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

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A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011 von Orth, Jeffrey D, Conrad, Tom M, Na, Jessica, Lerman, Joshua A, Nam, Hojung, Feist, Adam M, Palsson, Bernhard Ø

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

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Multi-omic data integration enables discovery of hidden biological regularities von Ebrahim, Ali, Brunk, Elizabeth, Tan, Justin, O'Brien, Edward J., Kim, Donghyuk, Szubin, Richard, Lerman, Joshua A., Lechner, Anna, Sastry, Anand, Bordbar, Aarash, Feist, Adam M., Palsson, Bernhard O.

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Network Context and Selection in the Evolution to Enzyme Specificity von Nam, Hojung, Lewis, Nathan E., Lerman, Joshua A., Lee, Dae-Hee, Chang, Roger L., Kim, Donghyuk, Palsson, Bernhard O.

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Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments von Monk, Jonathan M., Charusanti, Pep, Aziz, Ramy, Lerman, Joshua A., Premyodhin, Ned, Orth, Jeffrey D., Feist, Adam M., Palsson, Bernhard Ø.

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Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models von Palsson, Bernhard Ø, Lewis, Nathan E, Hixson, Kim K, Conrad, Tom M, Lerman, Joshua A, Charusanti, Pep, Polpitiya, Ashoka D, Adkins, Joshua N, Schramm, Gunnar, Purvine, Samuel O, Lopez-Ferrer, Daniel, Weitz, Karl K, Eils, Roland, König, Rainer, Smith, Richard D

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

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The genome organization of Thermotoga maritima reflects its lifestyle von Latif, Haythem, Lerman, Joshua A, Portnoy, Vasiliy A, Tarasova, Yekaterina, Nagarajan, Harish, Schrimpe-Rutledge, Alexandra C, Smith, Richard D, Adkins, Joshua N, Lee, Dae-Hee, Qiu, Yu, Zengler, Karsten

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BiGG Models: A platform for integrating, standardizing and sharing genome-scale models von King, Zachary A, Lu, Justin, Dräger, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A, Ebrahim, Ali, Palsson, Bernhard O, Lewis, Nathan E

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Do genome‐scale models need exact solvers or clearer standards? von Ebrahim, Ali, Almaas, Eivind, Bauer, Eugen, Bordbar, Aarash, Burgard, Anthony P, Chang, Roger L, Dräger, Andreas, Famili, Iman, Feist, Adam M, Fleming, Ronan MT, Fong, Stephen S, Hatzimanikatis, Vassily, Herrgård, Markus J, Holder, Allen, Hucka, Michael, Hyduke, Daniel, Jamshidi, Neema, Lee, Sang Yup, Le Novère, Nicolas, Lerman, Joshua A, Lewis, Nathan E, Ma, Ding, Mahadevan, Radhakrishnan, Maranas, Costas, Nagarajan, Harish, Navid, Ali, Nielsen, Jens, Nielsen, Lars K, Nogales, Juan, Noronha, Alberto, Pal, Csaba, Palsson, Bernhard O, Papin, Jason A, Patil, Kiran R, Price, Nathan D, Reed, Jennifer L, Saunders, Michael, Senger, Ryan S, Sonnenschein, Nikolaus, Sun, Yuekai, Thiele, Ines

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In silico method for modelling metabolism and gene product expression at genome scale von Lerman, Joshua A., Hyduke, Daniel R., Latif, Haythem, Portnoy, Vasiliy A., Lewis, Nathan E., Orth, Jeffrey D., Schrimpe-Rutledge, Alexandra C., Smith, Richard D., Adkins, Joshua N., Zengler, Karsten, Palsson, Bernhard O.

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Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence von Ho Sui, Shannan J, Lo, Raymond, Fernandes, Aalton R, Caulfield, Mackenzie D.G, Lerman, Joshua A, Xie, Lei, Bourne, Philip E, Baillie, David L, Brinkman, Fiona S.L

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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 von Fong, Nicole L., Lerman, Joshua A., Lam, Irene, Palsson, Bernhard O., Charusanti, Pep

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An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92 von Charusanti, Pep, Chauhan, Sadhana, McAteer, Kathleen, Lerman, Joshua A, Hyduke, Daniel R, Motin, Vladimir L, Ansong, Charles, Adkins, Joshua N, Palsson, Bernhard O

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BiGG Models: A platform for integrating, standardizing and sharing genome-scale models von King, Zachary A., Lu, Justin, Dräger, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A., Ebrahim, Ali, Palsson, Bernhard O., Lewis, Nathan E.

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BiGG Models: A platform for integrating, standardizing and sharing genome-scale models von King, Zachary A., Lu, Justin, Drager, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A., Ebrahim, Ali, Palsson, Bernhard O., Lewis, Nathan E.

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The Genome Organization of Thermotoga maritima Reflects Its Lifestyle: e1003485 von Latif, Haythem, Lerman, Joshua A, Portnoy, Vasiliy A, Tarasova, Yekaterina, Nagarajan, Harish, Schrimpe-Rutledge, Alexandra C, Smith, Richard D, Adkins, Joshua N, Lee, Dae-Hee, Qiu, Yu, Zengler, Karsten

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Do genome-scale models need exact solvers or clearer standards? von Ebrahim, Ali, Almaas, Eivind, Bauer, Eugen, Bordbar, Aarash, Burgard, Anthony P, Chang, Roger L, Dräger, Andreas, Famili, Iman, Feist, Adam M, Fleming, Ronan MT, Fong, Stephen S, Hatzimanikatis, Vassily, Herrgård, Markus J, Holder, Allen, Hucka, Michael, Hyduke, Daniel, Jamshidi, Neema, Lee, Sang Yup, Le Novère, Nicolas, Lerman, Joshua A, Lewis, Nathan E, Ma, Ding, Mahadevan, Radhakrishnan, Maranas, Costas, Nagarajan, Harish, Navid, Ali, Nielsen, Jens, Nielsen, Lars K, Nogales, Juan, Noronha, Alberto, Pal, Csaba, Palsson, Bernhard O, Papin, Jason A, Patil, Kiran R, Price, Nathan D, Reed, Jennifer L, Saunders, Michael, Senger, Ryan S, Sonnenschein, Nikolaus, Sun, Yuekai, Thiele, Ines

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BIOSYNTHESIS OF COMPOUNDS IN YEAST von YAP, Benjamin, LEAVELL, Michael, WALTER, Jessica, LERMAN, Joshua, A

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