-
1
-
-
58149179979
-
EcoCyc: A comprehensive view of E. coli biology
-
Keseler I, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus R, Johnson DA, Krummenacker M, Nolan L, Paley S, Paulsen I, Peralta-Gil M, Santos-Zavaleta A, Shearer A, Karp P. EcoCyc: A comprehensive view of E. coli biology. Nuc Acids Res 2009, 37:D464-70.
-
(2009)
Nuc Acids Res
, vol.37
-
-
Keseler, I.1
Bonavides-Martinez, C.2
Collado-Vides, J.3
Gama-Castro, S.4
Gunsalus, R.5
Johnson, D.A.6
Krummenacker, M.7
Nolan, L.8
Paley, S.9
Paulsen, I.10
Peralta-Gil, M.11
Santos-Zavaleta, A.12
Shearer, A.13
Karp, P.14
-
2
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
10.1038/msb4100155, 1911197, 17593909
-
Feist A, Henry C, Reed J, Krummenacker M, Joyce A, Karp P, Broadbelt L, Hatzimanikatis V, Palsson B. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 2007, 3:121-38. 10.1038/msb4100155, 1911197, 17593909.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 121-138
-
-
Feist, A.1
Henry, C.2
Reed, J.3
Krummenacker, M.4
Joyce, A.5
Karp, P.6
Broadbelt, L.7
Hatzimanikatis, V.8
Palsson, B.9
-
3
-
-
0036086784
-
Evaluation of computational metabolic-pathway predictions for H. pylori
-
10.1093/bioinformatics/18.5.715, 12050068
-
Paley S, Karp P. Evaluation of computational metabolic-pathway predictions for H. pylori. Bioinformatics 2002, 18(5):715-24. 10.1093/bioinformatics/18.5.715, 12050068.
-
(2002)
Bioinformatics
, vol.18
, Issue.5
, pp. 715-724
-
-
Paley, S.1
Karp, P.2
-
4
-
-
38549117301
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
-
Caspi R, Foerster H, Fulcher C, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer A, Tissier C, Walk T, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nuc Acids Res 2008, 36:D623-31.
-
(2008)
Nuc Acids Res
, vol.36
-
-
Caspi, R.1
Foerster, H.2
Fulcher, C.3
Kaipa, P.4
Krummenacker, M.5
Latendresse, M.6
Paley, S.7
Rhee, S.Y.8
Shearer, A.9
Tissier, C.10
Walk, T.11
Zhang, P.12
Karp, P.D.13
-
5
-
-
13244268322
-
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
-
10.1186/1471-2105-5-76, 446185, 15189570
-
Green M, Karp P. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 2004, 5:76. 10.1186/1471-2105-5-76, 446185, 15189570.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 76
-
-
Green, M.1
Karp, P.2
-
6
-
-
27244443126
-
MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research
-
10.1104/pp.105.060376, 1104157, 15888675
-
Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY. MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research. Plant Physiol 2005, 138:27-37. 10.1104/pp.105.060376, 1104157, 15888675.
-
(2005)
Plant Physiol
, vol.138
, pp. 27-37
-
-
Zhang, P.1
Foerster, H.2
Tissier, C.P.3
Mueller, L.4
Paley, S.5
Karp, P.D.6
Rhee, S.Y.7
-
7
-
-
84888285786
-
AraCyc Database
-
AraCyc Database. , http://www.arabidopsis.org/biocyc/
-
-
-
-
8
-
-
84888284597
-
YeastCyc Database
-
YeastCyc Database. , http://pathway.yeastgenome.org/
-
-
-
-
9
-
-
70049099900
-
MouseCyc Database
-
MouseCyc Database. , http://mousecyc.jax.org:8000/
-
-
-
-
10
-
-
65349131424
-
Reconstruction of metabolic pathways for the cattle genome
-
10.1186/1752-0509-3-33, 2669051, 19284618
-
Seo S, Lewin HA. Reconstruction of metabolic pathways for the cattle genome. BMC Syst Biol 2009, 3:33. 10.1186/1752-0509-3-33, 2669051, 19284618.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 33
-
-
Seo, S.1
Lewin, H.A.2
-
13
-
-
84888274363
-
IND software package
-
IND software package. , http://opensource.arc.nasa.gov/project/ind/
-
-
-
-
14
-
-
0002980086
-
Learning classification trees
-
Buntine W. Learning classification trees. Statistics and Computing 1992, 2:63-73.
-
(1992)
Statistics and Computing
, vol.2
, pp. 63-73
-
-
Buntine, W.1
-
16
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike H. A new look at the statistical model identification. IEEE Transactions on Automatic Control 1974, 19(6):716-723.
-
(1974)
IEEE Transactions on Automatic Control
, vol.19
, Issue.6
, pp. 716-723
-
-
Akaike, H.1
-
17
-
-
0000120766
-
Estimating the Dimension of a Model
-
Schwarz G. Estimating the Dimension of a Model. The Annals of Statistics 1978, 6(2):461-464.
-
(1978)
The Annals of Statistics
, vol.6
, Issue.2
, pp. 461-464
-
-
Schwarz, G.1
-
18
-
-
0030211964
-
Bagging Predictors
-
Breiman L. Bagging Predictors. Machine Learning 1996, 24(2):123-140.
-
(1996)
Machine Learning
, vol.24
, Issue.2
, pp. 123-140
-
-
Breiman, L.1
-
19
-
-
0035478854
-
Random Forests
-
Breiman L. Random Forests. Machine Learning 2001, 45:5-32.
-
(2001)
Machine Learning
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
20
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nuc Acids Res 2005, 33(17):5691-5702.
-
(2005)
Nuc Acids Res
, vol.33
, Issue.17
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
de Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
Fonstein, M.11
Frank, E.D.12
Gerdes, S.13
Glass, E.M.14
Goesmann, A.15
Hanson, A.16
Iwata-Reuyl, D.17
Jensen, R.18
Jamshidi, N.19
Krause, L.20
Kubal, M.21
Larsen, N.22
Linke, B.23
McHardy, A.C.24
Meyer, F.25
Neuweger, H.26
Olsen, G.27
Olson, R.28
Osterman, A.29
Portnoy, V.30
Pusch, G.D.31
Rodionov, D.A.32
Ruckert, C.33
Steiner, J.34
Stevens, R.35
Thiele, I.36
Vassieva, O.37
Ye, Y.38
Zagnitko, O.39
Vonstein, V.40
more..
-
21
-
-
34248632008
-
Toward the automated generation of genome-scale metabolic networks in the SEED
-
10.1186/1471-2105-8-139, 1868769, 17462086
-
DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A. Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007, 8:139. 10.1186/1471-2105-8-139, 1868769, 17462086.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 139
-
-
DeJongh, M.1
Formsma, K.2
Boillot, P.3
Gould, J.4
Rycenga, M.5
Best, A.6
-
22
-
-
27144524216
-
Automatic detection of subsystem/pathway variants in genome analysis
-
10.1093/bioinformatics/bti1052, 15961494
-
Ye Y, Osterman A, Overbeek R, Godzik A. Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics 2005, 21(Suppl 1):i478-i486. 10.1093/bioinformatics/bti1052, 15961494.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL 1
-
-
Ye, Y.1
Osterman, A.2
Overbeek, R.3
Godzik, A.4
-
23
-
-
58149177166
-
Reactome knowledgebase of human biological pathways and processes
-
Database
-
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P. Reactome knowledgebase of human biological pathways and processes. Nuc Acids Res 2009, (37 Database):D619-22.
-
(2009)
Nuc Acids Res
, Issue.37
-
-
Matthews, L.1
Gopinath, G.2
Gillespie, M.3
Caudy, M.4
Croft, D.5
de Bono, B.6
Garapati, P.7
Hemish, J.8
Hermjakob, H.9
Jassal, B.10
Kanapin, A.11
Lewis, S.12
Mahajan, S.13
May, B.14
Schmidt, E.15
Vastrik, I.16
Wu, G.17
Birney, E.18
Stein, L.19
D'Eustachio, P.20
more..
-
24
-
-
48449090785
-
KEGG Atlas mapping for global analysis of metabolic pathways
-
Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M. KEGG Atlas mapping for global analysis of metabolic pathways. Nuc Acids Res 2008, 36:W423-26.
-
(2008)
Nuc Acids Res
, vol.36
-
-
Okuda, S.1
Yamada, T.2
Hamajima, M.3
Itoh, M.4
Katayama, T.5
Bork, P.6
Goto, S.7
Kanehisa, M.8
-
25
-
-
33747139057
-
The Outcomes of Pathway Database Computations Depend on Pathway Ontology
-
Green M, Karp P. The Outcomes of Pathway Database Computations Depend on Pathway Ontology. Nuc Acids Res 2006, 34:3687-97.
-
(2006)
Nuc Acids Res
, vol.34
, pp. 3687-3697
-
-
Green, M.1
Karp, P.2
-
26
-
-
0028108519
-
Metabolic Flux Balancing: Basic concepts, Scientific and Practical Use
-
Varma A, Palsson B. Metabolic Flux Balancing: Basic concepts, Scientific and Practical Use. Bio/Technology 1994, 12:994-8.
-
(1994)
Bio/Technology
, vol.12
, pp. 994-998
-
-
Varma, A.1
Palsson, B.2
-
28
-
-
49549084189
-
An environmental perspective on large-scale genome clustering based on metabolic capabilities
-
10.1093/bioinformatics/btn302, 18689840
-
Kastenmuller G, Gasteiger J, Mewes HW. An environmental perspective on large-scale genome clustering based on metabolic capabilities. Bioinformatics 2008, 24(16):i56-62. 10.1093/bioinformatics/btn302, 18689840.
-
(2008)
Bioinformatics
, vol.24
, Issue.16
-
-
Kastenmuller, G.1
Gasteiger, J.2
Mewes, H.W.3
-
29
-
-
65249105934
-
Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes
-
10.1186/gb-2009-10-3-r28, 2690999, 19284550
-
Kastenmuller G, Schenk ME, Gasteiger J, Mewes HW. Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes. Genome Biol 2009, 10(3):R28. 10.1186/gb-2009-10-3-r28, 2690999, 19284550.
-
(2009)
Genome Biol
, vol.10
, Issue.3
-
-
Kastenmuller, G.1
Schenk, M.E.2
Gasteiger, J.3
Mewes, H.W.4
-
30
-
-
13244265575
-
IdentiCS - Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence
-
10.1186/1471-2105-5-112, 514700, 15312235
-
Sun J, Zeng AP. IdentiCS - Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics 2004, 5:112. 10.1186/1471-2105-5-112, 514700, 15312235.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 112
-
-
Sun, J.1
Zeng, A.P.2
-
31
-
-
14844349363
-
MetaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella
-
10.1093/nar/gki285, 552966, 15745999
-
Pinney JW, Shirley MW, McConkey GA, Westhead DR. metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Research 2005, 33(4):1399-1409. 10.1093/nar/gki285, 552966, 15745999.
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.4
, pp. 1399-1409
-
-
Pinney, J.W.1
Shirley, M.W.2
McConkey, G.A.3
Westhead, D.R.4
-
32
-
-
33847260244
-
Pathway Analyst -- Automated Metabolic Pathway Prediction
-
Pireddu L, Poulin B, Szafron D, Lu P, Wishart DS. Pathway Analyst -- Automated Metabolic Pathway Prediction. Computational Intelligence in Bioinformatics and Computational Biology, 2005. CIBCB '05. Proceedings of the 2005 IEEE Symposium on 2005, 1-8.
-
(2005)
Computational Intelligence in Bioinformatics and Computational Biology, 2005. CIBCB '05. Proceedings of the 2005 IEEE Symposium on
, pp. 1-8
-
-
Pireddu, L.1
Poulin, B.2
Szafron, D.3
Lu, P.4
Wishart, D.S.5
-
33
-
-
33747829918
-
The Path-A metabolic pathway prediction web server
-
10.1093/nar/gkl228, 1538809, 16845105
-
Pireddu L, Szafron D, Lu P, Greiner R. The Path-A metabolic pathway prediction web server. Nucleic Acids Research 2006, 34(suppl 2):W714-719. 10.1093/nar/gkl228, 1538809, 16845105.
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.SUPPL 2
-
-
Pireddu, L.1
Szafron, D.2
Lu, P.3
Greiner, R.4
-
34
-
-
0141850380
-
PathMiner: Predicting metabolic pathways by heuristic search
-
10.1093/bioinformatics/btg217, 2709535, 12967966
-
McShan D, Rao S, Shah I. PathMiner: Predicting metabolic pathways by heuristic search. Bioinformatics 2003, 19(13):1692-8. 10.1093/bioinformatics/btg217, 2709535, 12967966.
-
(2003)
Bioinformatics
, vol.19
, Issue.13
, pp. 1692-1698
-
-
McShan, D.1
Rao, S.2
Shah, I.3
-
35
-
-
35748980569
-
Mining biological networks for unknown pathways
-
10.1093/bioinformatics/btm409, 17766269
-
Cakmak A, Ozsoyoglu G. Mining biological networks for unknown pathways. Bioinformatics 2007, 23(20):2775-2783. 10.1093/bioinformatics/btm409, 17766269.
-
(2007)
Bioinformatics
, vol.23
, Issue.20
, pp. 2775-2783
-
-
Cakmak, A.1
Ozsoyoglu, G.2
-
36
-
-
29144446142
-
Supervised enzyme network inference from the integration of genomic data and chemical information
-
10.1093/bioinformatics/bti1012, 15961492
-
Yamanishi Y, Vert JP, Kanehisa M. Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics 2005, 21(suppl 1):i468-477. 10.1093/bioinformatics/bti1012, 15961492.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL 1
-
-
Yamanishi, Y.1
Vert, J.P.2
Kanehisa, M.3
|