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

von DeJongh, Matthew, Formsma, Kevin, Boillot, Paul, Gould, John, Rycenga, Matthew, Best, Aaron
Veröffentlicht 2007

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

von DeJongh, Matthew, Bockstege, Benjamin, Frybarger, Paul, Hazekamp, Nicholas, Kammeraad, Joshua, McGeehan, Travis
Veröffentlicht 2012

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

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

Gene set analyses for interpreting microarray experiments on prokaryotic organisms

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

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

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

A Bayesian Framework for the Classification of Microbial Gene Activity States

von 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
Veröffentlicht in Front Microbiol (2016)

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

von 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.
Veröffentlicht in Front Microbiol (2016)

The RAST Server: Rapid Annotations using Subsystems Technology

von 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
Veröffentlicht 2008-02-01

The RAST Server: Rapid Annotations using Subsystems Technology

von 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
Veröffentlicht 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

von 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
Veröffentlicht in 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

von 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
Veröffentlicht in Nucleic Acids Res (2020)

KBase: The United States Department of Energy Systems Biology Knowledgebase

von 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
Veröffentlicht in Nat Biotechnol (2018)