COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Por Ebrahim, Ali, Lerman, Joshua A, Palsson, Bernhard O, Hyduke, Daniel R
Publicado em 2013

Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant

Por Fong, Nicole L., Lerman, Joshua A., Lam, Irene, Palsson, Bernhard O., Charusanti, Pep
Publicado em 2013

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

Por O’Brien, Edward J, Lerman, Joshua A, Chang, Roger L, Hyduke, Daniel R, Palsson, Bernhard Ø
Publicado em 2013

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

Por Liu, Joanne K, O’Brien, Edward J, Lerman, Joshua A, Zengler, Karsten, Palsson, Bernhard O, Feist, Adam M
Publicado em 2014

A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011

Por Orth, Jeffrey D, Conrad, Tom M, Na, Jessica, Lerman, Joshua A, Nam, Hojung, Feist, Adam M, Palsson, Bernhard Ø
Publicado em 2011

Network context and selection in the evolution to enzyme specificity

Por Nam, Hojung, Lewis, Nathan E., Lerman, Joshua A., Lee, Dae-Hee, Chang, Roger L., Kim, Donghyuk, Palsson, Bernhard O.
Publicado em 2012

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Por Monk, Jonathan M., Charusanti, Pep, Aziz, Ramy K., Lerman, Joshua A., Premyodhin, Ned, Orth, Jeffrey D., Feist, Adam M., Palsson, Bernhard Ø.
Publicado em 2013

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Por King, Zachary A., Lu, Justin, Dräger, Andreas, Miller, Philip, Federowicz, Stephen, Lerman, Joshua A., Ebrahim, Ali, Palsson, Bernhard O., Lewis, Nathan E.
Publicado no Nucleic Acids Res (2016)

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92

Por Charusanti, Pep, Chauhan, Sadhana, McAteer, Kathleen, Lerman, Joshua A, Hyduke, Daniel R, Motin, Vladimir L, Ansong, Charles, Adkins, Joshua N, Palsson, Bernhard O
Publicado em 2011

Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence

Por 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.
Publicado no Int J Antimicrob Agents (2012)

The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

Por 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
Publicado em 2013

Multi-omic data integration enables discovery of hidden biological regularities

Por 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.
Publicado no Nat Commun (2016)

In silico method for modelling metabolism and gene product expression at genome scale

Por 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.
Publicado em 2012

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

Por 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, Palsson, Bernhard Ø
Publicado em 2010

Do genome-scale models need exact solvers or clearer standards?

Por 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
Publicado no Mol Syst Biol (2015)