COBRApy: COnstraints-Based Reconstruction and Analysis for Python

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

Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

por Federowicz, Stephen, Kim, Donghyuk, Ebrahim, Ali, Lerman, Joshua, Nagarajan, Harish, Cho, Byung-kwan, Zengler, Karsten, Palsson, Bernhard
Publicado 2014

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 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 2011

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 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 2011

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 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 2016

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 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 2015