Joshua A. Lerman
Joshua A. Lerman
Associate Director, Computational Biology at Amyris, Inc.
Verified email at amyris.com
Title
Cited by
Cited by
Year
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011
JD Orth, TM Conrad, J Na, JA Lerman, H Nam, AM Feist, BØ Palsson
Molecular systems biology 7 (1), 2011
9002011
COBRApy: constraints-based reconstruction and analysis for python
A Ebrahim, JA Lerman, BO Palsson, DR Hyduke
BMC systems biology 7 (1), 74, 2013
4542013
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models
NE Lewis, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, ...
Molecular systems biology 6 (1), 2010
4342010
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
ZA King, J Lu, A Dräger, P Miller, S Federowicz, JA Lerman, A Ebrahim, ...
Nucleic acids research 44 (D1), D515-D522, 2016
3822016
Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
EJ O'Brien*, JA Lerman*, RL Chang, DR Hyduke, BØ Palsson
Molecular systems biology 9 (1), 2013
3322013
Network context and selection in the evolution to enzyme specificity
H Nam, NE Lewis, JA Lerman, DH Lee, RL Chang, D Kim, BO Palsson
Science 337 (6098), 1101-1104, 2012
2272012
In silico method for modelling metabolism and gene product expression at genome scale
JA Lerman, DR Hyduke, H Latif, VA Portnoy, NE Lewis, JD Orth, ...
Nature communications 3 (1), 1-10, 2012
2212012
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
1952013
Multi-omic data integration enables discovery of hidden biological regularities
A Ebrahim, E Brunk, J Tan, EJ O'brien, D Kim, R Szubin, JA Lerman, ...
Nature communications 7 (1), 1-9, 2016
982016
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
JK Liu, EJ O’Brien, JA Lerman, K Zengler, BO Palsson, AM Feist
BMC systems biology 8 (1), 1-15, 2014
742014
Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence
SJH Sui, R Lo, AR Fernandes, MDG Caulfield, JA Lerman, L Xie, ...
International journal of antimicrobial agents 40 (3), 246-251, 2012
642012
Determining the control circuitry of redox metabolism at the genome-scale
S Federowicz, D Kim, A Ebrahim, J Lerman, H Nagarajan, B Cho, ...
PLoS Genet 10 (4), e1004264, 2014
462014
Do genome‐scale models need exact solvers or clearer standards?
A Ebrahim, E Almaas, E Bauer, A Bordbar, AP Burgard, RL Chang, ...
Molecular systems biology 11 (10), 831, 2015
432015
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92
P Charusanti, S Chauhan, K McAteer, JA Lerman, DR Hyduke, VL Motin, ...
BMC systems biology 5 (1), 163, 2011
372011
The genome organization of Thermotoga maritima reflects its lifestyle
H Latif*, JA Lerman*, VA Portnoy, Y Tarasova, H Nagarajan, ...
PLoS genetics 9 (4), e1003485, 2013
332013
Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion …
NL Fong, JA Lerman, I Lam, BO Palsson, P Charusanti
FEMS microbiology letters 342 (1), 62-69, 2013
82013
Multifunctional neck brace
P Gehlbach, B Benson, H Cortes, M Davenport, R Harrison, K Hwang, ...
US Patent App. 11/798,041, 2008
32008
Topping off a multiscale balancing act
J Lerman, BO Palsson
Science 330 (6007), 1058-1059, 2010
12010
Biosynthesis of compounds in yeast
J Walter, JA Lerman, M Leavell, B Yap
US Patent 10,519,475, 2019
2019
Method for in silico Modeling of Gene Product Expression and Metabolism
DR Hyduke, JA Lerman, BO Palsson, E O'brien
US Patent App. 14/399,129, 2015
2015
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Articles 1–20