KBase: The United States Department of Energy Systems Biology Knowledgebase

被引:964
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
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
收藏
页码:566 / 569
页数:4
相关论文
共 15 条
[1]   Global phenotypic characterization of bacteria [J].
Bochner, Barry R. .
FEMS MICROBIOLOGY REVIEWS, 2009, 33 (01) :191-205
[2]   MetaCyc: a multiorganism database of metabolic pathways and enzymes [J].
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. .
NUCLEIC ACIDS RESEARCH, 2006, 34 :D511-D516
[3]   Modeling central metabolism and energy biosynthesis across microbial life [J].
Edirisinghe, Janaka N. ;
Weisenhorn, Pamela ;
Conrad, Neal ;
Xia, Fangfang ;
Overbeek, Ross ;
Stevens, Rick L. ;
Henry, Christopher S. .
BMC GENOMICS, 2016, 17
[4]   Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation [J].
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. .
FRONTIERS IN MICROBIOLOGY, 2016, 7
[5]   Phytozome: a comparative platform for green plant genomics [J].
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. .
NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D1178-D1186
[6]   Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction [J].
Henry, Christopher S. ;
Bernstein, Hans C. ;
Weisenhorn, Pamela ;
Taylor, Ronald C. ;
Lee, Joon-Yong ;
Zucker, Jeremy ;
Song, Hyun-Seob .
JOURNAL OF CELLULAR PHYSIOLOGY, 2016, 231 (11) :2339-2345
[7]   KEGG: Kyoto Encyclopedia of Genes and Genomes [J].
Kanehisa, M ;
Goto, S .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :27-30
[8]   Jupyter Notebooks-a publishing format for reproducible computational workflows [J].
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 .
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 [J].
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 .
NATURE BIOTECHNOLOGY, 2017, 35 (01) :81-89
[10]  
Millman K.J., 2014, Implementing Reproducible Research, P149, DOI DOI 10.1201/9781315373461-6