-
1
-
-
34147174000
-
Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling
-
Bundy J.G., Papp B., Harmston R., Browne R.A., Clayson E.M., Burton N., Reece R.J., Oliver S.G., Brindle K.M. Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling. Genome Res. 2007, 17:510-519.
-
(2007)
Genome Res.
, vol.17
, pp. 510-519
-
-
Bundy, J.G.1
Papp, B.2
Harmston, R.3
Browne, R.A.4
Clayson, E.M.5
Burton, N.6
Reece, R.J.7
Oliver, S.G.8
Brindle, K.M.9
-
2
-
-
1242274402
-
Flux coupling analysis of genome-scale metabolic network reconstructions
-
Burgard A.P., Nikolaev E.V., Schilling C.H., Maranas C.D. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 2004, 14:301-312.
-
(2004)
Genome Res.
, vol.14
, pp. 301-312
-
-
Burgard, A.P.1
Nikolaev, E.V.2
Schilling, C.H.3
Maranas, C.D.4
-
3
-
-
8844231118
-
Metabolic pathway analysis of enzyme-deficient human red blood cells
-
Cakir T., Tacer C.S., Ulgen K.O. Metabolic pathway analysis of enzyme-deficient human red blood cells. BioSystems 2004, 78:49-67.
-
(2004)
BioSystems
, vol.78
, pp. 49-67
-
-
Cakir, T.1
Tacer, C.S.2
Ulgen, K.O.3
-
4
-
-
58049211936
-
Erratum: can sugars be produced from fatty acids? A test case for pathway analysis tools
-
de Figueiredo L.F., Schuster S., Kaleta C., Fell D.A. Erratum: can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics 2009, 25:152-158.
-
(2009)
Bioinformatics
, vol.25
, pp. 152-158
-
-
de Figueiredo, L.F.1
Schuster, S.2
Kaleta, C.3
Fell, D.A.4
-
5
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist A., Herrgard M., Thiele I., Reed J., Palsson B. Reconstruction of biochemical networks in microorganisms. Nat. Rev. Microbiol. 2009, 7:129-143.
-
(2009)
Nat. Rev. Microbiol.
, vol.7
, pp. 129-143
-
-
Feist, A.1
Herrgard, M.2
Thiele, I.3
Reed, J.4
Palsson, B.5
-
6
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist A.M., Henry C.S., Reed J.L., Krummenacker M., Joyce A.R., Karp P.D., Broadbelt L.J., Hatzimanikatis V., Palsson B.O. 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.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, B.O.9
-
7
-
-
45149111660
-
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
-
Feist A.M., Palsson B.O. 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
-
8
-
-
0022493181
-
Fat synthesis in adipose tissue, an examination of stoichiometric constraints
-
Fell D.A., Small J.R. Fat synthesis in adipose tissue, an examination of stoichiometric constraints. Biochem. J. 1986, 238:781-786.
-
(1986)
Biochem. J.
, vol.238
, pp. 781-786
-
-
Fell, D.A.1
Small, J.R.2
-
9
-
-
58449106341
-
Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism
-
Grafahrend-Belau E., Schreiber F., Koschützki 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
Koschützki, D.3
Junker, B.H.4
-
11
-
-
0029002581
-
Composite control of cell function: metabolic pathways behaving as single control units
-
Kholodenko B.N., Schuster S., Rohwer J.M., Cascante M., Westerhoff H.V. Composite control of cell function: metabolic pathways behaving as single control units. FEBS Lett. 1995, 368:1-4.
-
(1995)
FEBS Lett.
, vol.368
, pp. 1-4
-
-
Kholodenko, B.N.1
Schuster, S.2
Rohwer, J.M.3
Cascante, M.4
Westerhoff, H.V.5
-
12
-
-
1042269472
-
Minimal cut sets in biochemical reaction networks
-
Klamt S., Gilles E.D. Minimal cut sets in biochemical reaction networks. Bioinformatics 2004, 20:226-234.
-
(2004)
Bioinformatics
, vol.20
, pp. 226-234
-
-
Klamt, S.1
Gilles, E.D.2
-
13
-
-
34447551397
-
Structural and functional analysis of cellular networks with CellNetAnalyzer
-
Klamt S., Saez-Rodriguez J., Gilles E.D. Structural and functional analysis of cellular networks with CellNetAnalyzer. 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
-
14
-
-
0036039060
-
Combinatorial complexity of pathway analysis in metabolic networks
-
Klamt S., Stelling J. Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep. 2002, 29:233-236.
-
(2002)
Mol. Biol. Rep.
, vol.29
, pp. 233-236
-
-
Klamt, S.1
Stelling, J.2
-
15
-
-
0037308505
-
Two approaches for metabolic pathway analysis?
-
Klamt S., Stelling J.O. Two approaches for metabolic pathway analysis?. Trends Biotechnol. 2003, 21(2):64-69.
-
(2003)
Trends Biotechnol.
, vol.21
, Issue.2
, pp. 64-69
-
-
Klamt, S.1
Stelling, J.O.2
-
16
-
-
33750401814
-
A new approach to flux coupling analysis of metabolic networks
-
Larhlimi A., Bockmayr A. A new approach to flux coupling analysis of metabolic networks. Lect. Notes Comput. Sci. 2006, 4216:205-215.
-
(2006)
Lect. Notes Comput. Sci.
, vol.4216
, pp. 205-215
-
-
Larhlimi, A.1
Bockmayr, A.2
-
17
-
-
48249158278
-
The implications of human metabolic network topology for disease comorbidity
-
Lee D.S., Park J., Kay K.A., Christakis N.A., Oltvai Z.N., Barabasi A.L. The implications of human metabolic network topology for disease comorbidity. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:9880-9885.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 9880-9885
-
-
Lee, D.S.1
Park, J.2
Kay, K.A.3
Christakis, N.A.4
Oltvai, Z.N.5
Barabasi, A.L.6
-
18
-
-
0030571222
-
Pathway analysis, engineering, and physiological considerations for redirecting central metabolism
-
Liao J.C., Hou S.Y., Chao Y.P. Pathway analysis, engineering, and physiological considerations for redirecting central metabolism. Biotechnol. Bioeng. 1996, 52:129-140.
-
(1996)
Biotechnol. Bioeng.
, vol.52
, pp. 129-140
-
-
Liao, J.C.1
Hou, S.Y.2
Chao, Y.P.3
-
19
-
-
57849094907
-
Understanding human metabolic physiology: a genome-to-systems approach
-
Mo M.L., Palsson B.O. Understanding human metabolic physiology: a genome-to-systems approach. Trends Biotechnol. 2009, 27:37-44.
-
(2009)
Trends Biotechnol.
, vol.27
, pp. 37-44
-
-
Mo, M.L.1
Palsson, B.O.2
-
21
-
-
38949157812
-
Co-regulation of metabolic genes is better explained by flux coupling than by network distance
-
Notebaart R.A., Teusink B., Siezen R.J., Papp B. Co-regulation of metabolic genes is better explained by flux coupling than by network distance. PLoS Comput. Biol. 2008, 4:e26.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Notebaart, R.A.1
Teusink, B.2
Siezen, R.J.3
Papp, B.4
-
22
-
-
28444475529
-
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
-
Pal C., Papp B., Lercher M.J. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 2005, 37:1372-1375.
-
(2005)
Nat. Genet.
, vol.37
, pp. 1372-1375
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
23
-
-
27544449355
-
Horizontal gene transfer depends on gene content of the host
-
Pal C., Papp B., Lercher M.J. Horizontal gene transfer depends on gene content of the host. Bioinformatics 2005, 21:ii222-ii223.
-
(2005)
Bioinformatics
, vol.21
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
25
-
-
0036916269
-
Extreme pathway lengths and reaction participation in genome-scale metabolic networks
-
Papin J.A., Price N.D., Palsson B.O. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res. 2002, 12:1889-1900.
-
(2002)
Genome Res.
, vol.12
, pp. 1889-1900
-
-
Papin, J.A.1
Price, N.D.2
Palsson, B.O.3
-
26
-
-
8544223537
-
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks
-
Papin J.A., Reed J.L., Palsson B.O. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem. Sci. 2004, 29:641-647.
-
(2004)
Trends Biochem. Sci.
, vol.29
, pp. 641-647
-
-
Papin, J.A.1
Reed, J.L.2
Palsson, B.O.3
-
27
-
-
0344052685
-
METATOOL: for studying metabolic networks
-
Pfeiffer T., Sanchez-Valdenebro I., Nuno J.C., Montero F., Schuster S. METATOOL: for studying metabolic networks. Bioinformatics 1999, 15:251-257.
-
(1999)
Bioinformatics
, vol.15
, pp. 251-257
-
-
Pfeiffer, T.1
Sanchez-Valdenebro, I.2
Nuno, J.C.3
Montero, F.4
Schuster, S.5
-
28
-
-
0037317848
-
Elementary modes analysis of photosynthate metabolism in the chloroplast stroma
-
Poolman M.G., Fell D.A., Raines C.A. Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. Eur. J. Biochem. 2003, 270:430-439.
-
(2003)
Eur. J. Biochem.
, vol.270
, pp. 430-439
-
-
Poolman, M.G.1
Fell, D.A.2
Raines, C.A.3
-
30
-
-
0037385718
-
Genome-scale microbial in silico models: the constraints-based approach
-
Price N.D., Papin J.A., Schilling C.H., Palsson B.O. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 2003, 21:162-169.
-
(2003)
Trends Biotechnol.
, vol.21
, pp. 162-169
-
-
Price, N.D.1
Papin, J.A.2
Schilling, C.H.3
Palsson, B.O.4
-
31
-
-
55449096123
-
Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
-
Puchalka J., Oberhardt M.A., Godinho M., Bielecka A., Regenhardt D., Timmis K.N., Papin J.A., Martins Dos Santos V.A.P. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput. Biol. 2008, 4:e1000210.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Puchalka, J.1
Oberhardt, M.A.2
Godinho, M.3
Bielecka, A.4
Regenhardt, D.5
Timmis, K.N.6
Papin, J.A.7
Martins Dos Santos, V.A.P.8
-
32
-
-
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.O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 2003, 4:R54.
-
(2003)
Genome Biol.
, vol.4
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.O.4
-
33
-
-
0034615791
-
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
-
Schilling C.H., Letscher D., Palsson B.O. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 2000, 203:229-248.
-
(2000)
J. Theor. Biol.
, vol.203
, pp. 229-248
-
-
Schilling, C.H.1
Letscher, D.2
Palsson, B.O.3
-
34
-
-
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. Biotechnol. 2000, 18:326-332.
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
35
-
-
0000029295
-
On elementary flux modes in biochemical reaction systems at steady state
-
Schuster S., Hilgetag C. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 1994, 2:165-182.
-
(1994)
J. Biol. Syst.
, vol.2
, pp. 165-182
-
-
Schuster, S.1
Hilgetag, C.2
-
36
-
-
0035725112
-
Use of network analysis of metabolic systems in bioengineering
-
Schuster S., Klamt S., Weckwerth W., Moldenhauer F., Pfeiffer T. Use of network analysis of metabolic systems in bioengineering. Bioprocess Biosyst. Eng. 2001, 24:363-372.
-
(2001)
Bioprocess Biosyst. Eng.
, vol.24
, pp. 363-372
-
-
Schuster, S.1
Klamt, S.2
Weckwerth, W.3
Moldenhauer, F.4
Pfeiffer, T.5
-
37
-
-
61449254451
-
Principles of transcriptional regulation and evolution of the metabolic system in E. coli.
-
Seshasayee A.S.N., Fraser G.M., Babu M.M., Luscombe N.M. Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res. 2009, 19:79-91.
-
(2009)
Genome Res.
, vol.19
, pp. 79-91
-
-
Seshasayee, A.S.N.1
Fraser, G.M.2
Babu, M.M.3
Luscombe, N.M.4
-
38
-
-
76749140314
-
Improved computational performance of MFA using elementary metabolite units and flux coupling
-
Suthers P.F., Chang Y.J., Maranas C.D. Improved computational performance of MFA using elementary metabolite units and flux coupling. Metabolic Eng. 2010, 12:123-128.
-
(2010)
Metabolic Eng.
, vol.12
, pp. 123-128
-
-
Suthers, P.F.1
Chang, Y.J.2
Maranas, C.D.3
-
39
-
-
61449115916
-
A genome-scale metabolic reconstruction of Mycoplasma genitalium, i PS189
-
Suthers P.F., Dasika M.S., Kumar V.S., Denisov G., Glass J.I., Maranas C.D. A genome-scale metabolic reconstruction of Mycoplasma genitalium, i PS189. PLoS Comput. Biol. 2009, 5:e1000285.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Suthers, P.F.1
Dasika, M.S.2
Kumar, V.S.3
Denisov, G.4
Glass, J.I.5
Maranas, C.D.6
-
40
-
-
77956048572
-
Genome-scale metabolic networks
-
Terzer M., Maynard N.D., Covert M.W., Stelling J. Genome-scale metabolic networks. WIREs Syst. Biol. Med. 2009, 1:285-297.
-
(2009)
WIREs Syst. Biol. Med.
, vol.1
, pp. 285-297
-
-
Terzer, M.1
Maynard, N.D.2
Covert, M.W.3
Stelling, J.4
-
41
-
-
36348959154
-
Estimation of the number of extreme pathways for metabolic networks
-
Yeung M., Thiele I., Palsson B.O. Estimation of the number of extreme pathways for metabolic networks. BMC Bioinform. 2007, 8:363.
-
(2007)
BMC Bioinform.
, vol.8
, pp. 363
-
-
Yeung, M.1
Thiele, I.2
Palsson, B.O.3
|