Toward the automated generation of genome-scale metabolic networks in the SEED

Autor DeJongh, Matthew, Formsma, Kevin, Boillot, Paul, Gould, John, Rycenga, Matthew, Best, Aaron
Vydáno 2007

CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED

Autor DeJongh, Matthew, Bockstege, Benjamin, Frybarger, Paul, Hazekamp, Nicholas, Kammeraad, Joshua, McGeehan, Travis
Vydáno 2012

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

Autor Tintle, Nathan L, Sitarik, Alexandra, Boerema, Benjamin, Young, Kylie, Best, Aaron A, DeJongh, Matthew
Vydáno 2012

Gene set analyses for interpreting microarray experiments on prokaryotic organisms

Autor Tintle, Nathan L, Best, Aaron A, DeJongh, Matthew, Van Bruggen, Dirk, Heffron, Fred, Porwollik, Steffen, Taylor, Ronald C
Vydáno 2008

Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence

Autor Ravcheev, Dmitry A., Best, Aaron A., Tintle, Nathan, DeJongh, Matthew, Osterman, Andrei L., Novichkov, Pavel S., Rodionov, Dmitry A.
Vydáno 2011

A Bayesian Framework for the Classification of Microbial Gene Activity States

Autor Disselkoen, Craig, Greco, Brian, Cook, Kaitlyn, Koch, Kristin, Lerebours, Reginald, Viss, Chase, Cape, Joshua, Held, Elizabeth, Ashenafi, Yonatan, Fischer, Karen, Acosta, Allyson, Cunningham, Mark, Best, Aaron A., DeJongh, Matthew, Tintle, Nathan
Vydáno v Front Microbiol (2016)

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

Autor Faria, José P., Davis, James J., Edirisinghe, Janaka N., Taylor, Ronald C., Weisenhorn, Pamela, Olson, Robert D., Stevens, Rick L., Rocha, Miguel, Rocha, Isabel, Best, Aaron A., DeJongh, Matthew, Tintle, Nathan L., Parrello, Bruce, Overbeek, Ross, Henry, Christopher S.
Vydáno v Front Microbiol (2016)

The RAST Server: Rapid Annotations using Subsystems Technology

Autor Overbeek Ross A, Osterman Andrei L, Olson Robert, Olsen Gary J, Meyer Folker, Kubal Michael, Glass Elizabeth M, Gerdes Svetlana, Formsma Kevin, Edwards Robert A, Disz Terrence, DeJongh Matthew, Best Aaron A, Bartels Daniela, Aziz Ramy K, McNeil Leslie K, Paarmann Daniel, Paczian Tobias, Parrello Bruce, Pusch Gordon D, Reich Claudia, Stevens Rick, Vassieva Olga, Vonstein Veronika, Wilke Andreas, Zagnitko Olga
Vydáno 2008-02-01

The RAST Server: Rapid Annotations using Subsystems Technology

Autor Aziz, Ramy K, Bartels, Daniela, Best, Aaron A, DeJongh, Matthew, Disz, Terrence, Edwards, Robert A, Formsma, Kevin, Gerdes, Svetlana, Glass, Elizabeth M, Kubal, Michael, Meyer, Folker, Olsen, Gary J, Olson, Robert, Osterman, Andrei L, Overbeek, Ross A, McNeil, Leslie K, Paarmann, Daniel, Paczian, Tobias, Parrello, Bruce, Pusch, Gordon D, Reich, Claudia, Stevens, Rick, Vassieva, Olga, Vonstein, Veronika, Wilke, Andreas, Zagnitko, Olga
Vydáno 2008

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Autor Seaver, Samuel M D, Liu, Filipe, Zhang, Qizhi, Jeffryes, James, Faria, José P, Edirisinghe, Janaka N, Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E, Best, Aaron A, DeJongh, Matthew, Kimbrel, Jeffrey A, D’haeseleer, Patrik, McCorkle, Sean R, Bolton, Jay R, Pearson, Erik, Canon, Shane, Wood-Charlson, Elisha M, Cottingham, Robert W, Arkin, Adam P, Henry, Christopher S
Vydáno v Nucleic Acids Res (2020)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Autor Seaver, Samuel M D, Liu, Filipe, Zhang, Qizhi, Jeffryes, James, Faria, José P, Edirisinghe, Janaka N, Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E, Best, Aaron A, DeJongh, Matthew, Kimbrel, Jeffrey A, D’haeseleer, Patrik, McCorkle, Sean R, Bolton, Jay R, Pearson, Erik, Canon, Shane, Wood-Charlson, Elisha M, Cottingham, Robert W, Arkin, Adam P, Henry, Christopher S
Vydáno v Nucleic Acids Res (2020)

KBase: The United States Department of Energy Systems Biology Knowledgebase

Autor Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong
Vydáno v Nat Biotechnol (2018)