-
1
-
-
79952705856
-
Mining high-throughput experimental data to link gene and function
-
doi:10.1016/j.tibtech.2011.01.001
-
Blaby-Haas CE, de Crecy-Lagard V (2011) Mining high-throughput experimental data to link gene and function. Trends Biotechnol 29 (4):174-182. doi:10.1016/j.tibtech.2011.01.001
-
(2011)
Trends Biotechnol
, vol.29
, Issue.4
, pp. 174-182
-
-
Blaby-Haas, C.E.1
De Crecy-Lagard, V.2
-
2
-
-
72449145463
-
Unknown' proteins and 'orphan' enzymes: The missing half of the engineering parts list-and how to find it
-
doi:10.1042/BJ20091328
-
Hanson AD, Pribat A, Waller JC, de Crecy-Lagard V (2010) 'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list-and how to find it. Biochem J 425(1):1-11. doi:10.1042/BJ20091328
-
(2010)
Biochem J
, vol.425
, Issue.1
, pp. 1-11
-
-
Hanson, A.D.1
Pribat, A.2
Waller, J.C.3
De Crecy-Lagard, V.4
-
3
-
-
34547852439
-
A survey of orphan enzyme activities
-
doi:10.1186/1471-2105-8-244
-
Pouliot Y, Karp PD (2007) A survey of orphan enzyme activities. BMC Bioinformatics 8:244. doi:10.1186/1471-2105-8-244
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 244
-
-
Pouliot, Y.1
Karp, P.D.2
-
4
-
-
0037045398
-
ORF-FINDER: A vector for highthroughput gene identification
-
Rombel IT, Sykes KF, Rayner S, Johnston SA (2002) ORF-FINDER: a vector for highthroughput gene identification. Gene 282 (1-2):33-41
-
(2002)
Gene
, vol.282
, Issue.1-2
, pp. 33-41
-
-
Rombel, I.T.1
Sykes, K.F.2
Rayner, S.3
Johnston, S.A.4
-
5
-
-
33846844989
-
HORFeome v3.1: A resource of human open reading frames representing over 10,000 human genes
-
doi:10.1016/j.ygeno.2006.11.012
-
Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M (2007) hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 89(3):307-315. doi:10.1016/j.ygeno.2006.11.012
-
(2007)
Genomics
, vol.89
, Issue.3
, pp. 307-315
-
-
Lamesch, P.1
Li, N.2
Milstein, S.3
Fan, C.4
Hao, T.5
Szabo, G.6
Hu, Z.7
Venkatesan, K.8
Bethel, G.9
Martin, P.10
Rogers, J.11
Lawlor, S.12
McLaren, S.13
Dricot, A.14
Borick, H.15
Cusick, M.E.16
Vandenhaute, J.17
Dunham, I.18
Hill, D.E.19
Vidal, M.20
more..
-
6
-
-
34548246519
-
Protein annotation at genomic scale: The current status
-
doi:10.1021/cr068303k
-
Frishman D (2007) Protein annotation at genomic scale: the current status. Chem Rev 107(8):3448-3466. doi:10.1021/cr068303k
-
(2007)
Chem Rev
, vol.107
, Issue.8
, pp. 3448-3466
-
-
Frishman, D.1
-
7
-
-
79953077647
-
Protein function prediction: Towards integration of similarity metrics
-
doi:10.1016/j.sbi.2011.02.001
-
Erdin S, Lisewski AM, Lichtarge O (2011) Protein function prediction: towards integration of similarity metrics. Curr Opin Struct Biol 21(2):180-188. doi:10.1016/j.sbi.2011.02.001
-
(2011)
Curr Opin Struct Biol
, vol.21
, Issue.2
, pp. 180-188
-
-
Erdin, S.1
Lisewski, A.M.2
Lichtarge, O.3
-
8
-
-
84934439678
-
Inferring function from homology
-
doi:10.1007/978-1-60327-429-6-6
-
Emes RD (2008) Inferring function from homology. Methods Mol Biol 453:149-168. doi:10.1007/978-1-60327-429-6-6
-
(2008)
Methods Mol Biol
, vol.453
, pp. 149-168
-
-
Emes, R.D.1
-
9
-
-
34250790725
-
Estimating the annotation error rate of curated GO database sequence annotations
-
doi:10.1186/1471-2105-8-170
-
Jones CE, Brown AL, Baumann U (2007) Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 8:170. doi:10.1186/1471-2105-8-170
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 170
-
-
Jones, C.E.1
Brown, A.L.2
Baumann, U.3
-
10
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
doi:10.1038/nprot.2009.203
-
Thiele I, Palsson BO (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5(1):93-121. doi:10.1038/nprot.2009.203
-
(2010)
Nat Protoc
, vol.5
, Issue.1
, pp. 93-121
-
-
Thiele, I.1
Palsson, B.O.2
-
11
-
-
13444304389
-
GenBank
-
doi:10.1093/nar/gki063
-
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2005) GenBank. Nucleic Acids Res 33(Database issue): D34-D38. doi:10.1093/nar/gki063
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.DATABASE ISSUE
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
12
-
-
0025183708
-
Basic local alignment search tool
-
doi:10.1016/S0022-2836(05)80360-2
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410. doi:10.1016/S0022-2836(05) 80360-2
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
13
-
-
48449090786
-
NCBI BLAST: A better web interface
-
Web Server issue, doi:10.1093/nar/gkn201
-
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36(Web Server issue):W5-W9. doi:10.1093/nar/gkn201
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Johnson, M.1
Zaretskaya, I.2
Raytselis, Y.3
Merezhuk, Y.4
McGinnis, S.5
Madden, T.L.6
-
14
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27-30
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
15
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
doi:10.1093/nar/gkh063
-
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(Database issue):D277-D280. doi:10.1093/nar/gkh063
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.DATABASE ISSUE
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
16
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
doi:10.1093/nar/gkm882
-
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36(Database issue):D480-D484. doi:10.1093/nar/gkm882
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.DATABASE ISSUE
-
-
Kanehisa, M.1
Araki, M.2
Goto, S.3
Hattori, M.4
Hirakawa, M.5
Itoh, M.6
Katayama, T.7
Kawashima, S.8
Okuda, S.9
Tokimatsu, T.10
Yamanishi, Y.11
-
17
-
-
0043122944
-
ExPASy: The proteomics server for in-depth protein knowledge and analysis
-
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31 (13):3784-3788
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3784-3788
-
-
Gasteiger, E.1
Gattiker, A.2
Hoogland, C.3
Ivanyi, I.4
Appel, R.D.5
Bairoch, A.6
-
18
-
-
13444306342
-
The Swiss-Prot protein knowledgebase and ExPASy: Providing the plant community with high quality proteomic data and tools
-
doi:10.1016/j.plaphy.2004.10.009
-
Schneider M, Tognolli M, Bairoch A (2004) The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. Plant Physiol Biochem 42(12):1013-1021. doi:10.1016/j.plaphy.2004.10.009
-
(2004)
Plant Physiol Biochem
, vol.42
, Issue.12
, pp. 1013-1021
-
-
Schneider, M.1
Tognolli, M.2
Bairoch, A.3
-
19
-
-
77956696072
-
Highthroughput generation, optimization and analysis of genome-scale metabolic models
-
doi:10.1038/nbt.1672
-
Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL (2010) Highthroughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28(9):977-982. doi:10.1038/nbt.1672
-
(2010)
Nat Biotechnol
, vol.28
, Issue.9
, pp. 977-982
-
-
Henry, C.S.1
Dejongh, M.2
Best, A.A.3
Frybarger, P.M.4
Linsay, B.5
Stevens, R.L.6
-
20
-
-
84860490976
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/ genome databases
-
doi:10.1093/nar/gkr1014
-
Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M,Weerasinghe D, Zhang P, Karp PD (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/ genome databases. Nucleic Acids Res 40 (Database issue):D742-D753. doi:10.1093/nar/gkr1014
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
Caspi, R.1
Altman, T.2
Dreher, K.3
Fulcher, C.A.4
Subhraveti, P.5
Keseler, I.M.6
Kothari, A.7
Krummenacker, M.8
Latendresse, M.9
Mueller, L.A.10
Ong, Q.11
Paley, S.12
Pujar, A.13
Shearer, A.G.14
Travers, M.15
Weerasinghe, D.16
Zhang, P.17
Karp, P.D.18
-
21
-
-
80052719812
-
A survey of metabolic databases emphasizing the MetaCyc family
-
doi:10.1007/s00204-011-0705-2
-
Karp PD, Caspi R (2011) A survey of metabolic databases emphasizing the MetaCyc family. Arch Toxicol 85(9):1015-1033. doi:10.1007/s00204-011-0705-2
-
(2011)
Arch Toxicol
, vol.85
, Issue.9
, pp. 1015-1033
-
-
Karp, P.D.1
Caspi, R.2
-
22
-
-
9144264843
-
GeneDB: A resource for prokaryotic and eukaryotic organisms
-
doi:10.1093/nar/gkh007
-
Hertz-Fowler C, Peacock CS, Wood V, Aslett M, Kerhornou A, Mooney P, Tivey A, Berriman M, Hall N, Rutherford K, Parkhill J, Ivens AC, Rajandream MA, Barrell B (2004) GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res 32(Database issue):D339-D343. doi:10.1093/nar/gkh007
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.DATABASE ISSUE
-
-
Hertz-Fowler, C.1
Peacock, C.S.2
Wood, V.3
Aslett, M.4
Kerhornou, A.5
Mooney, P.6
Tivey, A.7
Berriman, M.8
Hall, N.9
Rutherford, K.10
Parkhill, J.11
Ivens, A.C.12
Rajandream, M.A.13
Barrell, B.14
-
23
-
-
84855499408
-
MetRxn: A knowledgebase of metabolites and reactions spanning metabolic models and databases
-
doi:10.1186/1471-2105-13-6
-
Kumar A, Suthers PF, Maranas CD (2012) MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics 13(1):6. doi:10.1186/1471-2105-13-6
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.1
, pp. 6
-
-
Kumar, A.1
Suthers, P.F.2
Maranas, C.D.3
-
24
-
-
9144232912
-
UniProt: The Universal Protein knowledgebase
-
doi:10.1093/nar/gkh131
-
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32(Database issue): D115-D119. doi:10.1093/nar/gkh131
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.DATABASE ISSUE
-
-
Apweiler, R.1
Bairoch, A.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
Ferro, S.6
Gasteiger, E.7
Huang, H.8
Lopez, R.9
Magrane, M.10
Martin, M.J.11
Natale, D.A.12
O'Donovan, C.13
Redaschi, N.14
Yeh, L.S.15
-
25
-
-
84862237958
-
MetaBase-The wiki-database of biological databases
-
doi:10.1093/nar/gkr109
-
Bolser DM, Chibon PY, Palopoli N, Gong S, Jacob D, Del Angel VD, Swan D, Bassi S, Gonzalez V, Suravajhala P, Hwang S, Romano P, Edwards R, Bishop B, Eargle J, Shtatland T, Provart NJ, Clements D, Renfro DP, Bhak D, Bhak J (2012) MetaBase-the wiki-database of biological databases. Nucleic Acids Res 40 (Database issue):D1250-D1254. doi:10.1093/nar/gkr109
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
Bolser, D.M.1
Chibon, P.Y.2
Palopoli, N.3
Gong, S.4
Jacob, D.5
Del Angel, V.D.6
Swan, D.7
Bassi, S.8
Gonzalez, V.9
Suravajhala, P.10
Hwang, S.11
Romano, P.12
Edwards, R.13
Bishop, B.14
Eargle, J.15
Shtatland, T.16
Provart, N.J.17
Clements, D.18
Renfro, D.P.19
Bhak, D.20
Bhak, J.21
more..
-
26
-
-
31544450286
-
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
-
doi:10.1038/msb4100050
-
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006:0008. doi:10.1038/msb4100050
-
(2006)
Mol Syst Biol
, vol.2006
, pp. 0008
-
-
Baba, T.1
Ara, T.2
Hasegawa, M.3
Takai, Y.4
Okumura, Y.5
Baba, M.6
Datsenko, K.A.7
Tomita, M.8
Wanner, B.L.9
Mori, H.10
-
27
-
-
73849087355
-
Update on the Keio collection of Escherichia coli single-gene deletion mutants
-
doi:10.1038/msb.2009.92
-
Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M,Wanner BL, Mori H (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol 5:335. doi:10.1038/msb.2009.92
-
(2009)
Mol Syst Biol
, vol.5
, pp. 335
-
-
Yamamoto, N.1
Nakahigashi, K.2
Nakamichi, T.3
Yoshino, M.4
Takai, Y.5
Touda, Y.6
Furubayashi, A.7
Kinjyo, S.8
Dose, H.9
Hasegawa, M.10
Datsenko, K.A.11
Nakayashiki, T.12
Tomita Mwanner, B.L.13
Mori, H.14
-
28
-
-
0346494858
-
DEG: A database of essential genes
-
doi:10.1093/nar/gkh024
-
Zhang R, Ou HY, Zhang CT (2004) DEG: a database of essential genes. Nucleic Acids Res 32(Database issue):D271-D272. doi:10.1093/nar/gkh024
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.DATABASE ISSUE
-
-
Zhang, R.1
Ou, H.Y.2
Zhang, C.T.3
-
29
-
-
58149197597
-
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
-
doi:10.1093/nar/gkn858
-
Zhang R, Lin Y (2009) DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 37(Database issue): D455-D458. doi:10.1093/nar/gkn858
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.DATABASE ISSUE
-
-
Zhang, R.1
Lin, Y.2
-
30
-
-
84862165032
-
OGEE: An online gene essentiality database
-
doi:10.1093/nar/gkr986
-
Chen WH, Minguez P, Lercher MJ, Bork P (2012) OGEE: an online gene essentiality database. Nucleic Acids Res 40(Database issue):D901-D906. doi:10.1093/nar/gkr986
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
-
-
Chen, W.H.1
Minguez, P.2
Lercher, M.J.3
Bork, P.4
-
31
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M,Wagner J,Wang J, Forum S (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524-531
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
Cuellar, A.A.11
Dronov, S.12
Gilles, E.D.13
Ginkel, M.14
Gor, V.15
Goryanin, I.I.16
Hedley, W.J.17
Hodgman, T.C.18
Hofmeyr, J.H.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Le Novere, N.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
Nakayama, Y.31
Nelson, M.R.32
Nielsen, P.F.33
Sakurada, T.34
Schaff, J.C.35
Shapiro, B.E.36
Shimizu, T.S.37
Spence, H.D.38
Stelling, J.39
Takahashi, K.40
Tomita, M.41
Wagner, J.42
Wang, J.43
Forum, S.44
more..
-
32
-
-
77951612556
-
BiGG: A Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
-
doi:10.1186/1471-2105-11-213
-
Schellenberger J, Park JO, Conrad TM, Palsson BO (2010) BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11:213. doi:10.1186/1471-2105-11-213
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson, B.O.4
-
33
-
-
79251546728
-
MEMOSys: Bioinformatics platform for genome-scale metabolic models
-
doi:10.1186/1752-0509-5-20
-
Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z (2011) MEMOSys: bioinformatics platform for genome-scale metabolic models. BMC Syst Biol 5:20. doi:10.1186/1752-0509-5-20
-
(2011)
BMC Syst Biol
, vol.5
, pp. 20
-
-
Pabinger, S.1
Rader, R.2
Agren, R.3
Nielsen, J.4
Trajanoski, Z.5
-
34
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0
-
doi:10.1038/nprot.2011.308
-
Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BO (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6 (9):1290-1307. doi:10.1038/nprot. 2011.308
-
(2011)
Nat Protoc
, vol.6
, Issue.9
, pp. 1290-1307
-
-
Schellenberger, J.1
Que, R.2
Fleming, R.M.3
Thiele, I.4
Orth, J.D.5
Feist, A.M.6
Zielinski, D.C.7
Bordbar, A.8
Lewis, N.E.9
Rahmanian, S.10
Kang, J.11
Hyduke, D.R.12
Palsson, B.O.13
-
35
-
-
33646884848
-
SBMLToolbox: An SBML toolbox for MATLAB users
-
doi:10.1093/bioinformatics/btl111
-
Keating SM, Bornstein BJ, Finney A, HuckaM (2006) SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics 22 (10):1275-1277. doi:10.1093/ bioinformatics/btl111
-
(2006)
Bioinformatics
, vol.22
, Issue.10
, pp. 1275-1277
-
-
Keating, S.M.1
Bornstein, B.J.2
Finney, A.3
Hucka, M.4
-
36
-
-
1642457253
-
The effects of alternate optimal solutions in constraintbased genome-scale metabolic models
-
Mahadevan R, Schilling CH (2003) The effects of alternate optimal solutions in constraintbased genome-scale metabolic models. Metab Eng 5(4):264-276
-
(2003)
Metab Eng
, vol.5
, Issue.4
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
37
-
-
84857999389
-
A metabolic network approach for the identification and prioritization of antimicrobial drug targets
-
doi:10.1016/j.tim.2011.12.004
-
Chavali AK, D'Auria KM, Hewlett EL, Pearson RD, Papin JA (2012) A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends Microbiol 20(3):113-123. doi:10.1016/j.tim. 2011.12.004
-
(2012)
Trends Microbiol
, vol.20
, Issue.3
, pp. 113-123
-
-
Chavali, A.K.1
D'Auria, K.M.2
Hewlett, E.L.3
Pearson, R.D.4
Papin, J.A.5
-
38
-
-
34547676311
-
Optimization based automated curation of metabolic reconstructions
-
doi:10.1186/1471-2105-8-212
-
Satish Kumar V, Dasika MS, Maranas CD (2007) Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8:212. doi:10.1186/1471-2105-8-212
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 212
-
-
Satish Kumar, V.1
Dasika, M.S.2
Maranas, C.D.3
-
39
-
-
33751226921
-
Systems approach to refining genome annotation
-
doi:10.1073/pnas.0603364103
-
Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO (2006) Systems approach to refining genome annotation. Proc Natl Acad Sci U S A 103(46):17480-17484. doi:10.1073/pnas. 0603364103
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, Issue.46
, pp. 17480-17484
-
-
Reed, J.L.1
Patel, T.R.2
Chen, K.H.3
Joyce, A.R.4
Applebee, M.K.5
Herring, C.D.6
Bui, O.T.7
Knight, E.M.8
Fong, S.S.9
Palsson, B.O.10
-
41
-
-
75849133666
-
Pathway Tools version 13.0: Integrated software for pathway/ genome informatics and systems biology
-
doi:10.1093/bib/bbp043
-
Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010) Pathway Tools version 13.0: integrated software for pathway/ genome informatics and systems biology. Brief Bioinform 11(1):40-79. doi:10.1093/bib/bbp043
-
(2010)
Brief Bioinform
, vol.11
, Issue.1
, pp. 40-79
-
-
Karp, P.D.1
Paley, S.M.2
Krummenacker, M.3
Latendresse, M.4
Dale, J.M.5
Lee, T.J.6
Kaipa, P.7
Gilham, F.8
Spaulding, A.9
Popescu, L.10
Altman, T.11
Paulsen, I.12
Keseler, I.M.13
Caspi, R.14
-
42
-
-
84856568013
-
Construction and completion of flux balance models from pathway databases
-
doi:10.1093/bioinformatics/btr681
-
Latendresse M, Krummenacker M, Trupp M, Karp PD (2012) Construction and completion of flux balance models from pathway databases. Bioinformatics 28(3):388-396. doi:10.1093/bioinformatics/btr681
-
(2012)
Bioinformatics
, vol.28
, Issue.3
, pp. 388-396
-
-
Latendresse, M.1
Krummenacker, M.2
Trupp, M.3
Karp, P.D.4
-
43
-
-
13244268322
-
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
-
doi:10.1186/1471-2105-5-76
-
Green ML, Karp PD (2004) A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5:76. doi:10.1186/1471-2105-5-76
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 76
-
-
Green, M.L.1
Karp, P.D.2
-
44
-
-
34547840249
-
Using genomecontext data to identify specific types of functional associations in pathway/genome databases
-
doi:10.1093/bioinformatics/btm213
-
Green ML, Karp PD (2007) Using genomecontext data to identify specific types of functional associations in pathway/genome databases. Bioinformatics 23(13):i205-i211. doi:10.1093/bioinformatics/btm213
-
(2007)
Bioinformatics
, vol.23
, Issue.13
-
-
Green, M.L.1
Karp, P.D.2
-
45
-
-
63549108441
-
GrowMatch: An automated method for reconciling in silico/ in vivo growth predictions
-
doi:10.1371/journal.pcbi.1000308
-
Kumar VS, Maranas CD (2009)GrowMatch: an automated method for reconciling in silico/ in vivo growth predictions. PLoS Comput Biol 5(3):e1000308. doi:10.1371/journal.pcbi.1000308
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.3
-
-
Kumar, V.S.1
Maranas, C.D.2
-
46
-
-
33746660425
-
Identification of genome-scale metabolic network models using experimentally measured flux profiles
-
doi:10.1371/journal.pcbi.0020072
-
Herrgard MJ, Fong SS, Palsson BO (2006) Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput Biol 2(7):e72. doi:10.1371/journal.pcbi.0020072
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.7
-
-
Herrgard, M.J.1
Fong, S.S.2
Palsson, B.O.3
-
47
-
-
17444382016
-
Exploring the diversity of complex metabolic networks
-
doi:10.1093/bioinformatics/bti213
-
Hatzimanikatis V, Li C, Ionita JA, Henry CS, Jankowski MD, Broadbelt LJ (2005) Exploring the diversity of complex metabolic networks. Bioinformatics 21(8):1603-1609. doi:10.1093/bioinformatics/bti213
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1603-1609
-
-
Hatzimanikatis, V.1
Li, C.2
Ionita, J.A.3
Henry, C.S.4
Jankowski, M.D.5
Broadbelt, L.J.6
-
48
-
-
79958821230
-
Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii
-
doi:10.1186/1471-2164-12-S1-S4
-
Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K (2011) Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. BMC Genomics 12(Suppl 1):S4. doi: 10.1186/1471-2164-12-S1-S4
-
(2011)
BMC Genomics
, vol.12
, Issue.SUPPL. 1
-
-
Ghamsari, L.1
Balaji, S.2
Shen, Y.3
Yang, X.4
Balcha, D.5
Fan, C.6
Hao, T.7
Yu, H.8
Papin, J.A.9
Salehi-Ashtiani, K.10
-
49
-
-
68349108021
-
Metabolic network analysis integrated with transcript verification for sequenced genomes
-
doi:10.1038/nmeth.1348
-
Manichaikul A, Ghamsari L, Hom EF, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, Papin JA (2009) Metabolic network analysis integrated with transcript verification for sequenced genomes. Nat Methods 6(8):589-592. doi: 10.1038/nmeth.1348
-
(2009)
Nat Methods
, vol.6
, Issue.8
, pp. 589-592
-
-
Manichaikul, A.1
Ghamsari, L.2
Hom, E.F.3
Lin, C.4
Murray, R.R.5
Chang, R.L.6
Balaji, S.7
Hao, T.8
Shen, Y.9
Chavali, A.K.10
Thiele, I.11
Yang, X.12
Fan, C.13
Mello, E.14
Hill, D.E.15
Vidal, M.16
Salehi-Ashtiani, K.17
Papin, J.A.18
-
50
-
-
80051537012
-
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism
-
doi:10.1038/msb.2011.52
-
Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, FuW, Shen Y, Hao T, Palsson BO, Salehi-Ashtiani K, Papin JA (2011) Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol 7:518. doi:10.1038/msb.2011.52
-
(2011)
Mol Syst Biol
, vol.7
, pp. 518
-
-
Chang, R.L.1
Ghamsari, L.2
Manichaikul, A.3
Hom, E.F.4
Balaji, S.5
Fuw Shen, Y.6
Hao, T.7
Palsson, B.O.8
Salehi-Ashtiani, K.9
Papin, J.A.10
-
51
-
-
78651335279
-
Systematizing the generation of missing metabolic knowledge
-
doi:10.1002/bit.22844
-
Orth JD, Palsson BO (2010) Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng 107(3):403-412. doi:10.1002/bit.22844
-
(2010)
Biotechnol Bioeng
, vol.107
, Issue.3
, pp. 403-412
-
-
Orth, J.D.1
Palsson, B.O.2
-
52
-
-
80053375237
-
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
-
doi:10.1186/1752-0509-5-155
-
Rolfsson O, Palsson BO, Thiele I (2011) The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst Biol 5:155. doi:10.1186/1752-0509-5-155
-
(2011)
BMC Syst Biol
, vol.5
, pp. 155
-
-
Rolfsson, O.1
Palsson, B.O.2
Thiele, I.3
-
53
-
-
65649126411
-
Flux balance analysis: Interrogating genomescale metabolic networks
-
doi:10.1007/978-1-59745-525-1-3
-
Oberhardt MA, Chavali AK, Papin JA (2009) Flux balance analysis: interrogating genomescale metabolic networks. Methods Mol Biol 500:61-80. doi:10.1007/978-1-59745-525-1-3
-
(2009)
Methods Mol Biol
, vol.500
, pp. 61-80
-
-
Oberhardt, M.A.1
Chavali, A.K.2
Papin, J.A.3
-
54
-
-
33751567092
-
Experimental and computational assessment of conditionally essential genes in Escherichia coli
-
doi:10.1128/JB.00740-06
-
Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006) Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol 188 (23):8259-8271. doi:10.1128/JB.00740-06
-
(2006)
J Bacteriol
, vol.188
, Issue.23
, pp. 8259-8271
-
-
Joyce, A.R.1
Reed, J.L.2
White, A.3
Edwards, R.4
Osterman, A.5
Baba, T.6
Mori, H.7
Lesely, S.A.8
Palsson, B.O.9
Agarwalla, S.10
-
55
-
-
77952886804
-
The biomass objective function
-
doi:10.1016/j.mib.2010.03.003
-
Feist AM, Palsson BO (2010) The biomass objective function. Curr Opin Microbiol 13 (3):344-349. doi:10.1016/j.mib.2010.03.003
-
(2010)
Curr Opin Microbiol
, vol.13
, Issue.3
, pp. 344-349
-
-
Feist, A.M.1
Palsson, B.O.2
-
56
-
-
41149169317
-
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major
-
doi:10.1038/msb.2008.15
-
Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA (2008) Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol Syst Biol 4:177. doi:10.1038/msb.2008.15
-
(2008)
Mol Syst Biol
, vol.4
, pp. 177
-
-
Chavali, A.K.1
Whittemore, J.D.2
Eddy, J.A.3
Williams, K.T.4
Papin, J.A.5
-
57
-
-
84862159261
-
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
-
doi:10.1186/1752-0509-6-30
-
Orth JD, Palsson BO (2012) Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst Biol 6(1):30. doi:10.1186/1752-0509-6-30
-
(2012)
BMC Syst Biol
, vol.6
, Issue.1
, pp. 30
-
-
Orth, J.D.1
Palsson, B.O.2
-
58
-
-
33846910173
-
Global reconstruction of the human metabolic network based on genomic and bibliomic data
-
doi:10.1073/pnas.0610772104
-
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BO (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104(6):1777-1782. doi:10.1073/pnas.0610772104
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, Issue.6
, pp. 1777-1782
-
-
Duarte, N.C.1
Becker, S.A.2
Jamshidi, N.3
Thiele, I.4
Mo, M.L.5
Vo, T.D.6
Srivas, R.7
Palsson, B.O.8
-
59
-
-
79952601486
-
Rapid amplification of cDNA ends (RACE)
-
doi:10.1007/978-1-59745-248-9-8
-
Yeku O, Frohman MA (2011) Rapid amplification of cDNA ends (RACE). Methods Mol Biol 703:107-122. doi:10.1007/978-1-59745-248-9-8
-
(2011)
Methods Mol Biol
, vol.703
, pp. 107-122
-
-
Yeku, O.1
Frohman, M.A.2
-
60
-
-
0024212067
-
Rapid production of full-length cDNAs from rare transcripts: Amplification using a single gene-specific oligonucleotide primer
-
Frohman MA, Dush MK, Martin GR (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A 85(23):8998-9002
-
(1988)
Proc Natl Acad Sci U S A
, vol.85
, Issue.23
, pp. 8998-9002
-
-
Frohman, M.A.1
Dush, M.K.2
Martin, G.R.3
-
61
-
-
33750298722
-
Prediction of genomic functional elements
-
doi:10.1146/annurev.genom.7.080505.115745
-
Jones SJ (2006) Prediction of genomic functional elements. Annu Rev Genomics Hum Genet 7:315-338. doi:10.1146/annurev.genom.7.080505.115745
-
(2006)
Annu Rev Genomics Hum Genet
, vol.7
, pp. 315-338
-
-
Jones, S.J.1
|