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
6182014
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
5282011
Using genome-scale models to predict biological capabilities
EJ O’Brien, JM Monk, BO Palsson
Cell 161 (5), 971-987, 2015
3982015
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
2032013
Optimizing genome-scale network reconstructions
J Monk, J Nogales, BO Palsson
Nature biotechnology 32 (5), 447-452, 2014
1732014
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
1572016
i ML1515, 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
1442017
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
1072016
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
702015
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
652016
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
552016
Search for production of [... formula...] resonances decaying to a lepton, neutrino and jets in [... formula...] collisions at [... formula...] TeV with the ATLAS detector
G Aad, B Abbott, J Abdallah, SA Khalek, R Aben, B Abi, M Abolins, ...
The European Physical journal. C, Particles and Fields 75 (5), 2015
472015
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), 1-9, 2018
442018
Predicting microbial growth
J Monk, BO Palsson
Science 344 (6191), 1448-1449, 2014
422014
Systems biology of the structural proteome
E Brunk, N Mih, J Monk, Z Zhang, EJ O’Brien, SE Bliven, K Chen, ...
BMC systems biology 10 (1), 1-16, 2016
352016
Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
C Lieven, ME Beber, BG Olivier, FT Bergmann, P Babaei, JA Bartell, ...
BioRxiv, 350991, 2018
342018
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
L Yang, J Tan, EJ O’Brien, JM Monk, D Kim, HJ Li, P Charusanti, ...
Proceedings of the National Academy of Sciences 112 (34), 10810-10815, 2015
332015
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), 1-12, 2018
282018
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
262020
łSearch for vectorlike B quarks in events with one isolated lepton, missing transverse momentum and jets at√ s= 8 TeV with the ATLAS detectorž
G Aad
Phys. Rev. D 91 (11), 112011, 2015
262015
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Articles 1–20