KBase: The United States department of energy systems biology knowledgebase

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

doi:10.1038/nbt.4163

KBase: The United States department of energy systems biology knowledgebase

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

MT School of Management

Research output: Contribution to journal › Letter › peer-review

184 Scopus citations

Original language	English (US)
Pages (from-to)	566-569
Number of pages	4
Journal	Nature Biotechnology
Volume	36
Issue number	7
DOIs	https://doi.org/10.1038/nbt.4163
State	Published - Jul 6 2018

All Science Journal Classification (ASJC) codes

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

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10.1038/nbt.4163

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Arkin, A. P., Cottingham, R. W., Henry, C. S., Harris, N. L., Stevens, R. L., Maslov, S., Dehal, P., Ware, D., Perez, F., Canon, S., Sneddon, M. W., Henderson, M. L., Riehl, W. J., Murphy-Olson, D., Chan, S. Y., Kamimura, R. T., Kumari, S., Drake, M. M., Brettin, T. S., ... Yu, D. (2018). KBase: The United States department of energy systems biology knowledgebase. Nature Biotechnology, 36(7), 566-569. https://doi.org/10.1038/nbt.4163

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. / KBase : The United States department of energy systems biology knowledgebase. In: Nature Biotechnology. 2018 ; Vol. 36, No. 7. pp. 566-569.

@article{3fb215895bef4e498deb5ba0fd288677,

title = "KBase: The United States department of energy systems biology knowledgebase",

author = "Arkin, {Adam P.} and Cottingham, {Robert W.} and Henry, {Christopher S.} and Harris, {Nomi L.} and Stevens, {Rick L.} and Sergei Maslov and Paramvir Dehal and Doreen Ware and Fernando Perez and Shane Canon and Sneddon, {Michael W.} and Henderson, {Matthew L.} and Riehl, {William J.} and Dan Murphy-Olson and Chan, {Stephen Y.} and Kamimura, {Roy T.} and Sunita Kumari and Drake, {Meghan M.} and Brettin, {Thomas S.} and Glass, {Elizabeth M.} and Dylan Chivian and Dan Gunter and Weston, {David J.} and Allen, {Benjamin H.} and Jason Baumohl and Best, {Aaron A.} and Ben Bowen and Brenner, {Steven E.} and Bun, {Christopher C.} and Chandonia, {John Marc} and Chia, {Jer Ming} and Ric Colasanti and Neal Conrad and Davis, {James J.} and Davison, {Brian H.} and Matthew Dejongh and Scott Devoid and Emily Dietrich and Inna Dubchak and Edirisinghe, {Janaka N.} and Gang Fang and Faria, {Jos{\'e} P.} and Frybarger, {Paul M.} and Wolfgang Gerlach and Mark Gerstein and Annette Greiner and James Gurtowski and Haun, {Holly L.} and Fei He and Rashmi Jain and Joachimiak, {Marcin P.} and Keegan, {Kevin P.} and Shinnosuke Kondo and Vivek Kumar and Land, {Miriam L.} and Folker Meyer and Marissa Mills and Novichkov, {Pavel S.} and Taeyun Oh and Olsen, {Gary J.} and Robert Olson and Bruce Parrello and Shiran Pasternak and Erik Pearson and Poon, {Sarah S.} and Price, {Gavin A.} and Srividya Ramakrishnan and Priya Ranjan and Ronald, {Pamela C.} and Schatz, {Michael C.} and Seaver, {Samuel M.D.} and Maulik Shukla and Sutormin, {Roman A.} and Syed, {Mustafa H.} and James Thomason and Tintle, {Nathan L.} and Daifeng Wang and Fangfang Xia and Hyunseung Yoo and Shinjae Yoo and Dantong Yu",

note = "Funding Information: F.P. declares competing interest related to his work for Plot.ly and research funding from Microsoft, Google, and Anaconda Inc. S.E.B. receives funding and has a research collaboration with Tata Consultancy Service that is unrelated to the KBase project. Funding Information: This work is supported by the Office of Biological and Environmental Research{\textquoteright}s Genomic Science program within the US Department of Energy Office of Science, under award numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886.",

year = "2018",

month = jul,

day = "6",

doi = "10.1038/nbt.4163",

language = "English (US)",

volume = "36",

pages = "566--569",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "7",

}

Arkin, AP, Cottingham, RW, Henry, CS, Harris, NL, Stevens, RL, Maslov, S, Dehal, P, Ware, D, Perez, F, Canon, S, Sneddon, MW, Henderson, ML, Riehl, WJ, Murphy-Olson, D, Chan, SY, Kamimura, RT, Kumari, S, Drake, MM, Brettin, TS, Glass, EM, Chivian, D, Gunter, D, Weston, DJ, Allen, BH, Baumohl, J, Best, AA, Bowen, B, Brenner, SE, Bun, CC, Chandonia, JM, Chia, JM, Colasanti, R, Conrad, N, Davis, JJ, Davison, BH, Dejongh, M, Devoid, S, Dietrich, E, Dubchak, I, Edirisinghe, JN, Fang, G, Faria, JP, Frybarger, PM, Gerlach, W, Gerstein, M, Greiner, A, Gurtowski, J, Haun, HL, He, F, Jain, R, Joachimiak, MP, Keegan, KP, Kondo, S, Kumar, V, Land, ML, Meyer, F, Mills, M, Novichkov, PS, Oh, T, Olsen, GJ, Olson, R, Parrello, B, Pasternak, S, Pearson, E, Poon, SS, Price, GA, Ramakrishnan, S, Ranjan, P, Ronald, PC, Schatz, MC, Seaver, SMD, Shukla, M, Sutormin, RA, Syed, MH, Thomason, J, Tintle, NL, Wang, D, Xia, F, Yoo, H, Yoo, S & Yu, D 2018, 'KBase: The United States department of energy systems biology knowledgebase', Nature Biotechnology, vol. 36, no. 7, pp. 566-569. https://doi.org/10.1038/nbt.4163

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.

In: Nature Biotechnology, Vol. 36, No. 7, 06.07.2018, p. 566-569.

Research output: Contribution to journal › Letter › peer-review

TY - JOUR

T1 - KBase

T2 - The United States department of energy systems biology knowledgebase

AU - Arkin, Adam P.

AU - Cottingham, Robert W.

AU - Henry, Christopher S.

AU - Harris, Nomi L.

AU - Stevens, Rick L.

AU - Maslov, Sergei

AU - Dehal, Paramvir

AU - Ware, Doreen

AU - Perez, Fernando

AU - Canon, Shane

AU - Sneddon, Michael W.

AU - Henderson, Matthew L.

AU - Riehl, William J.

AU - Murphy-Olson, Dan

AU - Chan, Stephen Y.

AU - Kamimura, Roy T.

AU - Kumari, Sunita

AU - Drake, Meghan M.

AU - Brettin, Thomas S.

AU - Glass, Elizabeth M.

AU - Chivian, Dylan

AU - Gunter, Dan

AU - Weston, David J.

AU - Allen, Benjamin H.

AU - Baumohl, Jason

AU - Best, Aaron A.

AU - Bowen, Ben

AU - Brenner, Steven E.

AU - Bun, Christopher C.

AU - Chandonia, John Marc

AU - Chia, Jer Ming

AU - Colasanti, Ric

AU - Conrad, Neal

AU - Davis, James J.

AU - Davison, Brian H.

AU - Dejongh, Matthew

AU - Devoid, Scott

AU - Dietrich, Emily

AU - Dubchak, Inna

AU - Edirisinghe, Janaka N.

AU - Fang, Gang

AU - Faria, José P.

AU - Frybarger, Paul M.

AU - Gerlach, Wolfgang

AU - Gerstein, Mark

AU - Greiner, Annette

AU - Gurtowski, James

AU - Haun, Holly L.

AU - He, Fei

AU - Jain, Rashmi

AU - Joachimiak, Marcin P.

AU - Keegan, Kevin P.

AU - Kondo, Shinnosuke

AU - Kumar, Vivek

AU - Land, Miriam L.

AU - Meyer, Folker

AU - Mills, Marissa

AU - Novichkov, Pavel S.

AU - Oh, Taeyun

AU - Olsen, Gary J.

AU - Olson, Robert

AU - Parrello, Bruce

AU - Pasternak, Shiran

AU - Pearson, Erik

AU - Poon, Sarah S.

AU - Price, Gavin A.

AU - Ramakrishnan, Srividya

AU - Ranjan, Priya

AU - Ronald, Pamela C.

AU - Schatz, Michael C.

AU - Seaver, Samuel M.D.

AU - Shukla, Maulik

AU - Sutormin, Roman A.

AU - Syed, Mustafa H.

AU - Thomason, James

AU - Tintle, Nathan L.

AU - Wang, Daifeng

AU - Xia, Fangfang

AU - Yoo, Hyunseung

AU - Yoo, Shinjae

AU - Yu, Dantong

N1 - Funding Information: F.P. declares competing interest related to his work for Plot.ly and research funding from Microsoft, Google, and Anaconda Inc. S.E.B. receives funding and has a research collaboration with Tata Consultancy Service that is unrelated to the KBase project. Funding Information: This work is supported by the Office of Biological and Environmental Research’s Genomic Science program within the US Department of Energy Office of Science, under award numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886.

PY - 2018/7/6

Y1 - 2018/7/6

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UR - http://www.scopus.com/inward/citedby.url?scp=85049776867&partnerID=8YFLogxK

U2 - 10.1038/nbt.4163

DO - 10.1038/nbt.4163

M3 - Letter

C2 - 29979655

AN - SCOPUS:85049776867

VL - 36

SP - 566

EP - 569

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 7

ER -

KBase: The United States department of energy systems biology knowledgebase

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