-
1
-
-
0034761603
-
Selection analyses of insertional mutants using subgenic-resolution arrays
-
Badarinarayana, V., Estep III, P.W., Shendure, J., Edwards, J., Tavazoie, S., Lam, F., and Church, G.M. 2001. Selection analyses of insertional mutants using subgenic-resolution arrays. Nat. Biotechnol. 19: 1060-1065.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 1060-1065
-
-
Badarinarayana, V.1
Estep III, P.W.2
Shendure, J.3
Edwards, J.4
Tavazoie, S.5
Lam, F.6
Church, G.M.7
-
2
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabasi, A.L. and Albert, R. 1999. Emergence of scaling in random networks. Science 286: 509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
3
-
-
0035812464
-
Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions
-
Burgard, A.P. and Maranas, C.D. 2001. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74: 364-375.
-
(2001)
Biotechnol. Bioeng.
, vol.74
, pp. 364-375
-
-
Burgard, A.P.1
Maranas, C.D.2
-
4
-
-
0034798879
-
Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments
-
Burgard, A.P., Vaidyaraman, S., and Maranas, C.D. 2001. Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnol. Prog. 17: 791-797.
-
(2001)
Biotechnol. Prog.
, vol.17
, pp. 791-797
-
-
Burgard, A.P.1
Vaidyaraman, S.2
Maranas, C.D.3
-
5
-
-
0242487787
-
OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
Burgard, A.P., Pharkya, P., and Maranas, C.D. 2003. OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84: 647-657.
-
(2003)
Biotechnol. Bioeng.
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
6
-
-
0037142769
-
Metabolic pathway analysis of a recombinant yeast for rational strain development
-
Carlson, R., Fell, D., and Srienc, F. 2002. Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol. Bioeng. 79: 121-134.
-
(2002)
Biotechnol. Bioeng.
, vol.79
, pp. 121-134
-
-
Carlson, R.1
Fell, D.2
Srienc, F.3
-
7
-
-
0037424661
-
Constraints-based models: Regulation of gene expression reduces the steady-state solution space
-
Covert, M.W. and Palsson, B.O. 2003. Constraints-based models: Regulation of gene expression reduces the steady-state solution space. J. Theor. Biol. 221: 309-325.
-
(2003)
J. Theor. Biol.
, vol.221
, pp. 309-325
-
-
Covert, M.W.1
Palsson, B.O.2
-
8
-
-
0035281870
-
Metabolic modeling of microbial strains in silico
-
Covert, M.W., Schilling, C.H., Famili, I., Edwards, J.S., Goryanin, I.I., Selkov, E., and Palsson, B.O. 2001. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26: 179-186.
-
(2001)
Trends Biochem. Sci.
, vol.26
, pp. 179-186
-
-
Covert, M.W.1
Schilling, C.H.2
Famili, I.3
Edwards, J.S.4
Goryanin, I.I.5
Selkov, E.6
Palsson, B.O.7
-
10
-
-
0033580813
-
Systems properties of the Haemophilus influenzae Rd metabolic genotype
-
Edwards, J.S. and Palsson, B.O. 1999. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274: 17410-17416.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 17410-17416
-
-
Edwards, J.S.1
Palsson, B.O.2
-
11
-
-
0034625143
-
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
-
Edwards, J.S. and Palsson, B.O. 2000. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. 97: 5528-5533.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 5528-5533
-
-
Edwards, J.S.1
Palsson, B.O.2
-
12
-
-
0035125986
-
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
-
Edwards, J.S., Ibarra, R.U., and Palsson, B.O. 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19: 125-130.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 125-130
-
-
Edwards, J.S.1
Ibarra, R.U.2
Palsson, B.O.3
-
13
-
-
0037335931
-
Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS
-
Fischer, E. and Sauer, U. 2003. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur. J. Biochem. 270: 880-891.
-
(2003)
Eur. J. Biochem.
, vol.270
, pp. 880-891
-
-
Fischer, E.1
Sauer, U.2
-
14
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
Forster, J., Famili, I., Fu, P.C., Palsson, B., and Nielsen, J. 2003. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13: 244-253.
-
(2003)
Genome Res.
, vol.13
, pp. 244-253
-
-
Forster, J.1
Famili, I.2
Fu, P.C.3
Palsson, B.4
Nielsen, J.5
-
16
-
-
0030748655
-
Construction and properties of aconitase mutants of Escherichia coli
-
Gruer, M.J., Bradbury, A.J., and Guest, J.R. 1997. Construction and properties of aconitase mutants of Escherichia coli. Microbiology 143 (Pt 6): 1837-1846.
-
(1997)
Microbiology
, vol.143
, Issue.PART 6
, pp. 1837-1846
-
-
Gruer, M.J.1
Bradbury, A.J.2
Guest, J.R.3
-
18
-
-
0015024317
-
Nalidixic acd-resistant mutants of Escherichia coli deficient in isocitrate dehydrogenase
-
Helling, R.B. and Kukora, J.S. 1971. Nalidixic acd-resistant mutants of Escherichia coli deficient in isocitrate dehydrogenase. J. Bacteriol. 105: 1224-1226.
-
(1971)
J. Bacteriol.
, vol.105
, pp. 1224-1226
-
-
Helling, R.B.1
Kukora, J.S.2
-
19
-
-
0037079023
-
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
-
Ibarra, R.U., Edwards, J.S., and Palsson, B.O. 2002. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189.
-
(2002)
Nature
, vol.420
, pp. 186-189
-
-
Ibarra, R.U.1
Edwards, J.S.2
Palsson, B.O.3
-
20
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., and Barabasi, A.L. 2000. The large-scale organization of metabolic networks. Nature 407: 651-654.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
21
-
-
0029002581
-
Composite control of cell function: Metabolic pathways behaving as single control units
-
Kholodenko, B.N., Schuster, S., Rohwer, J.M., Cascante, M., and Westerhoff, H.V. 1995. Composite control of cell function: Metabolic pathways behaving as single control units. FEBS Lett. 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
-
22
-
-
0036039060
-
Combinatorial complexity of pathway analysis in metabolic networks
-
Klamt, S. and Stelling, J. 2002. Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep. 29: 233-236.
-
(2002)
Mol. Biol. Rep.
, vol.29
, pp. 233-236
-
-
Klamt, S.1
Stelling, J.2
-
23
-
-
0037308505
-
Two approaches for metabolic pathway analysis?
-
Klamt, S. and Stelling, J. 2003. Two approaches for metabolic pathway analysis? Trends Biotechnol. 21: 64-69.
-
(2003)
Trends Biotechnol.
, vol.21
, pp. 64-69
-
-
Klamt, S.1
Stelling, J.2
-
24
-
-
0037316342
-
FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
-
Klamt, S., Stelling, J., Ginkel, M., and Gilles, E.D. 2003. FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19: 261-269.
-
(2003)
Bioinformatics
, vol.19
, pp. 261-269
-
-
Klamt, S.1
Stelling, J.2
Ginkel, M.3
Gilles, E.D.4
-
25
-
-
0017079114
-
Selection for citrate synthase deficiency in icd mutants of Escherichia coli
-
Lakshmi, T.M. and Helling, R.B. 1976. Selection for citrate synthase deficiency in icd mutants of Escherichia coli. J. Bacteriol. 127: 76-83.
-
(1976)
J. Bacteriol.
, vol.127
, pp. 76-83
-
-
Lakshmi, T.M.1
Helling, R.B.2
-
26
-
-
0037406237
-
Development of network-based pathway definitions: The need to analyze real metabolic networks
-
Palsson, B.O., Price, N.D., and Papin, J.A. 2003. Development of network-based pathway definitions: The need to analyze real metabolic networks. Trends Biotechnol. 21: 195-198.
-
(2003)
Trends Biotechnol.
, vol.21
, pp. 195-198
-
-
Palsson, B.O.1
Price, N.D.2
Papin, J.A.3
-
27
-
-
0036350955
-
The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy
-
Papin, J.A., Price, N.D., Edwards, J., and Palsson, B. 2002. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J. Theor. Biol. 215: 67-82.
-
(2002)
J. Theor. Biol.
, vol.215
, pp. 67-82
-
-
Papin, J.A.1
Price, N.D.2
Edwards, J.3
Palsson, B.4
-
28
-
-
0344052685
-
METATOOL: For studying metabolic networks
-
Pfeiffer, T., Sanchez-Valdenebro, I., Nuno, J.C., Montero, F., and Schuster, S. 1999. METATOOL: For studying metabolic networks. Bioinformatics 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
-
29
-
-
1242348578
-
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock
-
(in press)
-
Pharkya, P., Burgard, A.P., and Maranas, C.D. 2004. Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock. Biotechnol. Bioeng. (in press).
-
(2004)
Biotechnol. Bioeng.
-
-
Pharkya, P.1
Burgard, A.P.2
Maranas, C.D.3
-
30
-
-
0036100243
-
Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis
-
Price, N.D., Papin, J.A., and Palsson, B.O. 2002. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res. 12: 760-769.
-
(2002)
Genome Res.
, vol.12
, pp. 760-769
-
-
Price, N.D.1
Papin, J.A.2
Palsson, B.O.3
-
31
-
-
0037385718
-
Genome-scale microbial in silico models: The constraints-based approach
-
Price, N.D., Papin, J.A., Schilling, C.H., and Palsson, B. 2003. Genome-scale microbial in silico models: The constraints-based approach. Trends Biotechnol. 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.4
-
32
-
-
0037406843
-
Thirteen years of building constraint-based in silico models of Escherichia coli
-
Reed, J.L. and Palsson, B.O. 2003. Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol. 185: 2692-2699.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 2692-2699
-
-
Reed, J.L.1
Palsson, B.O.2
-
33
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
-
Reed, J.L., Vo, T.D., Schilling, C.H., and Palsson, B.C. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Gcnome Biol. 4: R54.
-
(2003)
Genome Biol.
, vol.4
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.C.4
-
34
-
-
0029884590
-
How to recognize monofunctional units in a metabolic system
-
Rohwer, J.M., Schuster, S., and Westerhoff, H.V. 1996. How to recognize monofunctional units in a metabolic system. J. Theor. Biol. 179: 213-228.
-
(1996)
J. Theor. Biol.
, vol.179
, pp. 213-228
-
-
Rohwer, J.M.1
Schuster, S.2
Westerhoff, H.V.3
-
35
-
-
0035162782
-
RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12
-
Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millan-Zarate, D., Diaz-Peredo, E., Sanchez-Solano, F., Perez-Rueda, E., Bonavides-Martinez, C., and Collado-Vides, J. 2001. RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29: 72-74.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 72-74
-
-
Salgado, H.1
Santos-Zavaleta, A.2
Gama-Castro, S.3
Millan-Zarate, D.4
Diaz-Peredo, E.5
Sanchez-Solano, F.6
Perez-Rueda, E.7
Bonavides-Martinez, C.8
Collado-Vides, J.9
-
36
-
-
0034615788
-
Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis
-
Schilling, C.H. and Palsson, B.O. 2000. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J. Theor. Biol. 203: 249-283.
-
(2000)
J. Theor. Biol.
, vol.203
, pp. 249-283
-
-
Schilling, C.H.1
Palsson, B.O.2
-
37
-
-
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., and Palsson, B.O. 2000. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203: 229-248.
-
(2000)
J. Theor. Biol.
, vol.203
, pp. 229-248
-
-
Schilling, C.H.1
Letscher, D.2
Palsson, B.O.3
-
38
-
-
0036330798
-
Genome-scale metabolic model of Helicobacter pylori 26695
-
Schilling, C.H., Covert, M.W., Famili, I., Church, G.M., Edwards, J.S., and Palsson, B.O. 2002. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184: 4582-4593.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 4582-4593
-
-
Schilling, C.H.1
Covert, M.W.2
Famili, I.3
Church, G.M.4
Edwards, J.S.5
Palsson, B.O.6
-
39
-
-
0000029295
-
On elementary flux modes in biochemical reaction systems at steady state
-
Schuster, S. and Hilgetag, C. 1994. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 2: 165-182.
-
(1994)
J. Biol. Syst.
, vol.2
, pp. 165-182
-
-
Schuster, S.1
Hilgetag, C.2
-
40
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
-
Schuster, S., Fell, D.A., and Dandekaf, T. 2000. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18: 326-332.
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
41
-
-
0036188159
-
Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae
-
Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I., and Dandekar, T. 2002. Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 18: 351-361.
-
(2002)
Bioinformatics
, vol.18
, pp. 351-361
-
-
Schuster, S.1
Pfeiffer, T.2
Moldenhauer, F.3
Koch, I.4
Dandekar, T.5
-
42
-
-
0037079050
-
Metabolic network structure determines key aspects of functionality and regulation
-
Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S., and Gilles, E.D. 2002. Metabolic network structure determines key aspects of functionality and regulation. Nature 420: 190-193.
-
(2002)
Nature
, vol.420
, pp. 190-193
-
-
Stelling, J.1
Klamt, S.2
Bettenbrock, K.3
Schuster, S.4
Gilles, E.D.5
-
43
-
-
0027223982
-
Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates
-
Varma, A., Boesch, B.W., and Palsson, B.O. 1993. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl. Environ. Microbiol. 59: 2465-2473.
-
(1993)
Appl. Environ. Microbiol.
, vol.59
, pp. 2465-2473
-
-
Varma, A.1
Boesch, B.W.2
Palsson, B.O.3
-
44
-
-
0035823264
-
The small world inside large metabolic networks
-
Wagner, A. and Fell, D.A. 2001. The small world inside large metabolic networks. Proc. R Soc. Lond. B Biol. Sci. 268: 1803-1810.
-
(2001)
Proc. R Soc. Lond. B Biol. Sci.
, vol.268
, pp. 1803-1810
-
-
Wagner, A.1
Fell, D.A.2
|