-
1
-
-
0037079054
-
Computational systems biology
-
Kitano H: Computational systems biology. Nature 2002, 420:206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
2
-
-
45149111660
-
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
-
Feist AM, Palsson BO: The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 2008, 26:659-667.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 659-667
-
-
Feist, A.M.1
Palsson, B.O.2
-
6
-
-
67449096729
-
Flux balance analysis of biological systems: Applications and challenges
-
Raman K, Chandra N: Flux balance analysis of biological systems: Applications and challenges. Brief Bioinform 2009, 10(4):435-449.
-
(2009)
Brief Bioinform
, vol.10
, Issue.4
, pp. 435-449
-
-
Raman, K.1
Chandra, N.2
-
7
-
-
0028146781
-
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
-
Varma A, Palsson BO: Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 1994, 60(10):3724-3731.
-
(1994)
Appl Environ Microbiol
, vol.60
, Issue.10
, pp. 3724-3731
-
-
Varma, A.1
Palsson, B.O.2
-
8
-
-
84892965416
-
Software applications toward quantitative metabolic flux analysis and modeling
-
Dandekar T, Fieselmann A, Majeed S, Ahmed Z: Software applications toward quantitative metabolic flux analysis and modeling. Brief Bioinform 2012, doi:10.1093/bib/bbs065.
-
(2012)
Brief Bioinform
-
-
Dandekar, T.1
Fieselmann, A.2
Majeed, S.3
Ahmed, Z.4
-
9
-
-
84892991094
-
Software applications for flux balance analysis
-
Lakshmanan M, Koh G, Chung BK, Lee DY: Software applications for flux balance analysis. Brief Bioinform 2012, 15:108-122.
-
(2012)
Brief Bioinform
, vol.15
, pp. 108-122
-
-
Lakshmanan, M.1
Koh, G.2
Chung, B.K.3
Lee, D.Y.4
-
10
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0
-
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: Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0. Nat Protoc 2011, 6:1290-1307.
-
(2011)
Nat Protoc
, vol.6
, 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
-
11
-
-
33747856186
-
Metatool 5.0: Fast and flexible elementary modes analysis
-
Von KA, Schuster S: Metatool 5.0: Fast and flexible elementary modes analysis. Bioinformatics 2006, 22:1930-1931.
-
(2006)
Bioinformatics
, vol.22
, pp. 1930-1931
-
-
Von, Ka1
Schuster, S.2
-
12
-
-
0037316342
-
FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
-
Klamt S, Stelling J, Ginkel M, Gilles ED: FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 2003, 19:261-269.
-
(2003)
Bioinformatics
, vol.19
, pp. 261-269
-
-
Klamt, S.1
Stelling, J.2
Ginkel, M.3
Gilles, E.D.4
-
13
-
-
0242475329
-
MetaFluxNet: The management of metabolic reaction information and quantitative metabolic flux analysis
-
Lee DY, Yun H, Park S, Lee SY: MetaFluxNet: The management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics 2003, 19:2144-2146.
-
(2003)
Bioinformatics
, vol.19
, pp. 2144-2146
-
-
Lee, D.Y.1
Yun, H.2
Park, S.3
Lee, S.Y.4
-
14
-
-
33645536317
-
SNA-a toolbox for the stoichiometric analysis of metabolic networks
-
Urbanczik R: SNA-a toolbox for the stoichiometric analysis of metabolic networks. BMC Bioinformatics 2006, 7:129.
-
(2006)
Bmc Bioinformatics
, vol.7
, pp. 129
-
-
Urbanczik, R.1
-
15
-
-
34447551397
-
Structural and functional analysis of cellular networks with Cell NetAnalyzer
-
Klamt S, Saez-Rodriguez J, Gilles ED: Structural and functional analysis of cellular networks with Cell NetAnalyzer. BMC Syst Biol 2007, 1:2.
-
(2007)
Bmc Syst Biol
, vol.1
, pp. 2
-
-
Klamt, S.1
Saez-Rodriguez, J.2
Gilles, E.D.3
-
16
-
-
35248849697
-
Integrated network reconstruction, visualization and analysis using YANAsquare
-
Schwarz R, Liang C, Kaleta C, Kuhnel M, Hoffmann E, Kuznetsov S, Hecker M, Griffiths G, Schuster S, Dandekar T: Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics 2007, 8:313.
-
(2007)
Bmc Bioinformatics
, vol.8
, pp. 313
-
-
Schwarz, R.1
Liang, C.2
Kaleta, C.3
Kuhnel, M.4
Hoffmann, E.5
Kuznetsov, S.6
Hecker, M.7
Griffiths, G.8
Schuster, S.9
Dandekar, T.10
-
17
-
-
77949264877
-
Quantifying food web flows using linear inverse models
-
van Oevelen D, Van den Meersche K, Meysman FJR, Soetaert K, Middelburg JJ, Vezina AF: Quantifying food web flows using linear inverse models. Ecosystems 2010, 13:32-45.
-
(2010)
Ecosystems
, vol.13
, pp. 32-45
-
-
Van Oevelen, D.1
Van Den Meersche, K.2
Meysman, F.J.R.3
Soetaert, K.4
Middelburg, J.J.5
Vezina, A.F.6
-
18
-
-
84887364569
-
Sybil: Efficient constrained based modelling in R
-
Gelius DG, Amer DA, Jonathan FC, Lercher M: Sybil: Efficient constrained based modelling in R. BMC Syst Biol 2013, 7:125.
-
(2013)
Bmc Syst Biol
, vol.7
, pp. 125
-
-
Gelius, D.G.1
Amer, D.A.2
Jonathan, F.C.3
Lercher, M.4
-
19
-
-
85100641998
-
BiGGR: Constraint based modeling in R using metabolic reconstruction databases
-
Gavai AK and Hettling H (2013). BiGGR: Constraint based modeling in R using metabolic reconstruction databases. R package version1.2.0, [http://www.bioconductor.org/]
-
(2013)
R Package version1.2.0
-
-
Gavai, A.K.1
Hettling, H.2
-
20
-
-
84863304598
-
-
R Core Team. Vienna, Austria: R Foundation for Statistical Computing
-
R Core Team: R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2014. URL http://www.R-project.org/.
-
(2014)
R: A Language and Environment for Statistical Computing
-
-
-
21
-
-
47649105109
-
The systems biology research tool: Evolvable open-source software
-
Wright J, Wagner A: The systems biology research tool: Evolvable open-source software. BMC Syst Biol 2008, 2:55.
-
(2008)
Bmc Syst Biol
, vol.2
, pp. 55
-
-
Wright, J.1
Wagner, A.2
-
22
-
-
84856247380
-
FAME, the flux analysis and modeling environment
-
Boele J, Olivier BG, Teusink B: FAME, the flux analysis and modeling environment. BMC Syst Biol 2012, 6:8.
-
(2012)
Bmc Syst Biol
, vol.6
, pp. 8
-
-
Boele, J.1
Olivier, B.G.2
Teusink, B.3
-
23
-
-
84864464109
-
MicrobesFlux: A web platform for drafting metabolic models from the KEGG database
-
Feng X, Xu Y, Chen Y, Tang YJ: MicrobesFlux: A web platform for drafting metabolic models from the KEGG database. BMC Syst Biol 2012, 6:94.
-
(2012)
Bmc Syst Biol
, vol.6
, pp. 94
-
-
Feng, X.1
Xu, Y.2
Chen, Y.3
Tang, Y.J.4
-
24
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S: KEGG: Kyoto encyclopedia of genes and genomes. MNucleic Acids Res 2000, 28:27-30.
-
(2000)
MNucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
25
-
-
85015538128
-
Flux-P: Automating metabolic flux analysis
-
Ebert BE, Lamprecht AL, Steffen B, Blank LM: Flux-P: Automating metabolic flux analysis. Metabolites 2012, 2:872-890.
-
(2012)
Metabolites
, vol.2
, pp. 872-890
-
-
Ebert, B.E.1
Lamprecht, A.L.2
Steffen, B.3
Blank, L.M.4
-
26
-
-
70350669876
-
WEbcoli: An interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model
-
Jung TS, Yeo HC, Reddy SG, Cho WS, Lee DY: WEbcoli: An interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model. Bioinformatics 2009, 25:2850-2852.
-
(2009)
Bioinformatics
, vol.25
, pp. 2850-2852
-
-
Jung, T.S.1
Yeo, H.C.2
Reddy, S.G.3
Cho, W.S.4
Lee, D.Y.5
-
27
-
-
84875144546
-
MetaNETX.org: A website and repository for accessing, analysing and manipulating metabolic networks
-
Ganter M, Bernard T, Moretti S, Stelling J, Pagni M: MetaNETX.org: A website and repository for accessing, analysing and manipulating metabolic networks. Bioinformatics 2013, 29:815-816.
-
(2013)
Bioinformatics
, vol.29
, pp. 815-816
-
-
Ganter, M.1
Bernard, T.2
Moretti, S.3
Stelling, J.4
Pagni, M.5
-
28
-
-
77951612556
-
BiGG: A Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
-
Schellenberger J, Park JO, Conrad TM, Palsson BO: BiGG: A Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 2010, 11:213.
-
(2010)
Bmc Bioinformatics
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson, B.O.4
-
29
-
-
84855499408
-
MetRxn: A knowledgebase of metabolites and reactions spanning metabolic models and databases
-
Kumar A, Suthers PF, Maranas CD: MetRxn: A knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics 2012, 13:6.
-
(2012)
Bmc Bioinformatics
, vol.13
, pp. 6
-
-
Kumar, A.1
Suthers, P.F.2
Maranas, C.D.3
-
30
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A: Galaxy: A platform for interactive large-scale genome analysis. Genome Res 2005, 15:1451-1455.
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
Miller, W.11
Kent, W.J.12
Nekrutenko, A.13
-
31
-
-
23644452487
-
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): An in silico genome-scale characterization of single- And double-deletion mutants
-
Thiele I, Vo TD, Price ND, Palsson BO: Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): An in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol 2005, 187:5818-5830.
-
(2005)
J Bacteriol
, vol.187
, pp. 5818-5830
-
-
Thiele, I.1
Vo, T.D.2
Price, N.D.3
Palsson, B.O.4
-
32
-
-
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 NN, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, et al: The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531.
-
(2003)
Bioinformatics
, vol.19
, 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, N.N.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
Al, E.31
more..
-
33
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
-
Reed JL, Vo TD, Schilling CH, Palsson BO: An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4:R54.
-
(2003)
Genome Biol
, vol.4
, pp. R54
-
-
Reed, J.L.1
Vo, T.D.2
Ch, S.3
Palsson, B.O.4
-
34
-
-
77950960250
-
OptFlux: An open-source software platform for in silico metabolic engineering
-
Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M: OptFlux: An open-source software platform for in silico metabolic engineering. BMC Syst Biol 2010, 4:45.
-
(2010)
Bmc Syst Biol
, vol.4
, pp. 45
-
-
Rocha, I.1
Maia, P.2
Evangelista, P.3
Vilaça, P.4
Soares, S.5
Pinto, J.P.6
Nielsen, J.7
Patil, K.R.8
Ferreira, E.C.9
Rocha, M.10
-
35
-
-
7744237727
-
Pyruvate formate and acetate kinase are essential for anaerobic growth of Escherichia coli on Xylose
-
Hasona A, Kim Y, Healy FG, Ingram LO, Shanmugam KT: Pyruvate formate and acetate kinase are essential for anaerobic growth of Escherichia coli on Xylose. J Bacteriol 2004, 186:7593-7600.
-
(2004)
J Bacteriol
, vol.186
, pp. 7593-7600
-
-
Hasona, A.1
Kim, Y.2
Healy, F.G.3
Ingram, L.O.4
Shanmugam, K.T.5
-
36
-
-
2442636351
-
Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery
-
Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB: Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery. Genome Res 2004, 14:917-924.
-
(2004)
Genome Res
, vol.14
, pp. 917-924
-
-
Yeh, I.1
Hanekamp, T.2
Tsoka, S.3
Karp, P.D.4
Altman, R.B.5
-
37
-
-
33747890136
-
Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks
-
Rahman SA, Schomburg D: Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks. Bioinformatics 2006, 22:1767-1774.
-
(2006)
Bioinformatics
, vol.22
, pp. 1767-1774
-
-
Rahman, S.A.1
Schomburg, D.2
-
38
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
Mahadevan R, Schilling CH: The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 2003, 5:264-276.
-
(2003)
Metab Eng
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Ch, S.2
|