KBase: The United States Department of Energy Systems Biology Knowledgebase

被引：891

作者：

Arkin, Adam P. ^{[1
,2
]}

Cottingham, Robert W. ^{[3
]}

Henry, Christopher S. ^{[4
]}

Harris, Nomi L. ^{[2
]}

Stevens, Rick L. ^{[5
,6
,7
]}

Maslov, Sergei ^{[8
,25
,26
]}

Dehal, Paramvir ^{[2
]}

Ware, Doreen ^{[9
]}

Perez, Fernando ^{[10
,11
,12
]}

Canon, Shane ^{[13
]}

Sneddon, Michael W. ^{[2
]}

Henderson, Matthew L. ^{[2
]}

Riehl, William J. ^{[2
]}

Murphy-Olson, Dan ^{[4
]}

Chan, Stephen Y. ^{[2
]}

Kamimura, Roy T. ^{[2
]}

Kumari, Sunita ^{[9
]}

Drake, Meghan M. ^{[3
]}

Brettin, Thomas S. ^{[7
]}

Glass, Elizabeth M. ^{[4
]}

Chivian, Dylan ^{[2
]}

Gunter, Dan ^{[10
]}

Weston, David J. ^{[3
]}

Allen, Benjamin H. ^{[3
]}

Baumohl, Jason ^{[2
]}

Best, Aaron A. ^{[14
]}

Bowen, Ben ^{[2
]}

Brenner, Steven E. ^{[15
]}

Bun, Christopher C. ^{[4
]}

Chandonia, John-Marc ^{[2
]}

Chia, Jer-Ming ^{[9
]}

Colasanti, Ric ^{[4
]}

Conrad, Neal ^{[7
]}

Davis, James J. ^{[7
]}

Davison, Brian H. ^{[3
]}

DeJongh, Matthew ^{[16
]}

Devoid, Scott ^{[4
]}

Dietrich, Emily ^{[7
]}

Dubchak, Inna ^{[2
]}

Edirisinghe, Janaka N. ^{[4
,6
]}

Fang, Gang ^{[17
,27
]}

Faria, Jose P. ^{[4
]}

Frybarger, Paul M. ^{[4
]}

Gerlach, Wolfgang ^{[4
]}

Gerstein, Mark ^{[17
]}

Greiner, Annette ^{[13
]}

Gurtowski, James ^{[9
]}

Haun, Holly L. ^{[3
]}

He, Fei ^{[8
,28
]}

Jain, Rashmi ^{[18
,19
,20
]}

机构：

[1] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA

[2] EO Lawrence Berkeley Natl Lab, Environm Genom & Syst Biol Div, Berkeley, CA 94720 USA

[3] Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA

[4] Argonne Natl Lab, Div Math & Comp Sci, 9700 S Cass Ave, Argonne, IL 60439 USA

[5] Univ Chicago, Dept Comp Sci, Chicago, IL 60637 USA

[6] Univ Chicago, Computat Inst, Chicago, IL 60637 USA

[7] Argonne Natl Lab, Comp Environm & Life Sci Directorate, 9700 S Cass Ave, Argonne, IL 60439 USA

[8] Brookhaven Natl Lab, Dept Biol, Upton, NY 11973 USA

[9] Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA

[10] EO Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA USA

[11] Univ Calif Berkeley, Berkeley Inst Data Sci, Berkeley, CA 94720 USA

[12] Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA

[13] EO Lawrence Berkeley Natl Lab, Natl Energy Res Sci Comp Ctr, Berkeley, CA USA

[14] Hope Coll, Dept Biol, Holland, MI 49423 USA

[15] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

[16] Hope Coll, Dept Comp Sci, Holland, MI 49423 USA

[17] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT USA

[18] Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA

[19] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA

[20] Lawrence Berkeley Natl Lab, Joint BioEnergy Inst, Berkeley, CA USA

[21] Univ Illinois, Dept Microbiol, Urbana, IL USA

[22] Univ Tennessee, Dept Plant Sci, Knoxville, TN USA

[23] Hope Coll, Dept Math, Holland, MI 49423 USA

[24] Brookhaven Natl Lab, Comp Sci & Math, Comp Sci Initiat, Upton, NY 11973 USA

[25] Univ Illinois, Dept Bioengn, Urbana, IL USA

[26] Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL USA

[27] New York Univ, Shanghai Campus, Shanghai, Peoples R China

[28] Kansas State Univ, Dept Plant Pathol, Throckmorton Hall, Manhattan, KS 66506 USA

[29] Insilicogen Inc, Yongin, Gyeonggi Do, South Korea

[30] Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD 21218 USA

[31] Mem Sloan Kettering Canc Ctr, 1275 York Ave, New York, NY 10021 USA

[32] Dordt Coll, Sioux Ctr, IA USA

[33] SUNY Stony Brook, Dept Biomed Informat, Stony Brook, NY 11794 USA

[34] New Jersey Inst Technol, Martin Tuchman Sch Management, Newark, NJ 07102 USA

来源：

NATURE BIOTECHNOLOGY | 2018年 / 36卷 / 07期

关键词：

DATABASE;

D O I：

10.1038/nbt.4163

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

引用

页码：566 / 569

页数：4

共 15 条

[1] Global phenotypic characterization of bacteria
Bochner, Barry R.
[J]. FEMS MICROBIOLOGY REVIEWS, 2009, 33 (01) : 191 - 205
[2] MetaCyc: a multiorganism database of metabolic pathways and enzymes
Caspi, Ron
Foerster, Hartmut
Fulcher, Carol A.
Hopkinson, Rebecca
Ingraham, John
Kaipa, Pallavi
Krummenacker, Markus
Paley, Suzanne
Pick, John
Rhee, Seung Y.
Tissier, Christophe
Zhang, Peifen
Karp, Peter D.
[J]. NUCLEIC ACIDS RESEARCH, 2006, 34 : D511 - D516
[3] Modeling central metabolism and energy biosynthesis across microbial life
Edirisinghe, Janaka N.
Weisenhorn, Pamela
Conrad, Neal
Xia, Fangfang
Overbeek, Ross
Stevens, Rick L.
Henry, Christopher S.
[J]. BMC GENOMICS, 2016, 17
[4] Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation
Faria, Jose 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.
[J]. FRONTIERS IN MICROBIOLOGY, 2016, 7
[5] Phytozome: a comparative platform for green plant genomics
Goodstein, David M.
Shu, Shengqiang
Howson, Russell
Neupane, Rochak
Hayes, Richard D.
Fazo, Joni
Mitros, Therese
Dirks, William
Hellsten, Uffe
Putnam, Nicholas
Rokhsar, Daniel S.
[J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) : D1178 - D1186
[6] Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction
Henry, Christopher S.
Bernstein, Hans C.
Weisenhorn, Pamela
Taylor, Ronald C.
Lee, Joon-Yong
Zucker, Jeremy
Song, Hyun-Seob
[J]. JOURNAL OF CELLULAR PHYSIOLOGY, 2016, 231 (11) : 2339 - 2345
[7] KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M
Goto, S
[J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 27 - 30
[8] Jupyter Notebooks-a publishing format for reproducible computational workflows
Kluyver, Thomas
Ragan-Kelley, Benjamin
Perez, Fernando
Granger, Brian
Bussonnier, Matthias
Frederic, Jonathan
Kelley, Kyle
Hamrick, Jessica
Grout, Jason
Corlay, Sylvain
Ivanov, Paul
Avila, Damin
Abdalla, Safia
Willing, Carol
[J]. POSITIONING AND POWER IN ACADEMIC PUBLISHING: PLAYERS, AGENTS AND AGENDAS, 2016, : 87 - 90
[9] Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Magnusdottir, Stefania
Heinken, Almut
Kutt, Laura
Ravcheev, Dmitry A.
Bauer, Eugen
Noronha, Alberto
Greenhalgh, Kacy
Jager, Christian
Baginska, Joanna
Wilmes, Paul
Fleming, Ronan M. T.
Thiele, Ines
[J]. NATURE BIOTECHNOLOGY, 2017, 35 (01) : 81 - 89
[10] Millman K.J., 2014, Implementing Reproducible Research, P149, DOI DOI 10.1201/9781315373461-6

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