Joshua A. Lerman

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Bernhard PalssonUCSDVerified email at eng.ucsd.edu
Nathan E LewisAssociate Professor, University of California, San DiegoVerified email at ucsd.edu
Ali EbrahimUniversity of California, San DiegoVerified email at ucsd.edu
Adam FeistUCSD / DTUVerified email at ucsd.edu
Jeff OrthComputational Biologist, X, the moonshot factoryVerified email at x.team
Joshua N. AdkinsPacific Northwest National LaboratoryVerified email at pnnl.gov
Pep CharusantiNNF Center for Biosustainability, Technical University of DenmarkVerified email at biosustain.dtu.dk
Edward J. O'BrienSr. Scientist, Seres TherapeuticsVerified email at serestherapeutics.com
Tom ConradSenior Biostatistician, EmmesVerified email at emmes.com
Richard D SmithChief Scientist and Battelle Fellow, Biological Sciences Division, PNNLVerified email at pnnl.gov
Karsten ZenglerUniversity of California, San DiegoVerified email at eng.ucsd.edu
Hojung NamAssociate Professor at Gwangju Institute of Science and Technology (GIST)Verified email at gist.ac.kr
Donghyuk KimAssociate Professor, School of Energy and Chemical Engineering, UNISTVerified email at unist.ac.kr
Roger Larken ChangAssistant Professor, Albert Einstein College of MedicineVerified email at einsteinmed.edu
Zachary A. KingVerified email at ucsd.edu
Dae-Hee LeeKorea Research Institute of Bioscience and Biotechnology(KRIBB)Verified email at kribb.re.kr
Andreas DrägerJuniorprofessor for Computational Systems Biology of Infection and Antimicrobial-ResistanceVerified email at uni-tuebingen.de
Ramy K. AzizProfessor of Microbiology & Immunology, CCHE 57357 and Faculty of Pharmacy, Cairo University, EgyptVerified email at pharma.cu.edu.eg
Jonathan MonkUC San DiegoVerified email at ucsd.edu
Harish NagarajanDirector, Systems Bioengineering at GenomaticaVerified email at genomatica.com

Joshua A. Lerman

Director of Computation, Bota Biosciences

Verified email at bota.bio

systems microbiology metabolic engineering synthetic biology bioinformatics data integration


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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	1175	2011
COBRApy: constraints-based reconstruction and analysis for python A Ebrahim, JA Lerman, BO Palsson, DR Hyduke BMC systems biology 7, 1-6, 2013	909	2013
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	710	2016
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	660	2010
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	466	2013
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), 929, 2012	312	2012
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	288	2012
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	282	2013
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), 13091, 2016	149	2016
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	106	2014
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	92	2012
Determining the control circuitry of redox metabolism at the genome-scale S Federowicz, D Kim, A Ebrahim, J Lerman, H Nagarajan, B Cho, ... PLoS genetics 10 (4), e1004264, 2014	69	2014
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	57	2015
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	44	2013
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), 1-13, 2011	44	2011
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	12	2013
Multifunctional neck brace P Gehlbach, B Benson, H Cortes, M Davenport, R Harrison, K Hwang, ... US Patent App. 11/798,041, 2008	5	2008
Biosynthesis of compounds in yeast J Walter, JA Lerman, M Leavell, B Yap US Patent 10,519,475, 2019	2	2019
An Automated Scientist to Design and Optimize Microbial Strains for the Industrial Production of Small Molecules AH Singh, BB Kaufmann-Malaga, JA Lerman, DP Dougherty, Y Zhang, ... bioRxiv, 2023.01. 03.521657, 2023	1	2023
Topping off a multiscale balancing act J Lerman, BO Palsson Science 330 (6007), 1058-1059, 2010	1	2010

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