KBase: The United States Department of Energy Systems Biology Knowledgebase

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

doi:10.1038/nbt.4163

Title: KBase: The United States Department of Energy Systems Biology Knowledgebase

Journal Article · Fri Jul 06 00:00:00 EDT 2018 · Nature Biotechnology

DOI:https://doi.org/10.1038/nbt.4163· OSTI ID:1474150

; Cottingham, Robert W.; Henry, Christopher S.;

; Stevens, Rick L.; Maslov, Sergei; Dehal, Paramvir;

;

; 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. more »

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science - Office of Biological and Environmental Research; USDOE Office of Science (SC)

DOE Contract Number:: AC02-06CH11357

OSTI ID:: 1474150

Journal Information:: Nature Biotechnology, Vol. 36, Issue 7; ISSN 1087-0156

Publisher:: Springer Nature

Country of Publication:: United States

Language:: English

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Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota Magnúsdóttir, Stefanía; Heinken, Almut; Kutt, Laura Nature Biotechnology, Vol. 35, Issue 1 https://doi.org/10.1038/nbt.3703	journal	November 2016
Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING Henry, Christopher S.; Bernstein, Hans C.; Weisenhorn, Pamela Journal of Cellular Physiology, Vol. 231, Issue 11 https://doi.org/10.1002/jcp.25428	journal	June 2016
Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions St. James, Andrew; Crockett, Zachary Cornell Univ., Ithaca, NY (United States);Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States) https://doi.org/10.25982/51077.6/1637903	dataset	January 2020
Viral Annotation Pipeline in KBase Bolduc, Benjamin; Wood-Charlson, Elisha; Dehal, Paramvir Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); The Ohio State University; U.S. Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States) https://doi.org/10.25982/59912.37/1635154	dataset	January 2020
MetaCyc: a multiorganism database of metabolic pathways and enzymes Krieger, C. J. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh100	journal	January 2004
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Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes Vangelisti, Alberto; Guidi, Lucia; Cavallini, Andrea Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-58878-8	journal	February 2020
Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation Faria, José P.; Davis, James J.; Edirisinghe, Janaka N. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01819	journal	November 2016

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Viral Annotation Pipeline in KBase Bolduc, Benjamin; Wood-Charlson, Elisha; Dehal, Paramvir Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); The Ohio State University; U.S. Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States) https://doi.org/10.25982/59912.37/1635154	dataset	January 2020
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Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics Lima, Alex Ranieri Jerônimo; Siqueira, Andrei Santos; Vasconcelos, Janaina Mota de Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02811	journal	November 2018
A Comparison of Microbial Genome Web Portals Karp, Peter D.; Ivanova, Natalia; Krummenacker, Markus Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00208	journal	February 2019
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation Pelicaen, Rudy; Gonze, Didier; Teusink, Bas Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02801	journal	December 2019

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