsai, DF Lee, J Monk, J Su, K Ratnakumar, J Ding, Y Ge, ...
Cell 145 (2), 183-197, 2011
6562011
iML1515, a knowledgebase that computes Escherichia coli traits
JM Monk, CJ Lloyd, E Brunk, N Mih, A Sastry, Z King, R Takeuchi, ...
Nature biotechnology 35 (10), 904-908, 2017
4522017
MEMOTE for standardized genome-scale metabolic model testing
C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ...
Nature biotechnology 38 (3), 272-276, 2020
3282020
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
JM Monk, P Charusanti, RK Aziz, JA Lerman, N Premyodhin, JD Orth, ...
Proceedings of the National Academy of Sciences 110 (50), 20338-20343, 2013
3132013
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira
DE Fouts, MA Matthias, H Adhikarla, B Adler, L Amorim-Santos, DE Berg, ...
PLoS neglected tropical diseases 10 (2), e0004403, 2016
2952016
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity
E Bosi, JM Monk, RK Aziz, M Fondi, V Nizet, BŘ Palsson
Proceedings of the National Academy of Sciences 113 (26), E3801-E3809, 2016
2442016
Optimizing genome-scale network reconstructions
J Monk, J Nogales, BO Palsson
Nature biotechnology 32 (5), 447-452, 2014
2342014
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
ES Kavvas, E Catoiu, N Mih, JT Yurkovich, Y Seif, N Dillon, D Heckmann, ...
Nature communications 9 (1), 4306, 2018
1642018
High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities
J Nogales, J Mueller, S Gudmundsson, FJ Canalejo, E Duque, J Monk, ...
Environmental microbiology 22 (1), 255-269, 2020
1362020
Multi-omics quantification of species variation of Escherichia coli links molecular features with strain phenotypes
JM Monk, A Koza, MA Campodonico, D Machado, JM Seoane, ...
Cell systems 3 (3), 238-251. e12, 2016
1212016
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
Y Seif, E Kavvas, JC Lachance, JT Yurkovich, SP Nuccio, X Fang, ...
Nature communications 9 (1), 3771, 2018
1132018
Model-driven discovery of underground metabolic functions in Escherichia coli
GI Guzmán, J Utrilla, S Nurk, E Brunk, JM Monk, A Ebrahim, BO Palsson, ...
Proceedings of the National Academy of Sciences 112 (3), 929-934, 2015
1052015
Characterizing strain variation in engineered E. coli using a multi-omics-based workflow
E Brunk, KW George, J Alonso-Gutierrez, M Thompson, E Baidoo, ...
Cell systems 2 (5), 335-346, 2016
952016
Cellular responses to reactive oxygen species are predicted from molecular mechanisms
L Yang, N Mih, A Anand, JH Park, J Tan, JT Yurkovich, JM Monk, CJ Lloyd, ...
Proceedings of the National Academy of Sciences 116 (28), 14368-14373, 2019
892019
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
JC Lachance, CJ Lloyd, JM Monk, L Yang, AV Sastry, Y Seif, BO Palsson, ...
PLoS computational biology 15 (4), e1006971, 2019
762019
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes
CJ Norsigian, X Fang, Y Seif, JM Monk, BO Palsson
Nature protocols 15 (1), 1-14, 2020
622020
A biochemically-interpretable machine learning classifier for microbial GWAS
ES Kavvas, L Yang, JM Monk, D Heckmann, BO Palsson
Nature communications 11 (1), 2580, 2020
592020
Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ...
BioRxiv, 350991, 2018
592018
The system can't perform the operation now. Try again later.
Articles 1–20