-
1
-
-
84864932596
-
Fifteen years of large scale metabolic modeling of yeast: Developments and impacts
-
Osterlund, T., Nookaew, I. & Nielsen, J. Fifteen years of large scale metabolic modeling of yeast: Developments and impacts. Biotechnol. Adv. 30, 979-988 (2012).
-
(2012)
Biotechnol. Adv
, vol.30
, pp. 979-988
-
-
Osterlund, T.1
Nookaew, I.2
Nielsen, J.3
-
2
-
-
78649631909
-
The application of flux balance analysis in systems biology. Wiley Interdiscip
-
Gianchandani, E. P., Chavali, A. K. & Papin, J. A. The application of flux balance analysis in systems biology. Wiley Interdiscip. Rev. Syst. Biol. Med. 2, 372-382 (2010).
-
(2010)
Rev. Syst. Biol. Med
, vol.2
, pp. 372-382
-
-
Gianchandani, E.P.1
Chavali, A.K.2
Papin, J.A.3
-
3
-
-
73149122136
-
Applications of genome-scale metabolic reconstructions
-
Oberhardt, M. A., Palsson, B. . & Papin, J. A. Applications of genome-scale metabolic reconstructions. Mol. Syst. Biol. 5, 320; DOI:10.1038/msb.2009.77 (2009).
-
(2009)
Mol. Syst. Biol
, vol.5
, pp. 320
-
-
Oberhardt, M.A.1
Palsson, B.2
Papin, J.A.3
-
4
-
-
84858439602
-
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
-
Lewis N.E. Nagarajan H. Palsson B. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods Nat. Rev. Microbiol 2012 10 291-305
-
(2012)
Nat. Rev. Microbiol
, vol.10
, pp. 291-305
-
-
Lewis, N.E.1
Nagarajan, H.2
Palsson, B.3
-
5
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
-
Schuster, S., Fell, D. A. &Dandekar, T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotech. 18, 326-332 (2000).
-
(2000)
Nat. Biotech
, vol.18
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
6
-
-
84884172916
-
Elementary flux modes in a nutshell: Properties, calculation and applications
-
Zanghellini, J., Ruckerbauer, D. E., Hanscho, M. & Jungreuthmayer, C. Elementary flux modes in a nutshell: Properties, calculation and applications. Biotechnol. J. 8, 1009-1016; DOI:10.1002/biot.201200269 (2013).
-
(2013)
Biotechnol. J
, vol.8
, pp. 1009-1016
-
-
Zanghellini, J.1
Ruckerbauer, D.E.2
Hanscho, M.3
Jungreuthmayer, C.4
-
7
-
-
0036039060
-
Combinatorial complexity of pathway analysis in metabolic networks
-
Klamt, S. & Stelling, J. Combinatorial Complexity of Pathway Analysis in Metabolic Networks. Mol. Biol. Rep. 29, 233-236 (2002).
-
(2002)
Mol. Biol. Rep
, vol.29
, pp. 233-236
-
-
Klamt, S.1
Stelling, J.2
-
8
-
-
57049122976
-
Modes and cuts in metabolic networks: Complexity and algorithms
-
Acunã, V. et al. Modes and cuts in metabolic networks: Complexity and algorithms. Biosystems 95, 51-60; DOI:10.1016/j.biosystems.2008.06.015 (2009).
-
(2009)
Biosystems
, vol.95
, pp. 51-60
-
-
Acunã, V.1
-
9
-
-
84901356026
-
Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition
-
Hunt, K. A., Folsom, J. P., Taffs, R. L. & Carlson, R. P. Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition. Bioinformatics 30, 1569-1578; DOI:10.1093/bioinformatics/btu021 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1569-1578
-
-
Hunt, K.A.1
Folsom, J.P.2
Taffs, R.L.3
Carlson, R.P.4
-
10
-
-
75849164426
-
Computing the shortest elementary flux modes in genome-scale metabolic networks
-
De Figueiredo, L. F. et al. Computing the Shortest Elementary Flux Modes in Genome-Scale Metabolic Networks. Bioinformatics 25, 3158-3165; DOI:10.1093/bioinformatics/btp564 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 3158-3165
-
-
De Figueiredo, L.F.1
-
11
-
-
84866443920
-
-
Random sampling of elementary flux modes in large-scale metabolic networks
-
Machado, D., Soons, Z., Patil, K. R., Ferreira, E. C. & Rocha, I. Random sampling of elementary flux modes in large-scale metabolic networks. Bioinformatics 28, i515-i521 (2012).
-
Bioinformatics
, vol.28
, pp. 2012
-
-
MacHado, D.1
Soons, Z.2
Patil, K.R.3
Ferreira, E.C.4
Rocha, I.5
-
12
-
-
84856560417
-
Efmevolver: Computing elementary flux modes in genome-scale metabolic networks
-
(Gesellschaft für Informatik Bonn
-
Kaleta, C., De Figueiredo, L. F., Behre, J. & Schuster, S. Efmevolver: computing elementary flux modes in genome-scale metabolic networks. Lecture Notes in Informatics (LNI)-Proceedings of the German Conference on Bioinformatics, P-157, 179-190; (Gesellschaft für Informatik, Bonn, 2009).
-
(2009)
Lecture Notes in Informatics (LNI)-Proceedings of the German Conference on Bioinformatics P-157 179-190
-
-
Kaleta, C.1
De Figueiredo, L.F.2
Behre, J.3
Schuster, S.4
-
13
-
-
84904992252
-
Direct calculation of Elementary Flux Modes satisfying several biological constraints in genome-scale metabolic networks
-
Pey, J. & Planes, F. J. Direct calculation of Elementary Flux Modes satisfying several biological constraints in genome-scale metabolic networks. Bioinformatics 30, 2197-2203; DOI:10.1093/bioinformatics/btu193 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2197-2203
-
-
Pey, J.1
Planes, F.J.2
-
14
-
-
84866090747
-
Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks
-
Kelk, S. M., Olivier, B. G., Stougie, L. & Bruggeman, F. J. Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Sci. Rep. 2, 580; DOI:10.1038/srep00580 (2012).
-
(2012)
Sci. Rep
, vol.2
, pp. 580
-
-
Kelk, S.M.1
Olivier, B.G.2
Stougie, L.3
Bruggeman, F.J.4
-
15
-
-
84878346520
-
Efmtool: Speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic
-
Jungreuthmayer, C., Ruckerbauer, D. E. & Zanghellini, J. regEfmtool: Speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic. Biosystems 113, 37-39; DOI:10.1016/j.biosystems.2013.04.002 (2013).
-
(2013)
Biosystems
, vol.113
, pp. 37-39
-
-
Jungreuthmayer, C.1
Ruckerbauer, D.E.2
Zanghellini, J.3
-
16
-
-
0037008673
-
Transcriptional Regulation in Constraints-based Metabolic Models of Escherichia coli
-
Covert, M. W. & Palsson, B. . Transcriptional Regulation in Constraints-based Metabolic Models of Escherichia coli. J. Biol. Chem. 277, 28058-28064 (2002).
-
(2002)
J. Biol. Chem
, vol.277
, pp. 28058-28064
-
-
Covert, M.W.1
Palsson, B.2
-
17
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist, A. M. et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 3, 121; DOI:10.1038/msb4100155 (2007).
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 121
-
-
Feist, A.M.1
-
18
-
-
77953514760
-
Which metabolic pathways generate and characterize the flux space? a comparison among elementary modes extreme pathways and minimal generators
-
Llaneras, F. & Picó, J.Which Metabolic Pathways Generate and Characterize the Flux Space? A Comparison among Elementary Modes, Extreme Pathways and Minimal Generators. J. Biomed. Biotechnol. 2010, 753904; DOI:10.1155/2010/753904 (2010).
-
(2010)
J. Biomed. Biotechnol
, vol.2010
, pp. 753904
-
-
Llaneras, F.1
Picó, J.2
-
19
-
-
13244292328
-
Computation of elementary modes: A unifying framework and the new binary approach
-
Gagneur, J. & Klamt, S. Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 5, 175; DOI:10.1186/1471-2105-5-175 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 175
-
-
Gagneur, J.1
Klamt, S.2
-
20
-
-
33745433792
-
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data
-
Kümmel, A., Panke, S. & Heinemann, M. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol. Syst. Biol. 2, 2006.0034; DOI:10.1038/msb4100074 (2006).
-
(2006)
Mol. Syst. Biol
, vol.2
, Issue.2006
, pp. 0034
-
-
Kümmel, A.1
Panke, S.2
Heinemann, M.3
-
22
-
-
84861128104
-
System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes
-
Jol, S. J., Kümmel, A., Terzer, M., Stelling, J. & Heinemann, M. System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes. PLoS Comput. Biol. 8, e1002415; DOI:10.1371/journal.pcbi.1002415 (2012).
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002415
-
-
Jol, S.J.1
Kümmel, A.2
Terzer, M.3
Stelling, J.4
Heinemann, M.5
-
23
-
-
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 24, 2229-2235; DOI:10.1093/bioinformatics/btn401 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 2229-2235
-
-
Terzer, M.1
Stelling, J.2
-
25
-
-
84927781592
-
Reconstruction anduse of microbial metabolic networks: The core escherichia coli metabolic model as an educational guide
-
Orth, J. D., Fleming, R. M. T.&Palsson, B. . Reconstruction andUse of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide. EcoSal 28, 245-248; (2010).
-
(2010)
EcoSal
, vol.28
, pp. 245-248
-
-
Orth, J.D.1
Fleming, R.M.T.2
Palsson, B.3
-
26
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
-
Reed, J. L., Vo, T. D., Schilling, C. H. & Palsson, B. . An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4, R54; DOI:10.1186/gb-2003-4-9-r54 (2003).
-
(2003)
Genome Biol
, vol.4
, pp. R54
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.4
-
27
-
-
0034625143
-
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
-
Edwards, J. S. & Palsson, B. O. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. U.S.A. 97, 5528-5533 (2000).
-
(2000)
Proc. Natl. Acad. Sci. U.S.A
, vol.97
, pp. 5528-5533
-
-
Edwards, J.S.1
Palsson, B.O.2
-
28
-
-
68049100110
-
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
-
Bennett, B. D. et al. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 5, 593-599; DOI:10.1038/nchembio.186 (2009).
-
(2009)
Nat. Chem. Biol
, vol.5
, pp. 593-599
-
-
Bennett, B.D.1
-
29
-
-
33847797256
-
Thermodynamics-based metabolic flux analysis
-
Henry, C. S., Broadbelt, L. J. & Hatzimanikatis, V. Thermodynamics-Based Metabolic Flux Analysis. Biophys. J. 92, 1792-1805 (2007).
-
(2007)
Biophys. J
, vol.92
, pp. 1792-1805
-
-
Henry, C.S.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
30
-
-
84861429699
-
Quilibrator-the biochemical thermodynamics calculator
-
Flamholz, A., Noor, E., Bar-Even, A. & Milo, R. eQuilibrator-the biochemical thermodynamics calculator. Nucleic. Acids. Res. 40, D770-D775; DOI:10.1093/nar/gkr874 (2012).
-
(2012)
Nucleic. Acids. Res
, vol.40
, pp. D770-D775
-
-
Flamholz, A.1
Noor, E.2
Bar-Even, A.3
Milo, R.4
-
31
-
-
84947909628
-
Double description method revisited
-
Manoussakis I. (ed.) (Springer, Berlin/Heidelberg)
-
Fukuda, K. & Prodon, A. Double description method revisited. In Combinatorics and Computer Science, Manoussakis, I. (ed.), 91-111; (Springer, Berlin/Heidelberg) 1996.
-
(1996)
Combinatorics and Computer Science
, pp. 91-111
-
-
Fukuda, K.1
Prodon, A.2
-
32
-
-
0028129875
-
Why does Escherichia coli have two primary pathways for synthesis of glutamate?
-
Helling, R. B. Why does Escherichia coli have two primary pathways for synthesis of glutamate? J. Bacteriol. 176, 4664-4668 (1994).
-
(1994)
J Bacteriol
, vol.176
, pp. 4664-4668
-
-
Helling, R.B.1
-
33
-
-
0031752273
-
Pathway Choice in Glutamate Synthesis inEscherichia coli
-
Helling, R. B. Pathway Choice in Glutamate Synthesis inEscherichia coli. J. Bacteriol. 180, 4571-4575 (1998).
-
(1998)
J. Bacteriol
, vol.180
, pp. 4571-4575
-
-
Helling, R.B.1
-
35
-
-
33746083686
-
Quantitative elementary mode analysis of metabolic path-ways: The example of yeast glycolysis
-
Schwartz, J.-M. & Kanehisa, M. Quantitative elementary mode analysis of metabolic path-ways: the example of yeast glycolysis. BMC Bioinformatics 7, 1-20; DOI:10.1186/1471-2105-7-186 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 1-20
-
-
Schwartz, J.-M.1
Kanehisa, M.2
-
36
-
-
84880997617
-
Selection of human tissue-specific elementary flux modes using gene expression data
-
Rezola, A. et al. Selection of human tissue-specific elementary flux modes using gene expression data. Bioinformatics 29, 2009-2016; DOI:10.1093/bioinformatics/btt328 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 2009-2016
-
-
Rezola, A.1
-
37
-
-
84880341305
-
Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models
-
Hamilton, J. J., Dwivedi, V. & Reed, J. L. Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models. Biophys. J. 105, 512-522; DOI:10.1016/j.bpj.2013.06.011 (2013).
-
(2013)
Biophys. J
, vol.105
, pp. 512-522
-
-
Hamilton, J.J.1
Dwivedi, V.2
Reed, J.L.3
-
38
-
-
36248990302
-
Including metabolite concentrations into flux balance analysis: Thermodynamic realizability as a constraint on flux distributions in metabolic networks
-
Hoppe, A., Hoffmann, S. & Holzhütter, H.-G. Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMC Syst. Biol. 1, 23; DOI:10.1186/1752-0509-1-23 (2007).
-
(2007)
BMC Syst. Biol
, vol.1
, pp. 23
-
-
Hoppe, A.1
Hoffmann, S.2
Holzhütter, H.-G.3
-
40
-
-
80155143484
-
Metabolic network analysis of perfused livers under fed and fasted states: Incorporating thermodynamic and futile-cycle-associated regulatory constraints
-
Orman, M. A., Androulakis, I. P., Berthiaume, F. & Ierapetritou, M. G.Metabolic network analysis of perfused livers under fed and fasted states: Incorporating thermodynamic and futile-cycle-associated regulatory constraints. J. Theor. Biol. 293, 101-110; DOI:10.1016/j.jtbi.2011.10.019 (2012).
-
(2012)
J. Theor. Biol
, vol.293
, pp. 101-110
-
-
Orman, M.A.1
Androulakis, I.P.2
Berthiaume, F.3
Ierapetritou, M.G.4
-
41
-
-
79961245535
-
Analysis of amino acid supplementation effects on hepatocyte cultures using flux balance analysis
-
Yang, H., Roth, C. M. & Ierapetritou, M. G. Analysis of Amino Acid Supplementation Effects on Hepatocyte Cultures Using Flux Balance Analysis. OMICS 15, 449-460; DOI:10.1089/omi.2010.0070 (2011).
-
(2011)
OMICS
, vol.15
, pp. 449-460
-
-
Yang, H.1
Roth, C.M.2
Ierapetritou, M.G.3
-
42
-
-
77951109180
-
Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design
-
Boghigian, B. A., Shi, H., Lee, K. & Pfeifer, B. A. Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design. BMC Syst. Biol. 4, 49; DOI:10.1186/1752-0509-4-49 (2010).
-
(2010)
BMC Syst. Biol
, vol.4
, pp. 49
-
-
Boghigian, B.A.1
Shi, H.2
Lee, K.3
Pfeifer, B.A.4
-
43
-
-
77957225963
-
Effects of glucose and insulin on HepG2-C3A cell metabolism
-
Iyer, V. V., Yang, H., Ierapetritou, M. G. & Roth, C. M. Effects of glucose and insulin on HepG2-C3A cell metabolism. Biotechnol. Bioeng. 107, 347-356; DOI:10.1002/bit.22799 (2010).
-
(2010)
Biotechnol. Bioeng.
, vol.107
, pp. 347-356
-
-
Iyer, V.V.1
Yang, H.2
Ierapetritou, M.G.3
Roth, C.M.4
-
44
-
-
84880781653
-
Consistent estimation of gibbs energy using component contributions
-
Noor, E., Haraldsdóttir, H. S., Milo, R. & Fleming, R. M. T. Consistent estimation of gibbs energy using component contributions. PLoS Comput. Biol. 9, e1003098; DOI:10.1371/journal.pcbi.1003098 (2013).
-
(2013)
PLoS Comput. Biol
, vol.9
, pp. e1003098
-
-
Noor, E.1
Haraldsdóttir, H.S.2
Milo, R.3
Fleming, R.M.T.4
-
45
-
-
34247612307
-
Multiple high-throughput analyses monitor the response of E. Coli to perturbations
-
Ishii, N. et al. Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations. Science 316, 593-597 (2007).
-
(2007)
Science
, vol.316
, pp. 593-597
-
-
Ishii, N.1
-
46
-
-
78649281194
-
Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks
-
Jol, S. J., Kümmel, A., Hatzimanikatis, V., Beard, D. A. & Heinemann, M. Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks. Biophys. J. 99, 3139-3144; DOI:10.1016/j.bpj.2010.09.043 (2010).
-
(2010)
Biophys. J.
, vol.99
, pp. 3139-3144
-
-
Jol, S.J.1
Kümmel, A.2
Hatzimanikatis, V.3
Beard, D.A.4
Heinemann, M.5
|