Joshua A. Lerman

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Ali EbrahimUniversity of California, San DiegoVerified email at ucsd.edu
Nathan E LewisProfessor, University of California, San DiegoVerified email at ucsd.edu
Adam FeistUC San Diego (UCSD) / Technical University of Denmark (DTU)Verified email at ucsd.edu
Joshua N. AdkinsPacific Northwest National LaboratoryVerified email at pnnl.gov
Jeff OrthComputational Biologist, X, the moonshot factoryVerified email at x.team
Pep CharusantiNNF Center for Biosustainability, Technical University of DenmarkVerified email at biosustain.dtu.dk
Edward J. O'BrienDirector, Translational Computational Biology, Seres TherapeuticsVerified email at serestherapeutics.com
Richard D SmithChief Scientist and Battelle Fellow, Biological Sciences Division, PNNL; retired 2/2024Verified email at pnnl.gov
Tom ConradSenior Biostatistician, EmmesVerified email at emmes.com
Hojung NamProfessor 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
Zachary A. KingVerified email at ucsd.edu
Roger Larken ChangAssistant Professor, Albert Einstein College of MedicineVerified email at einsteinmed.edu
Andreas DrägerProfessor for Data Analytics and BioinformaticsVerified email at informatik.uni-halle.de
Dae-Hee LeeKorea Research Institute of Bioscience and Biotechnology(KRIBB)Verified email at kribb.re.kr
Ramy K. AzizProf., Microbiology & Immunology, Faculty of Pharmacy, Cairo University/ Head, MARC Biolabs, 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
Aarash BordbarSinopia BiosciencesVerified email at sinopiabio.com
Elizabeth BrunkAssistant Professor at UNC Chapel HillVerified email at med.unc.edu

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	1301	2011
COBRApy: constraints-based reconstruction and analysis for python A Ebrahim, JA Lerman, BO Palsson, DR Hyduke BMC systems biology 7, 1-6, 2013	1242	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	948	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	819	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	537	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	354	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	329	2013
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	314	2012
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	171	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, 1-15, 2014	113	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	110	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	84	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	64	2015
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, 1-13, 2011	56	2011
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	53	2013
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	15	2013
Multifunctional neck brace P Gehlbach, B Benson, H Cortes, M Davenport, R Harrison, K Hwang, ... US Patent App. 11/798,041, 2008	7	2008
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	6	2023
Biosynthesis of compounds in yeast J Walter, JA Lerman, M Leavell, B Yap US Patent 10,519,475, 2019	3	2019
Topping off a multiscale balancing act J Lerman, BO Palsson Science 330 (6007), 1058-1059, 2010	2	2010

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