-
2
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist A.M., Herrgard M.J., Thiele I., Reed J.L., Palsson B.O. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 2009, 7:129-143.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.O.5
-
3
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele I., Palsson B.O. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 2010, 5:93-121.
-
(2010)
Nat Protoc
, vol.5
, pp. 93-121
-
-
Thiele, I.1
Palsson, B.O.2
-
4
-
-
78651286166
-
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
-
Blake J.A., Bult C.J., Kadin J.A., Richardson J.E., Eppig J.T., Mouse Genome Database G. The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res 2011, 39:D842-D848.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Blake, J.A.1
Bult, C.J.2
Kadin, J.A.3
Richardson, J.E.4
Eppig, J.T.5
Mouse Genome Database, G.6
-
5
-
-
58449106341
-
Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism
-
Grafahrend-Belau E., Schreiber F., Koschuetzki D., Junker B.H. Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol 2009, 149:585-598.
-
(2009)
Plant Physiol
, vol.149
, pp. 585-598
-
-
Grafahrend-Belau, E.1
Schreiber, F.2
Koschuetzki, D.3
Junker, B.H.4
-
6
-
-
44949247269
-
Dynamic analysis of integrated signaling, metabolic, and regulatory networks
-
Lee J.M., Gianchandani E.P., Eddy J.A., Papin J.A. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput Biol 2008, 4.
-
(2008)
PLoS Comput Biol
, pp. 4
-
-
Lee, J.M.1
Gianchandani, E.P.2
Eddy, J.A.3
Papin, J.A.4
-
7
-
-
76749149000
-
Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation
-
Meadows A.L., Karnik R., Lam H., Forestell S., Snedecor B. Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation. Metab Eng 2010, 12:150-160.
-
(2010)
Metab Eng
, vol.12
, pp. 150-160
-
-
Meadows, A.L.1
Karnik, R.2
Lam, H.3
Forestell, S.4
Snedecor, B.5
-
8
-
-
57749200993
-
Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue
-
Coquin L., Feala J.D., McCulloch A.D., Paternostro G. Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue. Mol Syst Biol 2008, 4.
-
(2008)
Mol Syst Biol
, pp. 4
-
-
Coquin, L.1
Feala, J.D.2
McCulloch, A.D.3
Paternostro, G.4
-
9
-
-
71049135169
-
Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysis
-
Feala J.D., Coquin L., Zhou D., Haddad G.G., Paternostro G., McCulloch A.D. Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysis. BMC Syst Biol 2009, 3.
-
(2009)
BMC Syst Biol
, pp. 3
-
-
Feala, J.D.1
Coquin, L.2
Zhou, D.3
Haddad, G.G.4
Paternostro, G.5
McCulloch, A.D.6
-
10
-
-
77957260797
-
Why does yeast ferment? A flux balance analysis study
-
Simeonidis E., Murabito E., Smallbone K., Westerhoff H.V. Why does yeast ferment? A flux balance analysis study. Biochem Soc Trans 2010, 38:1225-1229.
-
(2010)
Biochem Soc Trans
, vol.38
, pp. 1225-1229
-
-
Simeonidis, E.1
Murabito, E.2
Smallbone, K.3
Westerhoff, H.V.4
-
11
-
-
77049084742
-
Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models
-
Jamshidi N., Palsson B.O. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. Biophys J 2010, 98:175-185.
-
(2010)
Biophys J
, vol.98
, pp. 175-185
-
-
Jamshidi, N.1
Palsson, B.O.2
-
12
-
-
79956206621
-
'Closing the loop' in biological systems modeling-from the in silico to the in vitro
-
Kiparissides A., Koutinas M., Kontoravdi C., Mantalaris A., Pistikopoulos E.N. 'Closing the loop' in biological systems modeling-from the in silico to the in vitro. Automatica 2011, 47:1147-1155.
-
(2011)
Automatica
, vol.47
, pp. 1147-1155
-
-
Kiparissides, A.1
Koutinas, M.2
Kontoravdi, C.3
Mantalaris, A.4
Pistikopoulos, E.N.5
-
13
-
-
58149460015
-
Effective quenching processes for physiologically valid metabolite profiling of suspension cultured mammalian cells
-
Sellick C.A., Hansen R., Maqsood A.R., Dunn W.B., Stephens G.M., Goodacre R., Dickson A.J. Effective quenching processes for physiologically valid metabolite profiling of suspension cultured mammalian cells. Anal Chem 2009, 81:174-183.
-
(2009)
Anal Chem
, vol.81
, pp. 174-183
-
-
Sellick, C.A.1
Hansen, R.2
Maqsood, A.R.3
Dunn, W.B.4
Stephens, G.M.5
Goodacre, R.6
Dickson, A.J.7
-
14
-
-
77954457415
-
Towards quantitative metabolomics of mammalian cells: development of a metabolite extraction protocol
-
Dietmair S., Timmins N.E., Gray P.P., Nielsen L.K., Kromer J.O. Towards quantitative metabolomics of mammalian cells: development of a metabolite extraction protocol. Anal Biochem 2010, 404:155-164.
-
(2010)
Anal Biochem
, vol.404
, pp. 155-164
-
-
Dietmair, S.1
Timmins, N.E.2
Gray, P.P.3
Nielsen, L.K.4
Kromer, J.O.5
-
15
-
-
77956417789
-
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
-
Jerby L., Shlomi T., Ruppin E. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 2010, 6.
-
(2010)
Mol Syst Biol
, pp. 6
-
-
Jerby, L.1
Shlomi, T.2
Ruppin, E.3
-
16
-
-
77956333400
-
Systematic integration of experimental data and models in systems biology
-
Li P., Dada J.O., Jameson D., Spasic I., Swainston N., Carroll K., Dunn W., Khan F., Malys N., Messiha H.L., et al. Systematic integration of experimental data and models in systems biology. BMC Bioinform 2010, 11.
-
(2010)
BMC Bioinform
, pp. 11
-
-
Li, P.1
Dada, J.O.2
Jameson, D.3
Spasic, I.4
Swainston, N.5
Carroll, K.6
Dunn, W.7
Khan, F.8
Malys, N.9
Messiha, H.L.10
-
17
-
-
78349239648
-
An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models
-
Barua D., Kim J., Reed J.L. An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models. PLoS Comput Biol 2010, 6:e1000970.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Barua, D.1
Kim, J.2
Reed, J.L.3
-
18
-
-
79959687662
-
An integrated approach to characterize genetic interaction networks in yeast metabolism
-
656-U182
-
Szappanos B., Kovacs K., Szamecz B., Honti F., Costanzo M., Baryshnikova A., Gelius-Dietrich G., Lercher M.J., Jelasity M., Myers C.L., et al. An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet 2011, 43. 656-U182.
-
(2011)
Nat Genet
, vol.43
-
-
Szappanos, B.1
Kovacs, K.2
Szamecz, B.3
Honti, F.4
Costanzo, M.5
Baryshnikova, A.6
Gelius-Dietrich, G.7
Lercher, M.J.8
Jelasity, M.9
Myers, C.L.10
-
19
-
-
78049255973
-
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
-
Chandrasekaran S., Price N.D. Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci USA 2010, 107:17845-17850.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 17845-17850
-
-
Chandrasekaran, S.1
Price, N.D.2
-
20
-
-
77951612556
-
BiGG: a biochemical genetic and genomic knowledge base of large scale metabolic reconstructions
-
Schellenberger J., Park J.O., Conrad T.M., Palsson B.O. BiGG: a biochemical genetic and genomic knowledge base of large scale metabolic reconstructions. BMC Bioinform 2010, 11:213.
-
(2010)
BMC Bioinform
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson, B.O.4
-
21
-
-
77953934646
-
BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models
-
Li C., Donizelli M., Rodriguez N., Dharuri H., Endler L., Chelliah V., Li L., He E., Henry A., Stefan M.I., et al. BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010, 4.
-
(2010)
BMC Syst Biol
, pp. 4
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.8
Henry, A.9
Stefan, M.I.10
-
22
-
-
77957687260
-
Mathematical modeling of monolignol biosynthesis in Populus xylem
-
Lee Y., Voit E.O. Mathematical modeling of monolignol biosynthesis in Populus xylem. Math Biosci 2010, 228:78-89.
-
(2010)
Math Biosci
, vol.228
, pp. 78-89
-
-
Lee, Y.1
Voit, E.O.2
-
23
-
-
66249096326
-
Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae
-
Hjersted J.L., Henson M.A. Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae. IET Syst Biol 2009, 3:167-179.
-
(2009)
IET Syst Biol
, vol.3
, pp. 167-179
-
-
Hjersted, J.L.1
Henson, M.A.2
-
25
-
-
77952797285
-
Streamlining the construction of large-scale dynamic models using generic kinetic equations
-
Adiamah D.A., Handl J., Schwartz J.-M. Streamlining the construction of large-scale dynamic models using generic kinetic equations. Bioinformatics 2010, 26:1324-1331.
-
(2010)
Bioinformatics
, vol.26
, pp. 1324-1331
-
-
Adiamah, D.A.1
Handl, J.2
Schwartz, J.-M.3
-
26
-
-
77954196484
-
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
-
Liebermeister W., Uhlendorf J., Klipp E. Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation. Bioinformatics 2010, 26:1528-1534.
-
(2010)
Bioinformatics
, vol.26
, pp. 1528-1534
-
-
Liebermeister, W.1
Uhlendorf, J.2
Klipp, E.3
-
27
-
-
58149156532
-
Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws-a promising method for speeding up the kinetic modelling of complex metabolic networks
-
Bulik S., Grimbs S., Huthmacher C., Selbig J., Holzhuetter H.G. Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws-a promising method for speeding up the kinetic modelling of complex metabolic networks. Febs J 2009, 276:410-424.
-
(2009)
Febs J
, vol.276
, pp. 410-424
-
-
Bulik, S.1
Grimbs, S.2
Huthmacher, C.3
Selbig, J.4
Holzhuetter, H.G.5
-
28
-
-
77649176477
-
Towards a genome-scale kinetic model of cellular metabolism
-
Smallbone K., Simeonidis E., Swainston N., Mendes P. Towards a genome-scale kinetic model of cellular metabolism. BMC Syst Biol 2010, 4:6.
-
(2010)
BMC Syst Biol
, vol.4
, pp. 6
-
-
Smallbone, K.1
Simeonidis, E.2
Swainston, N.3
Mendes, P.4
-
29
-
-
79959406807
-
-
Berthoumieux S., Brilli M., de Jong H., Kahn D., Cinquemani E. Bioinformatics 2011, 27:i186-i195.
-
(2011)
Bioinformatics
, vol.27
-
-
Berthoumieux, S.1
Brilli, M.2
de Jong, H.3
Kahn, D.4
Cinquemani, E.5
-
30
-
-
78650525718
-
Dynamic model of CHO cell metabolism
-
Nolan R.P., Lee K. Dynamic model of CHO cell metabolism. Metab Eng 2011, 13:108124.
-
(2011)
Metab Eng
, vol.13
, pp. 108124
-
-
Nolan, R.P.1
Lee, K.2
-
31
-
-
79957618816
-
Construction of kinetic models for metabolic reaction networks: Lessons learned in analysing short-term stimulus response data
-
Nikerel I.E., Canelas A.B., Jol S.J., Verheijen P.J.T., Heijnen J.J. Construction of kinetic models for metabolic reaction networks: Lessons learned in analysing short-term stimulus response data. Math Computer Model Dyn Syst 2011, 17:243.
-
(2011)
Math Computer Model Dyn Syst
, vol.17
, pp. 243
-
-
Nikerel, I.E.1
Canelas, A.B.2
Jol, S.J.3
Verheijen, P.J.T.4
Heijnen, J.J.5
-
32
-
-
79955137362
-
An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data
-
Canelas A.B., Ras C., ten Pierick A., van Gulik W.M., Heijnen J.J. An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data. Metab Eng 2011, 13:294-306.
-
(2011)
Metab Eng
, vol.13
, pp. 294-306
-
-
Canelas, A.B.1
Ras, C.2
ten Pierick, A.3
van Gulik, W.M.4
Heijnen, J.J.5
-
33
-
-
47949099328
-
CellDesigner 3.5: a versatile modeling tool for biochemical networks
-
Funahashi A., Matsuoka Y., Jouraku A., Morohashi M., Kikuchi N., Kitano H. CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proc IEEE 2008, 96:1254.
-
(2008)
Proc IEEE
, vol.96
, pp. 1254
-
-
Funahashi, A.1
Matsuoka, Y.2
Jouraku, A.3
Morohashi, M.4
Kikuchi, N.5
Kitano, H.6
-
34
-
-
84856481385
-
-
SimBiology©: Version 3.4. The Mathworks, Inc.; 2011 (R2011a).
-
SimBiology©: Version 3.4. The Mathworks, Inc.; 2011 (R2011a).
-
(2011)
-
-
-
35
-
-
65649138437
-
Computational modeling of biochemical networks using COPASI
-
Mendes P., Hoops S., Sahle S., Gauges R., Dada J., Kummer U. Computational modeling of biochemical networks using COPASI. Methods Mol Biol 2009, 500:17-59.
-
(2009)
Methods Mol Biol
, vol.500
, pp. 17-59
-
-
Mendes, P.1
Hoops, S.2
Sahle, S.3
Gauges, R.4
Dada, J.5
Kummer, U.6
-
36
-
-
79953279638
-
Systems biology: the next frontier for bioinformatics
-
Likic V.A., McConville M.J., Lithgow T., Bacic A. Systems biology: the next frontier for bioinformatics. Adv Bioinform 2010, 2010:10.
-
(2010)
Adv Bioinform
, vol.2010
, pp. 10
-
-
Likic, V.A.1
McConville, M.J.2
Lithgow, T.3
Bacic, A.4
-
37
-
-
84856481387
-
-
Nature Publishing Group
-
Bordbar A., Feist A., Palsson B., Hyduke D., Zielinski D., Thiele I., Schellenberger J., Orth J., Kang J., Lewis N., et al. COBRA Toolbox 2.0. Protocol Exchange 2011, Nature Publishing Group.
-
(2011)
COBRA Toolbox 2.0. Protocol Exchange
-
-
Bordbar, A.1
Feist, A.2
Palsson, B.3
Hyduke, D.4
Zielinski, D.5
Thiele, I.6
Schellenberger, J.7
Orth, J.8
Kang, J.9
Lewis, N.10
-
38
-
-
78650541419
-
Von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
-
Fleming R.M.T., Thiele I. von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics 2011, 27:142-143.
-
(2011)
Bioinformatics
, vol.27
, pp. 142-143
-
-
Fleming, R.M.T.1
Thiele, I.2
-
39
-
-
77953887264
-
Arcadia: a visualization tool for metabolic pathways
-
Villéger A.C., Pettifer S.R., Kell D.B. Arcadia: a visualization tool for metabolic pathways. Bioinformatics 2010, 26:1470-1471.
-
(2010)
Bioinformatics
, vol.26
, pp. 1470-1471
-
-
Villéger, A.C.1
Pettifer, S.R.2
Kell, D.B.3
-
40
-
-
77956511014
-
MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format
-
Forth T., McConkey G.A., Westhead D.R. MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format. Bioinformatics 2010, 26:2352-2353.
-
(2010)
Bioinformatics
, vol.26
, pp. 2352-2353
-
-
Forth, T.1
McConkey, G.A.2
Westhead, D.R.3
-
41
-
-
79551582182
-
A command line tool and graphics user interface for constraint based modelling of genome scale metabolic reaction networks
-
Gevorgyan A., Bushell M.E., Avignone-Rossa C., Kierzek A.M., Surrey F.B.A. A command line tool and graphics user interface for constraint based modelling of genome scale metabolic reaction networks. Bioinformatics 2010, 27:433-434.
-
(2010)
Bioinformatics
, vol.27
, pp. 433-434
-
-
Gevorgyan, A.1
Bushell, M.E.2
Avignone-Rossa, C.3
Kierzek, A.M.4
Surrey, F.B.A.5
-
42
-
-
79952789318
-
An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228
-
Liao Y.C., Huang T.W., Chen F.C., Charusanti P., Hong J.S.J., Chang H.Y., Tsai S.F., Palsson B.O., Hsiung C.A. An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. J Bacteriol 2011, 193:1710-1717.
-
(2011)
J Bacteriol
, vol.193
, pp. 1710-1717
-
-
Liao, Y.C.1
Huang, T.W.2
Chen, F.C.3
Charusanti, P.4
Hong, J.S.J.5
Chang, H.Y.6
Tsai, S.F.7
Palsson, B.O.8
Hsiung, C.A.9
-
43
-
-
77954743150
-
Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production
-
Sohn S.B., Graf A.B., Kim T.Y., Gasser B., Maurer M., Ferrer P., Mattanovich D., Lee S.Y. Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production. Biotechnol J 2010, 5:705-715.
-
(2010)
Biotechnol J
, vol.5
, pp. 705-715
-
-
Sohn, S.B.1
Graf, A.B.2
Kim, T.Y.3
Gasser, B.4
Maurer, M.5
Ferrer, P.6
Mattanovich, D.7
Lee, S.Y.8
-
44
-
-
77955534569
-
Integration of metabolic databases for the reconstruction of genome-scale metabolic networks
-
Radrich K., Tsuruoka Y., Dobson P., Gevorgyan A., Swainston N., Baart G., Schwartz J.-M. Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. BMC Syst Biol 2010, 4.
-
(2010)
BMC Syst Biol
, pp. 4
-
-
Radrich, K.1
Tsuruoka, Y.2
Dobson, P.3
Gevorgyan, A.4
Swainston, N.5
Baart, G.6
Schwartz, J.-M.7
-
45
-
-
72949118860
-
Genome-scale modeling and in silico analysis of mouse cell metabolic network
-
Selvarasu S., Karimi I.A., Ghim G.H., Lee D.Y. Genome-scale modeling and in silico analysis of mouse cell metabolic network. Mol BioSystems 2009, 6:152.
-
(2009)
Mol BioSystems
, vol.6
, pp. 152
-
-
Selvarasu, S.1
Karimi, I.A.2
Ghim, G.H.3
Lee, D.Y.4
-
46
-
-
66349098682
-
Update of the LIPID MAPS comprehensive classification system for lipids
-
Fahy E., Subramaniam S., Murphy R.C., Nishijima M., Raetz C.R.H., Shimizu T., Spener F., van Meer G., Wakelam M.J.O., Dennis E.A. Update of the LIPID MAPS comprehensive classification system for lipids. J Lipid Res 2009, 50:S9-S14.
-
(2009)
J Lipid Res
, vol.50
-
-
Fahy, E.1
Subramaniam, S.2
Murphy, R.C.3
Nishijima, M.4
Raetz, C.R.H.5
Shimizu, T.6
Spener, F.7
van Meer, G.8
Wakelam, M.J.O.9
Dennis, E.A.10
-
47
-
-
58149202163
-
HMDB: a knowledgebase for the human metabolome
-
Wishart D.S., Knox C., Guo A.C., Eisner R., Young N., Gautam B., Hau D.D., Psychogios N., Dong E., Bouatra S., et al. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 2009, 37:D603-D610.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Wishart, D.S.1
Knox, C.2
Guo, A.C.3
Eisner, R.4
Young, N.5
Gautam, B.6
Hau, D.D.7
Psychogios, N.8
Dong, E.9
Bouatra, S.10
-
48
-
-
84856477798
-
-
Nature Pub. Group
-
Ma H., Sorokin A., Mazein A., Selkov A., Selkov E., Demin O., Goryanin I. The Edinburgh Human Metabolic Network Reconstruction and its Functional Analysis 2007, Nature Pub. Group.
-
(2007)
The Edinburgh Human Metabolic Network Reconstruction and its Functional Analysis
-
-
Ma, H.1
Sorokin, A.2
Mazein, A.3
Selkov, A.4
Selkov, E.5
Demin, O.6
Goryanin, I.7
|