Publications by authors named "Joshua Lerman"

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Multi-omic data integration enables discovery of hidden biological regularities.
Ali Ebrahim, Elizabeth Brunk, Justin Tan, Edward J O'Brien, Donghyuk Kim, Joshua A Lerman

Nat Commun· October 2016

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BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
Zachary A King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A Lerman

Nucleic Acids Res· January 2016

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Do genome-scale models need exact solvers or clearer standards?
Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P Burgard, Joshua A Lerman

Mol Syst Biol· October 2015

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Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.
Joanne K Liu, Edward J O'Brien, Joshua A Lerman, Karsten Zengler, Bernhard O Palsson

BMC Syst Biol· September 2014

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Determining the control circuitry of redox metabolism at the genome-scale.
Stephen Federowicz, Donghyuk Kim, Ali Ebrahim, Joshua Lerman, Harish Nagarajan

PLoS Genet· April 2014

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Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.
Jonathan M Monk, Pep Charusanti, Ramy K Aziz, Joshua A Lerman, Ned Premyodhin

Proc Natl Acad Sci U S A· December 2013

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Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.
Edward J O'Brien, Joshua A Lerman, Roger L Chang, Daniel R Hyduke, Bernhard Ø Palsson

Mol Syst Biol· October 2013

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COBRApy: COnstraints-Based Reconstruction and Analysis for Python.
Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson, Daniel R Hyduke

BMC Syst Biol· August 2013

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Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant.
Nicole L Fong, Joshua A Lerman, Irene Lam, Bernhard O Palsson, Pep Charusanti

FEMS Microbiol Lett· May 2013

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The genome organization of Thermotoga maritima reflects its lifestyle.
Haythem Latif, Joshua A Lerman, Vasiliy A Portnoy, Yekaterina Tarasova, Harish Nagarajan

PLoS Genet· April 2013

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Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence.
Shannan J Ho Sui, Raymond Lo, Aalton R Fernandes, Mackenzie D G Caulfield, Joshua A Lerman

Int J Antimicrob Agents· September 2012

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Network context and selection in the evolution to enzyme specificity.
Hojung Nam, Nathan E Lewis, Joshua A Lerman, Dae-Hee Lee, Roger L Chang

Science· August 2012

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In silico method for modelling metabolism and gene product expression at genome scale.
Joshua A Lerman, Daniel R Hyduke, Haythem Latif, Vasiliy A Portnoy, Nathan E Lewis

Nat Commun· July 2012

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A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.
Jeffrey D Orth, Tom M Conrad, Jessica Na, Joshua A Lerman, Hojung Nam

Mol Syst Biol· October 2011

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An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.
Pep Charusanti, Sadhana Chauhan, Kathleen McAteer, Joshua A Lerman, Daniel R Hyduke

BMC Syst Biol· October 2011

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Microbiology. Topping off a multiscale balancing act.
Joshua Lerman, Bernhard O Palsson

Science· November 2010

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Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.
Nathan E Lewis, Kim K Hixson, Tom M Conrad, Joshua A Lerman, Pep Charusanti

Mol Syst Biol· July 2010

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