-
1
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BO. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 2009, 7(2):129-143.
-
(2009)
Nat Rev Microbiol
, vol.7
, Issue.2
, pp. 129-143
-
-
Feist, A.M.1
Herrgård, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.O.5
-
2
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
2238879, 18077471
-
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, 36:D480-D484. 2238879, 18077471.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
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
-
3
-
-
38549117301
-
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
-
2238876, 17965431
-
Caspi R, Foerster H, Fulcher C, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee S, Shearer A, Tissier C, Walk T, Zhang P, Karp P. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 2008, 36:D623-D631. 2238876, 17965431.
-
(2008)
Nucleic 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.8
Shearer, A.9
Tissier, C.10
Walk, T.11
Zhang, P.12
Karp, P.13
-
4
-
-
67549123519
-
Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel anti-microbial drug targets
-
19376871
-
Lee DS, Burd H, Liu J, Almaas E, Wiest O, Barabási AL, Oltvai ZN, Kapatral V. Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel anti-microbial drug targets. J Bacteriol 2009, 191(12):4015-4024. 19376871.
-
(2009)
J Bacteriol
, vol.191
, Issue.12
, pp. 4015-4024
-
-
Lee, D.S.1
Burd, H.2
Liu, J.3
Almaas, E.4
Wiest, O.5
Barabási, A.L.6
Oltvai, Z.N.7
Kapatral, V.8
-
5
-
-
15044342010
-
Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts
-
Blank LM, Lehmbeck F, Sauer U. Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Research 2005, 5:545-558.
-
(2005)
FEMS Yeast Research
, vol.5
, pp. 545-558
-
-
Blank, L.M.1
Lehmbeck, F.2
Sauer, U.3
-
6
-
-
14844289540
-
Illuminating drug discovery with biological pathways
-
Apic G, Ignjatovic T, Boyer S, Russell R. Illuminating drug discovery with biological pathways. FEBS Letters 2005, 579(8):1872-1877.
-
(2005)
FEBS Letters
, vol.579
, Issue.8
, pp. 1872-1877
-
-
Apic, G.1
Ignjatovic, T.2
Boyer, S.3
Russell, R.4
-
7
-
-
45749090110
-
An analytic and systematic framework for estimating metabolic flux ratios from 13 C tracer experiments
-
2430715, 18534038
-
Rantanen A, Rousu J, Jouhten P, Zamboni N, Maaheimo H, Ukkonen E. An analytic and systematic framework for estimating metabolic flux ratios from 13 C tracer experiments. BMC Bioinformatics 2008, 9:266. 2430715, 18534038.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 266
-
-
Rantanen, A.1
Rousu, J.2
Jouhten, P.3
Zamboni, N.4
Maaheimo, H.5
Ukkonen, E.6
-
8
-
-
8744224466
-
OptStrain: a computational framework for redesign of microbial production systems
-
525696, 15520298
-
Pharkya P, Burgard AP, Maranas CD. OptStrain: a computational framework for redesign of microbial production systems. Genome Res 2004, 14(11):2367-2376. 525696, 15520298.
-
(2004)
Genome Res
, vol.14
, Issue.11
, pp. 2367-2376
-
-
Pharkya, P.1
Burgard, A.P.2
Maranas, C.D.3
-
9
-
-
84855621976
-
A computational method for reconstructing gapless metabolic networks
-
Communications in Computer and Information Science, Springer
-
Pitkänen E, Rantanen A, Rousu J, Ukkonen E. A computational method for reconstructing gapless metabolic networks. Proceedings of the 2nd International Conference on Bioinformatics Research and Development (BIRD'08) 2008, 13. Communications in Computer and Information Science, Springer.
-
(2008)
Proceedings of the 2nd International Conference on Bioinformatics Research and Development (BIRD'08)
, vol.13
-
-
Pitkänen, E.1
Rantanen, A.2
Rousu, J.3
Ukkonen, E.4
-
11
-
-
9544253891
-
Genome-Scale Models Of Microbial Cells: Evaluating The Consequences Of Constraints
-
Price ND, Reed JL, Palsson BO. Genome-Scale Models Of Microbial Cells: Evaluating The Consequences Of Constraints. Nature Reviews Microbiology 2004, 2:886-897.
-
(2004)
Nature Reviews Microbiology
, vol.2
, pp. 886-897
-
-
Price, N.D.1
Reed, J.L.2
Palsson, B.O.3
-
12
-
-
34547676311
-
Optimization based automated curation of metabolic reconstructions
-
17584497, 1933441
-
Kumar VS, Dasika MS, Maranas CD. Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 2007, 8(212). 17584497, 1933441.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.212
-
-
Kumar, V.S.1
Dasika, M.S.2
Maranas, C.D.3
-
13
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
-
Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnology 2000, 18:326-332.
-
(2000)
Nature Biotechnology
, vol.18
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
14
-
-
0037881782
-
Metabolic reconstruction using shortest paths
-
Arita M. Metabolic reconstruction using shortest paths. Simulation Practice and Theory 2000, 8:109-125.
-
(2000)
Simulation Practice and Theory
, vol.8
, pp. 109-125
-
-
Arita, M.1
-
15
-
-
23144466440
-
Metabolic PathFinding: inferring relevant pathways in biochemical networks
-
1160198, 15980483
-
Croes D, Couche F, Wodak SJ, van Helden J. Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Research 2005, 33:W326-W330. 1160198, 15980483.
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Croes, D.1
Couche, F.2
Wodak, S.J.3
van Helden, J.4
-
16
-
-
16344376028
-
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
-
Rahman SA, Advani P, Schunk R, Schrader R, Schomburg D. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics 2005, 21(7):1189-1193.
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 1189-1193
-
-
Rahman, S.A.1
Advani, P.2
Schunk, R.3
Schrader, R.4
Schomburg, D.5
-
18
-
-
51749088153
-
MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization
-
2530881, 18635573
-
Blum T, Kohlbacher O. MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics 2008, 24(18). 2530881, 18635573.
-
(2008)
Bioinformatics
, vol.24
, Issue.18
-
-
Blum, T.1
Kohlbacher, O.2
-
20
-
-
49949089557
-
A critical examination of stoichiometric and path-finding approaches to metabolic pathways
-
Planes FJ, Beasley JE. A critical examination of stoichiometric and path-finding approaches to metabolic pathways. Briefings in Bioinformatics 2008, 9(5):422-436.
-
(2008)
Briefings in Bioinformatics
, vol.9
, Issue.5
, pp. 422-436
-
-
Planes, F.J.1
Beasley, J.E.2
-
21
-
-
55949089680
-
An introduction to metabolic networks and their structural analysis
-
18989046
-
Lacroix V, Cottret L, Thebault P, Sagot MF. An introduction to metabolic networks and their structural analysis. IEEE Transactions on Computational Biology and Bioinformatics 2008, 5(4):594-617. 18989046.
-
(2008)
IEEE Transactions on Computational Biology and Bioinformatics
, vol.5
, Issue.4
, pp. 594-617
-
-
Lacroix, V.1
Cottret, L.2
Thebault, P.3
Sagot, M.F.4
-
22
-
-
52949098408
-
Large scale computation of elementary flux modes with bit pattern trees
-
Terzer M, Stelling J. Large scale computation of elementary flux modes with bit pattern trees. Bioinformatics 2008, 24(19):2229-2235.
-
(2008)
Bioinformatics
, vol.24
, Issue.19
, pp. 2229-2235
-
-
Terzer, M.1
Stelling, J.2
-
23
-
-
0141843591
-
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways
-
Hattori M, Okuno Y, Goto S, Kanehisa M. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. Journal of the American Chemical Society 2003, 125:11853-11865.
-
(2003)
Journal of the American Chemical Society
, vol.125
, pp. 11853-11865
-
-
Hattori, M.1
Okuno, Y.2
Goto, S.3
Kanehisa, M.4
-
24
-
-
0035823264
-
The small world inside large metabolic networks
-
11522199, 1088812
-
Wagner A, Fell DA. The small world inside large metabolic networks. Proc R Soc Lond B 2001, 268(1478):1803-1810. 11522199, 1088812.
-
(2001)
Proc R Soc Lond B
, vol.268
, Issue.1478
, pp. 1803-1810
-
-
Wagner, A.1
Fell, D.A.2
-
25
-
-
30344456708
-
Inferring meaningful pathways in weighted metabolic networks
-
Croes D, Couche F, Wodak S, van Helden J. Inferring meaningful pathways in weighted metabolic networks. J Mol Biol 2006, 356:222-236.
-
(2006)
J Mol Biol
, vol.356
, pp. 222-236
-
-
Croes, D.1
Couche, F.2
Wodak, S.3
van Helden, J.4
-
26
-
-
47549099578
-
Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks
-
Blum T, Kohlbacher O. Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks. Journal of Computational Biology 2008, 15(6):565-576.
-
(2008)
Journal of Computational Biology
, vol.15
, Issue.6
, pp. 565-576
-
-
Blum, T.1
Kohlbacher, O.2
-
27
-
-
45249101693
-
RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions
-
Kotera M, Hattori M, Oh MA, Yamamoto R, Komeno T, Yabuzaki J. RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions. Genome Inf 2004, 15:P062.
-
(2004)
Genome Inf
, vol.15
-
-
Kotera, M.1
Hattori, M.2
Oh, M.A.3
Yamamoto, R.4
Komeno, T.5
Yabuzaki, J.6
-
28
-
-
0037079050
-
Metabolic network structure determines key aspects of functionality and regulation
-
Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002, 420(6912):190-193.
-
(2002)
Nature
, vol.420
, Issue.6912
, pp. 190-193
-
-
Stelling, J.1
Klamt, S.2
Bettenbrock, K.3
Schuster, S.4
Gilles, E.D.5
-
29
-
-
0033670135
-
Pathway analysis in metabolic databases via differential metabolic display (DMD)
-
Küffner R, Zimmer R, Lengauer T. Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 2000, 16(9):825-836.
-
(2000)
Bioinformatics
, vol.16
, Issue.9
, pp. 825-836
-
-
Küffner, R.1
Zimmer, R.2
Lengauer, T.3
-
30
-
-
31144448020
-
Algorithmic approaches for computing elementary modes in large biochemical reaction networks
-
Klamt S, Gagneur J, von Kamp A. Algorithmic approaches for computing elementary modes in large biochemical reaction networks. IEE Proceedings Systems Biology 2005, 152(4):249-255.
-
(2005)
IEE Proceedings Systems Biology
, vol.152
, Issue.4
, pp. 249-255
-
-
Klamt, S.1
Gagneur, J.2
von Kamp, A.3
-
31
-
-
33747856186
-
Metatool 5.0: fast and flexible elementary modes analysis
-
von Kamp A, Schuster S. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 2006, 22(15):1930-1931.
-
(2006)
Bioinformatics
, vol.22
, Issue.15
, pp. 1930-1931
-
-
von Kamp, A.1
Schuster, S.2
-
32
-
-
25444515956
-
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities
-
1175843, 15929789
-
Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T. YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics 2005, 6(135). 1175843, 15929789.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.135
-
-
Schwarz, R.1
Musch, P.2
von Kamp, A.3
Engels, B.4
Schirmer, H.5
Schuster, S.6
Dandekar, T.7
-
33
-
-
55749088074
-
Can sugars be produced from fatty acids? A test case for pathway analysis tools
-
de Figueiredo LF, Schuster S, Kaleta C, Fell DA. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics 2008, 24(22):2615-2621.
-
(2008)
Bioinformatics
, vol.24
, Issue.22
, pp. 2615-2621
-
-
de Figueiredo, L.F.1
Schuster, S.2
Kaleta, C.3
Fell, D.A.4
-
34
-
-
0000663732
-
Finding the K Shortest Loopless Paths in a Network
-
Yen JY. Finding the K Shortest Loopless Paths in a Network. Management Science 1971, 17(11):712-716.
-
(1971)
Management Science
, vol.17
, Issue.11
, pp. 712-716
-
-
Yen, J.Y.1
-
35
-
-
0032108018
-
Finding the k shortest paths
-
Eppstein D. Finding the k shortest paths. SIAM J Computing 1998, 28(2):652-673.
-
(1998)
SIAM J Computing
, vol.28
, Issue.2
, pp. 652-673
-
-
Eppstein, D.1
-
36
-
-
71949089406
-
13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose
-
Jouhten P, Pitkänen E, Pakula T, Saloheimo M, Penttilä M, Maaheimo H. 13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose. 2009, , http://www.biomedcentral.com/1752-0509/3/104
-
(2009)
-
-
Jouhten, P.1
Pitkänen, E.2
Pakula, T.3
Saloheimo, M.4
Penttilä, M.5
Maaheimo, H.6
-
37
-
-
77950630179
-
Towards structured output prediction of enzyme function
-
19091049, 2654971
-
Astikainen K, Holm L, Pitkänen E, Szedmak S, Rousu J. Towards structured output prediction of enzyme function. BMC proceedings, BioMed Central Ltd 2008, 2:S2. 19091049, 2654971.
-
(2008)
BMC proceedings, BioMed Central Ltd
, vol.2
-
-
Astikainen, K.1
Holm, L.2
Pitkänen, E.3
Szedmak, S.4
Rousu, J.5
-
39
-
-
0031554635
-
Bidirectional Reaction Steps in Metabolic Networks: I. Modeling and Simulation of Carbon Isotope Labeling Experiments
-
Wiechert W, de Graaf AA. Bidirectional Reaction Steps in Metabolic Networks: I. Modeling and Simulation of Carbon Isotope Labeling Experiments. Biotechnology and Bioengineering 1997, 55:101-117.
-
(1997)
Biotechnology and Bioengineering
, vol.55
, pp. 101-117
-
-
Wiechert, W.1
de Graaf, A.A.2
-
41
-
-
2142678730
-
Computing the K Shortest Paths: a New Algorithm and an Experimental Comparison
-
LNCS, Springer-Verlag
-
Jiminez V, Marzal A. Computing the K Shortest Paths: a New Algorithm and an Experimental Comparison. Algorithm Engineering 1999, 15-29. LNCS, Springer-Verlag.
-
(1999)
Algorithm Engineering
, pp. 15-29
-
-
Jiminez, V.1
Marzal, A.2
-
42
-
-
66749140138
-
ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis
-
Pitkänen E, Åkerlund A, Rantanen A, Jouhten P, Ukkonen E. ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis. Journal of Integrative Bioinformatics 2008, 5(2):102.
-
(2008)
Journal of Integrative Bioinformatics
, vol.5
, Issue.2
, pp. 102
-
-
Pitkänen, E.1
Åkerlund, A.2
Rantanen, A.3
Jouhten, P.4
Ukkonen, E.5
-
43
-
-
0042093610
-
The connectivity structure, giant strong component and centrality of metabolic networks
-
Ma HW, Zeng AP. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003, 19(11):1423-1430.
-
(2003)
Bioinformatics
, vol.19
, Issue.11
, pp. 1423-1430
-
-
Ma, H.W.1
Zeng, A.P.2
-
45
-
-
1242319556
-
The metabolic world of Escherichia coli is not small
-
341771, 14757824
-
Arita M. The metabolic world of Escherichia coli is not small. PNAS 2004, 101(6):1543-1547. 341771, 14757824.
-
(2004)
PNAS
, vol.101
, Issue.6
, pp. 1543-1547
-
-
Arita, M.1
-
46
-
-
43449098828
-
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei
-
Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barbote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei. Nat Biotechnol 2008, 26:553-560.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 553-560
-
-
Martinez, D.1
Berka, R.M.2
Henrissat, B.3
Saloheimo, M.4
Arvas, M.5
Baker, S.E.6
Chapman, J.7
Chertkov, O.8
Coutinho, P.M.9
Cullen, D.10
Danchin, E.G.11
Grigoriev, I.V.12
Harris, P.13
Jackson, M.14
Kubicek, C.P.15
Han, C.S.16
Ho, I.17
Larrondo, L.F.18
de Leon, A.L.19
Magnuson, J.K.20
Merino, S.21
Misra, M.22
Nelson, B.23
Putnam, N.24
Robbertse, B.25
Salamov, A.A.26
Schmoll, M.27
Terry, A.28
Thayer, N.29
Westerholm-Parvinen, A.30
Schoch, C.L.31
Yao, J.32
Barbote, R.33
Nelson, M.A.34
Detter, C.35
Bruce, D.36
Kuske, C.R.37
Xie, G.38
Richardson, P.39
Rokhsar, D.S.40
Lucas, S.M.41
Rubin, E.M.42
Dunn-Coleman, N.43
Ward, M.44
Brettin, T.S.45
more..
-
47
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
146917, 9254694
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
48
-
-
33846041078
-
The Universal Protein Resource (UniProt)
-
1669721, 17142230
-
Consortium TU The Universal Protein Resource (UniProt). Nucleic Acids Res 2007, 35:D193-197. 1669721, 17142230.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
-
49
-
-
0001648656
-
Nucleic acids, purines, pyrimidines (nucleotide synthesis)
-
Hartman SC, Buchanan JM. Nucleic acids, purines, pyrimidines (nucleotide synthesis). Annu Rev Biochem 1959, 28:365-410.
-
(1959)
Annu Rev Biochem
, vol.28
, pp. 365-410
-
-
Hartman, S.C.1
Buchanan, J.M.2
|