-
1
-
-
0037133671
-
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
-
H Akashi T Gojobori 2002 Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis Proc Natl Acad Sci USA 99 3695 3700
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 3695-3700
-
-
Akashi, H.1
Gojobori, T.2
-
2
-
-
6044265058
-
Integration of gene expression data into genome-scale metabolic models
-
M Akesson J Forster J Nielsen 2004 Integration of gene expression data into genome-scale metabolic models Metab Eng 6 285 293
-
(2004)
Metab Eng
, vol.6
, pp. 285-293
-
-
Akesson, M.1
Forster, J.2
Nielsen, J.3
-
3
-
-
0036286631
-
Energy balance for analysis of complex metabolic networks
-
DA Beard SD Liang H Qian 2002 Energy balance for analysis of complex metabolic networks Biophys J 83 79 86
-
(2002)
Biophys J
, vol.83
, pp. 79-86
-
-
Beard, D.A.1
Liang, S.D.2
Qian, H.3
-
4
-
-
27744506402
-
Amplified expression of fructose 1, 6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources
-
J Becker C Klopprogge O Zelder E Heinzle C Wittmann 2005 Amplified expression of fructose 1, 6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources Appl Environ Microbiol 71 8587 8596
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 8587-8596
-
-
Becker, J.1
Klopprogge, C.2
Zelder, O.3
Heinzle, E.4
Wittmann, C.5
-
5
-
-
73249151004
-
Metabolic engineering of the tricarboxylic acid cycle for improved lysine production by Corynebacterium glutamicum
-
J Becker C Klopprogge H Schroder C Wittmann 2009 Metabolic engineering of the tricarboxylic acid cycle for improved lysine production by Corynebacterium glutamicum Appl Environ Microbiol 75 7866 7869
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 7866-7869
-
-
Becker, J.1
Klopprogge, C.2
Schroder, H.3
Wittmann, C.4
-
6
-
-
25444467580
-
13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast
-
13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast Genome Biol 6 R49
-
(2005)
Genome Biol
, vol.6
, pp. 49
-
-
Blank, L.M.1
Kuepfer, L.2
Sauer, U.3
-
7
-
-
48649109598
-
Metabolic capacity estimation of Escherichia coli as a platform for redox biocatalysis: Constraint-based modeling and experimental verification
-
LM Blank BE Ebert B Bühler A Schmid 2008 Metabolic capacity estimation of Escherichia coli as a platform for redox biocatalysis: constraint-based modeling and experimental verification Biotechnol Bioeng 100 1050 1065
-
(2008)
Biotechnol Bioeng
, vol.100
, pp. 1050-1065
-
-
Blank, L.M.1
Ebert, B.E.2
Bühler, B.3
Schmid, A.4
-
8
-
-
34249942028
-
Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes
-
JG Bragg A Wagner 2007 Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes Proc Biol Sci 274 1063 1070
-
(2007)
Proc Biol Sci
, vol.274
, pp. 1063-1070
-
-
Bragg, J.G.1
Wagner, A.2
-
9
-
-
58149354386
-
Protein material costs: Single atoms can make an evolutionary difference
-
JG Bragg A Wagner 2009 Protein material costs: single atoms can make an evolutionary difference Trends Genet 25 5 8
-
(2009)
Trends Genet
, vol.25
, pp. 5-8
-
-
Bragg, J.G.1
Wagner, A.2
-
11
-
-
0037142769
-
Metabolic pathway analysis of a recombinant yeast for rational strain development
-
R Carlson D Fell F Srienc 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
-
13
-
-
34247254436
-
Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants
-
HS Choi TY Kim DY Lee SY Lee 2007 Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants J Biotechnol 129 696 705
-
(2007)
J Biotechnol
, vol.129
, pp. 696-705
-
-
Choi, H.S.1
Kim, T.Y.2
Lee, D.Y.3
Lee, S.Y.4
-
14
-
-
0037008673
-
Transcriptional regulation in constraints-based metabolic models of Escherichia coli
-
MW Covert BO Palsson 2002 Transcriptional regulation in constraints-based metabolic models of Escherichia coli J Biol Chem 277 28058 28064
-
(2002)
J Biol Chem
, vol.277
, pp. 28058-28064
-
-
Covert, M.W.1
Palsson, B.O.2
-
15
-
-
0032087026
-
Selection costs of amino acid substitutions in ColE1 and ColIa gene clusters harbored by Escherichia coli
-
CL Craig RS Weber 1998 Selection costs of amino acid substitutions in ColE1 and ColIa gene clusters harbored by Escherichia coli Mol Biol Evol 15 774 776
-
(1998)
Mol Biol Evol
, vol.15
, pp. 774-776
-
-
Craig, C.L.1
Weber, R.S.2
-
17
-
-
67349280647
-
Amino acid metabolic origin as an evolutionary influence on protein sequence in yeast
-
BL de Bivort EO Perlstein S Kunes SL Schreiber 2009 Amino acid metabolic origin as an evolutionary influence on protein sequence in yeast J Mol Evol 68 490 497
-
(2009)
J Mol Evol
, vol.68
, pp. 490-497
-
-
De Bivort, B.L.1
Perlstein, E.O.2
Kunes, S.3
Schreiber, S.L.4
-
18
-
-
33749250188
-
Rapid metabolism of glucose detected with FRET glucose nanosensors in epidermal cells and intact roots of Arabidopsis RNA-silencing mutants
-
K Deuschle B Chaudhuri S Okumoto I Lager S Lalonde WB Frommer 2006 Rapid metabolism of glucose detected with FRET glucose nanosensors in epidermal cells and intact roots of Arabidopsis RNA-silencing mutants Plant Cell 18 2314 2325
-
(2006)
Plant Cell
, vol.18
, pp. 2314-2325
-
-
Deuschle, K.1
Chaudhuri, B.2
Okumoto, S.3
Lager, I.4
Lalonde, S.5
Frommer, W.B.6
-
20
-
-
35648967032
-
Microtiter plates as mini-bioreactors: Miniaturization of fermentation methods
-
WA Duetz 2007 Microtiter plates as mini-bioreactors: miniaturization of fermentation methods Trends Microbiol 15 469 475
-
(2007)
Trends Microbiol
, vol.15
, pp. 469-475
-
-
Duetz, W.A.1
-
21
-
-
0035424201
-
Using proteins in their natural environment: Potential and limitations of microbial whole-cell hydroxylations in applied biocatalysis
-
WA Duetz JB van Beilen B Witholt 2001 Using proteins in their natural environment: potential and limitations of microbial whole-cell hydroxylations in applied biocatalysis Curr Opin Biotechnol 12 419 425
-
(2001)
Curr Opin Biotechnol
, vol.12
, pp. 419-425
-
-
Duetz, W.A.1
Van Beilen, J.B.2
Witholt, B.3
-
22
-
-
0034625143
-
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
-
JS Edwards BO Palsson 2000 The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities Proc Natl Acad Sci U S A 97 5528 5533
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 5528-5533
-
-
Edwards, J.S.1
Palsson, B.O.2
-
23
-
-
0035125986
-
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
-
JS Edwards RU Ibarra BO Palsson 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
-
25
-
-
14244256095
-
Experimental identification and quantification of glucose metabolism in seven bacterial species
-
T Fuhrer E Fischer U Sauer 2005 Experimental identification and quantification of glucose metabolism in seven bacterial species J Bacteriol 187 1581 1590
-
(2005)
J Bacteriol
, vol.187
, pp. 1581-1590
-
-
Fuhrer, T.1
Fischer, E.2
Sauer, U.3
-
26
-
-
24044432264
-
Lysine and glutamate production by Corynebacterium glutamicum on glucose, fructose and sucrose: Roles of malic enzyme and fructose-1, 6-bisphosphatase
-
T Georgi D Rittmann VF Wendisch 2005 Lysine and glutamate production by Corynebacterium glutamicum on glucose, fructose and sucrose: roles of malic enzyme and fructose-1, 6-bisphosphatase Metab Eng 7 291 301
-
(2005)
Metab Eng
, vol.7
, pp. 291-301
-
-
Georgi, T.1
Rittmann, D.2
Wendisch, V.F.3
-
28
-
-
0020486135
-
A role for mRNA secondary structure in the control of translation initiation
-
MN Hall J Gabay M Debarbouille M Schwartz 1982 A role for mRNA secondary structure in the control of translation initiation Nature 295 616 618
-
(1982)
Nature
, vol.295
, pp. 616-618
-
-
Hall, M.N.1
Gabay, J.2
Debarbouille, M.3
Schwartz, M.4
-
29
-
-
0015989446
-
A linear steady-state treatment of enzymatic chains. General properties, control and effector strength
-
Heinrich R, Rapoport TA (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur J Biochem 42(1):89-95
-
(1974)
Eur J Biochem
, vol.42
, Issue.1
, pp. 89-95
-
-
Heinrich, R.1
Rapoport, T.A.2
-
30
-
-
3242795003
-
The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks
-
HG Holzhutter 2004 The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks Eur J Biochem 271 2905 2922
-
(2004)
Eur J Biochem
, vol.271
, pp. 2905-2922
-
-
Holzhutter, H.G.1
-
31
-
-
0037079023
-
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
-
RU Ibarra JS Edwards BO Palsson 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
-
32
-
-
33745013345
-
A genome-based approach to create a minimally mutated Corynebacterium glutamicum strain for efficient L-lysine production
-
M Ikeda J Ohnishi M Hayashi S Mitsuhashi 2006 A genome-based approach to create a minimally mutated Corynebacterium glutamicum strain for efficient L-lysine production J Ind Microbiol Biotech 33 610 615
-
(2006)
J Ind Microbiol Biotech
, vol.33
, pp. 610-615
-
-
Ikeda, M.1
Ohnishi, J.2
Hayashi, M.3
Mitsuhashi, S.4
-
33
-
-
34247584154
-
Expression of the Escherichia coli pntAB genes encoding a membrane-bound transhydrogenase in Corynebacterium glutamicum improves L-lysine formation
-
A Kabus T Georgi VF Wendisch M Bott 2007 Expression of the Escherichia coli pntAB genes encoding a membrane-bound transhydrogenase in Corynebacterium glutamicum improves L-lysine formation Appl Microbiol Biotechnol 75 47 53
-
(2007)
Appl Microbiol Biotechnol
, vol.75
, pp. 47-53
-
-
Kabus, A.1
Georgi, T.2
Wendisch, V.F.3
Bott, M.4
-
34
-
-
0027301842
-
A universal method for achieving increases in metabolite production
-
H Kacser L Acerenza 1993 A universal method for achieving increases in metabolite production Eur J Biochem 216 361 367
-
(1993)
Eur J Biochem
, vol.216
, pp. 361-367
-
-
Kacser, H.1
Acerenza, L.2
-
37
-
-
0033816775
-
Predicted highly expressed genes of diverse prokaryotic genomes
-
S Karlin J Mrazek 2000 Predicted highly expressed genes of diverse prokaryotic genomes J Bacteriol 182 5238 5250
-
(2000)
J Bacteriol
, vol.182
, pp. 5238-5250
-
-
Karlin, S.1
Mrazek, J.2
-
38
-
-
0034888743
-
Characterizations of highly expressed genes of four fast-growing bacteria
-
S Karlin J Mrazek A Campbell D Kaiser 2001 Characterizations of highly expressed genes of four fast-growing bacteria J Bacteriol 183 5025 5040
-
(2001)
J Bacteriol
, vol.183
, pp. 5025-5040
-
-
Karlin, S.1
Mrazek, J.2
Campbell, A.3
Kaiser, D.4
-
39
-
-
58249089508
-
In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network
-
KR Kjeldsen J Nielsen 2009 In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network Biotechnol Bioeng 102 583 597
-
(2009)
Biotechnol Bioeng
, vol.102
, pp. 583-597
-
-
Kjeldsen, K.R.1
Nielsen, J.2
-
40
-
-
0037197159
-
Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria
-
S Klamt S Schuster ED Gilles 2002 Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria Biotechnol Bioeng 77 734 751
-
(2002)
Biotechnol Bioeng
, vol.77
, pp. 734-751
-
-
Klamt, S.1
Schuster, S.2
Gilles, E.D.3
-
41
-
-
0037316342
-
FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
-
S Klamt J Stelling M Ginkel ED Gilles 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
-
42
-
-
33847307148
-
Bayesian-based selection of metabolic objective functions
-
AL Knorr R Jain R Srivastava 2007 Bayesian-based selection of metabolic objective functions Bioinformatics 23 351 357
-
(2007)
Bioinformatics
, vol.23
, pp. 351-357
-
-
Knorr, A.L.1
Jain, R.2
Srivastava, R.3
-
43
-
-
0038514074
-
Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression
-
MA Koffas GY Jung G Stephanopoulos 2003 Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression Metab Eng 5 32 41
-
(2003)
Metab Eng
, vol.5
, pp. 32-41
-
-
Koffas, M.A.1
Jung, G.Y.2
Stephanopoulos, G.3
-
44
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
G Kudla AW Murray D Tollervey JB Plotkin 2009 Coding-sequence determinants of gene expression in Escherichia coli Science 324 255 258
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
45
-
-
25844463806
-
Metabolic functions of duplicate genes in Saccharomyces cerevisiae
-
L Kuepfer U Sauer LM Blank 2005 Metabolic functions of duplicate genes in Saccharomyces cerevisiae Genome Res 15 1421 1430
-
(2005)
Genome Res
, vol.15
, pp. 1421-1430
-
-
Kuepfer, L.1
Sauer, U.2
Blank, L.M.3
-
46
-
-
33745433792
-
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data
-
0034
-
Kummel A, Panke S, Heinemann M (2006a) Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol 2:2006.0034
-
(2006)
Mol Syst Biol
, vol.2
, pp. 2006
-
-
Kummel, A.1
Panke, S.2
Heinemann, M.3
-
47
-
-
33845238737
-
Systematic assignment of thermodynamic constraints in metabolic network models
-
A Kummel S Panke M Heinemann 2006 Systematic assignment of thermodynamic constraints in metabolic network models BMC Bioinformatics 7 512
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 512
-
-
Kummel, A.1
Panke, S.2
Heinemann, M.3
-
48
-
-
0034661295
-
Recursive MILP model for finding all the alternate optima in LP models for metabolic networks
-
S Lee C Phalakornkule MM Domach IE Grossmann 2000 Recursive MILP model for finding all the alternate optima in LP models for metabolic networks Comput Chem Eng 24 711 716
-
(2000)
Comput Chem Eng
, vol.24
, pp. 711-716
-
-
Lee, S.1
Phalakornkule, C.2
Domach, M.M.3
Grossmann, I.E.4
-
49
-
-
29144484729
-
Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation
-
SJ Lee DY Lee TY Kim BH Kim J Lee SY Lee 2005 Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation Appl Environ Microbiol 71 7880 7887
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 7880-7887
-
-
Lee, S.J.1
Lee, D.Y.2
Kim, T.Y.3
Kim, B.H.4
Lee, J.5
Lee, S.Y.6
-
50
-
-
42149149798
-
From genome sequence to integrated bioprocess for succinic acid production by Mannheimia succiniciproducens
-
SY Lee JM Kim H Song JW Lee TY Kim YS Jang 2008 From genome sequence to integrated bioprocess for succinic acid production by Mannheimia succiniciproducens Appl Microbiol Biotechnol 79 11 22
-
(2008)
Appl Microbiol Biotechnol
, vol.79
, pp. 11-22
-
-
Lee, S.Y.1
Kim, J.M.2
Song, H.3
Lee, J.W.4
Kim, T.Y.5
Jang, Y.S.6
-
51
-
-
62949232967
-
Low contents of carbon and nitrogen in highly abundant proteins: Evidence of selection for the economy of atomic composition
-
N Li J Lv DK Niu 2009 Low contents of carbon and nitrogen in highly abundant proteins: evidence of selection for the economy of atomic composition J Mol Evol 68 248 255
-
(2009)
J Mol Evol
, vol.68
, pp. 248-255
-
-
Li, N.1
Lv, J.2
Niu, D.K.3
-
52
-
-
15344340751
-
Metabolic engineering of aerobic succinate production systems in Escherichia coli to improve process productivity and achieve the maximum theoretical succinate yield
-
H Lin GN Bennett KY San 2005 Metabolic engineering of aerobic succinate production systems in Escherichia coli to improve process productivity and achieve the maximum theoretical succinate yield Metab Eng 7 116 127
-
(2005)
Metab Eng
, vol.7
, pp. 116-127
-
-
Lin, H.1
Bennett, G.N.2
San, K.Y.3
-
53
-
-
0036786891
-
Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures
-
J Ma A Campbell S Karlin 2002 Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures J Bacteriol 184 5733 5745
-
(2002)
J Bacteriol
, vol.184
, pp. 5733-5745
-
-
Ma, J.1
Campbell, A.2
Karlin, S.3
-
54
-
-
67349177730
-
Detection of volatile metabolites of Escherichia coli by multi capillary column coupled ion mobility spectrometry
-
S Maddula LM Blank A Schmid JI Baumbach 2009 Detection of volatile metabolites of Escherichia coli by multi capillary column coupled ion mobility spectrometry Anal Bioanal Chem 394 791 800
-
(2009)
Anal Bioanal Chem
, vol.394
, pp. 791-800
-
-
Maddula, S.1
Blank, L.M.2
Schmid, A.3
Baumbach, J.I.4
-
55
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
R Mahadevan CH Schilling 2003 The effects of alternate optimal solutions in constraint-based genome-scale metabolic models Metab Eng 5 264 276
-
(2003)
Metab Eng
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
56
-
-
0025405421
-
Simple constrained-optimization view of acetate overflow in E. coli
-
RA Majewski MM Domach 1990 Simple constrained-optimization view of acetate overflow in E. coli Biotechnol Bioeng 35 732 738
-
(1990)
Biotechnol Bioeng
, vol.35
, pp. 732-738
-
-
Majewski, R.A.1
Domach, M.M.2
-
57
-
-
68549090718
-
High throughput in biotechnology: From shake-flasks to fully instrumented microfermentors
-
MP Marques JM Cabral P Fernandes 2009 High throughput in biotechnology: from shake-flasks to fully instrumented microfermentors Recent Pat Biotechnol 3 124 140
-
(2009)
Recent Pat Biotechnol
, vol.3
, pp. 124-140
-
-
Marques, M.P.1
Cabral, J.M.2
Fernandes, P.3
-
58
-
-
0030050268
-
Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing
-
A Marx AA de Graaf W Wiechert L Eggeling H Sahm 1996 Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing Biotechnol Bioeng 49 111 129
-
(1996)
Biotechnol Bioeng
, vol.49
, pp. 111-129
-
-
Marx, A.1
De Graaf, A.A.2
Wiechert, W.3
Eggeling, L.4
Sahm, H.5
-
59
-
-
0022350091
-
The game of the pentose phosphate cycle
-
E Melendez-Hevia A Isidoro 1985 The game of the pentose phosphate cycle J Theor Biol 117 251 263
-
(1985)
J Theor Biol
, vol.117
, pp. 251-263
-
-
Melendez-Hevia, E.1
Isidoro, A.2
-
60
-
-
33751394915
-
Disruption of malate:quinone oxidoreductase increases L-lysine production by Corynebacterium glutamicum
-
DOI 10.1271/bbb.60298
-
S Mitsuhashi M Hayashi J Ohnishi M Ikeda 2006 Disruption of malate:quinone oxidoreductase increases L-lysine production by Corynebacterium glutamicum Biosci Biotechnol Biochem 70 2803 2806 (Pubitemid 44819862)
-
(2006)
Bioscience, Biotechnology and Biochemistry
, vol.70
, Issue.11
, pp. 2803-2806
-
-
Mitsuhashi, S.1
Hayashi, M.2
Ohnishi, J.3
Ikeda, M.4
-
61
-
-
66149122278
-
Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p
-
JF Moxley MC Jewett MR Antoniewicz SG Villas-Boas H Alper RT Wheeler L Tong AG Hinnebusch T Ideker J Nielsen, et al. 2009 Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p Proc Natl Acad Sci USA 106 6477 6482
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 6477-6482
-
-
Moxley, J.F.1
Jewett, M.C.2
Antoniewicz, M.R.3
Villas-Boas, S.G.4
Alper, H.5
Wheeler, R.T.6
Tong, L.7
Hinnebusch, A.G.8
Ideker, T.9
Nielsen, J.10
-
63
-
-
73949135027
-
Comparison of quantitative metabolite imaging tools and carbon-13 techniques for fluxomics
-
T Niittylae B Chaudhuri U Sauer WB Frommer 2009 Comparison of quantitative metabolite imaging tools and carbon-13 techniques for fluxomics Methods Mol Biol 553 355 372
-
(2009)
Methods Mol Biol
, vol.553
, pp. 355-372
-
-
Niittylae, T.1
Chaudhuri, B.2
Sauer, U.3
Frommer, W.B.4
-
64
-
-
38749100629
-
Visualizing regulatory interactions in metabolic networks
-
S Noack A Wahl E Qeli W Wiechert 2007 Visualizing regulatory interactions in metabolic networks BMC Biol 5 46
-
(2007)
BMC Biol
, vol.5
, pp. 46
-
-
Noack, S.1
Wahl, A.2
Qeli, E.3
Wiechert, W.4
-
67
-
-
11144261828
-
A novel gnd mutation leading to increased L-lysine production in Corynebacterium glutamicum
-
J Ohnishi R Katahira S Mitsuhashi S Kakita M Ikeda 2005 A novel gnd mutation leading to increased L-lysine production in Corynebacterium glutamicum FEMS Microbiol Lett 242 265 274
-
(2005)
FEMS Microbiol Lett
, vol.242
, pp. 265-274
-
-
Ohnishi, J.1
Katahira, R.2
Mitsuhashi, S.3
Kakita, S.4
Ikeda, M.5
-
69
-
-
62149111135
-
FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data
-
J Paananen G Wong 2009 FORG3D: force-directed 3D graph editor for visualization of integrated genome scale data BMC Syst Biol 3 26
-
(2009)
BMC Syst Biol
, vol.3
, pp. 26
-
-
Paananen, J.1
Wong, G.2
-
71
-
-
2942624207
-
Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast
-
B Papp C Pal LD Hurst 2004 Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast Nature 429 661 664
-
(2004)
Nature
, vol.429
, pp. 661-664
-
-
Papp, B.1
Pal, C.2
Hurst, L.D.3
-
72
-
-
0034680782
-
In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum
-
S Petersen AA de Graaf L Eggeling M Mollney W Wiechert H Sahm 2000 In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum J Biol Chem 275 35932 35941
-
(2000)
J Biol Chem
, vol.275
, pp. 35932-35941
-
-
Petersen, S.1
De Graaf, A.A.2
Eggeling, L.3
Mollney, M.4
Wiechert, W.5
Sahm, H.6
-
75
-
-
25444464110
-
Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein
-
GP Raghava JH Han 2005 Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein BMC Bioinformatics 6 59
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 59
-
-
Raghava, G.P.1
Han, J.H.2
-
77
-
-
0035017810
-
Flux-balance analysis of mitochondrial energy metabolism: Consequences of systemic stoichiometric constraints
-
R Ramakrishna JS Edwards A McCulloch BO Palsson 2001 Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints Am J Physiol-Reg I 280 R695 R704
-
(2001)
Am J Physiol-Reg i
, vol.280
-
-
Ramakrishna, R.1
Edwards, J.S.2
McCulloch, A.3
Palsson, B.O.4
-
78
-
-
4644220226
-
Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: Assessment of correlated reaction subsets that comprise network states
-
JL Reed BO Palsson 2004 Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states Genome Res 14 1797 1805
-
(2004)
Genome Res
, vol.14
, pp. 1797-1805
-
-
Reed, J.L.1
Palsson, B.O.2
-
79
-
-
33747369422
-
Batch culture characterization and metabolic flux analysis of succinate-producing Escherichia coli strains
-
AM Sanchez GN Bennett KY San 2006 Batch culture characterization and metabolic flux analysis of succinate-producing Escherichia coli strains Metab Eng 8 209 226
-
(2006)
Metab Eng
, vol.8
, pp. 209-226
-
-
Sanchez, A.M.1
Bennett, G.N.2
San, K.Y.3
-
80
-
-
33846061120
-
13C-based flux analysis
-
13C-based flux analysis Mol Syst Biol 2 62
-
(2006)
Mol Syst Biol
, vol.2
, pp. 62
-
-
Sauer, U.1
-
81
-
-
0032753923
-
Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism
-
U Sauer DR Lasko J Fiaux M Hochuli R Glaser T Szyperski K Wüthrich JE Bailey 1999 Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism J Bacteriol 181 6679 6688 (Pubitemid 29517982)
-
(1999)
Journal of Bacteriology
, vol.181
, Issue.21
, pp. 6679-6688
-
-
Sauer, U.1
Lasko, D.R.2
Fiaux, J.3
Hochuli, M.4
Glaser, R.5
Szyperski, T.6
Wuthrich, K.7
Bailey, J.E.8
-
83
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
R Schuetz L Kuepfer U Sauer 2007 Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli Mol Syst Biol 3 119
-
(2007)
Mol Syst Biol
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
84
-
-
35248849697
-
Integrated network reconstruction, visualization and analysis using YANAsquare
-
R Schwarz C Liang C Kaleta M Kuhnel E Hoffmann S Kuznetsov M Hecker G Griffiths S Schuster T Dandekar 2007 Integrated network reconstruction, visualization and analysis using YANAsquare BMC Bioinformatics 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
-
85
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
D Segre D Vitkup GM Church 2002 Analysis of optimality in natural and perturbed metabolic networks Proc Natl Acad Sci USA 99 15112 15117
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 15112-15117
-
-
Segre, D.1
Vitkup, D.2
Church, G.M.3
-
86
-
-
19644386033
-
Regulatory on/off minimization of metabolic flux changes after genetic perturbations
-
T Shlomi O Berkman E Ruppin 2005 Regulatory on/off minimization of metabolic flux changes after genetic perturbations Proc Natl Acad Sci USA 102 7695 7700
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 7695-7700
-
-
Shlomi, T.1
Berkman, O.2
Ruppin, E.3
-
88
-
-
34548043216
-
Improving lysine production by Corynebacterium glutamicum through DNA microarray-based identification of novel target genes
-
G Sindelar VF Wendisch 2007 Improving lysine production by Corynebacterium glutamicum through DNA microarray-based identification of novel target genes Appl Microbiol Biotechnol 76 677 689
-
(2007)
Appl Microbiol Biotechnol
, vol.76
, pp. 677-689
-
-
Sindelar, G.1
Wendisch, V.F.2
-
89
-
-
52949098408
-
Large-scale computation of elementary flux modes with bit pattern trees
-
M Terzer J Stelling 2008 Large-scale computation of elementary flux modes with bit pattern trees Bioinformatics 24 2229 2235
-
(2008)
Bioinformatics
, vol.24
, pp. 2229-2235
-
-
Terzer, M.1
Stelling, J.2
-
90
-
-
27944487902
-
Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes
-
BP Tu A Kudlicki M Rowicka SL McKnight 2005 Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes Science 310 1152 1158
-
(2005)
Science
, vol.310
, pp. 1152-1158
-
-
Tu, B.P.1
Kudlicki, A.2
Rowicka, M.3
McKnight, S.L.4
-
92
-
-
0028764687
-
Linear constraint relations in biochemical reaction systems: I. Classification of the calculability and the balanceability of conversion rates
-
RT van der Heijden JJ Heijnen C Hellinga B Romein KC Luyben 1994 Linear constraint relations in biochemical reaction systems: I. Classification of the calculability and the balanceability of conversion rates Biotechnol Bioeng 43 3 10
-
(1994)
Biotechnol Bioeng
, vol.43
, pp. 3-10
-
-
Van Der Heijden, R.T.1
Heijnen, J.J.2
Hellinga, C.3
Romein, B.4
Luyben, K.C.5
-
93
-
-
0028973161
-
A metabolic network stoichiometry analysis of microbia growth and product formation
-
WM van Gulik JJ Heijnen 1995 A metabolic network stoichiometry analysis of microbia growth and product formation Biotechnol Bioeng 48 681 698
-
(1995)
Biotechnol Bioeng
, vol.48
, pp. 681-698
-
-
Van Gulik, W.M.1
Heijnen, J.J.2
-
94
-
-
15044347498
-
Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites
-
WA van Winden JC van Dam C Ras RJ Kleijn JL Vinke WM van Gulik JJ Heijnen 2005 Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites FEMS Yeast Res 5 559 568
-
(2005)
FEMS Yeast Res
, vol.5
, pp. 559-568
-
-
Van Winden, W.A.1
Van Dam, J.C.2
Ras, C.3
Kleijn, R.J.4
Vinke, J.L.5
Van Gulik, W.M.6
Heijnen, J.J.7
-
95
-
-
0028146781
-
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
-
A Varma BO Palsson 1994 Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 Appl Environ Microbiol 60 3724 3731
-
(1994)
Appl Environ Microbiol
, vol.60
, pp. 3724-3731
-
-
Varma, A.1
Palsson, B.O.2
-
96
-
-
0036210809
-
Effects of growth mode and pyruvate carboxylase on succinic acid production by metabolically engineered strains of Escherichia coli
-
GN Vemuri MA Eiteman E Altman 2002 Effects of growth mode and pyruvate carboxylase on succinic acid production by metabolically engineered strains of Escherichia coli Appl Environ Microbiol 68 1715 1727
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 1715-1727
-
-
Vemuri, G.N.1
Eiteman, M.A.2
Altman, E.3
-
97
-
-
0036309458
-
Succinate production in dual-phase Escherichia coli fermentations depends on the time of transition from aerobic to anaerobic conditions
-
GN Vemuri MA Eiteman E Altman 2002 Succinate production in dual-phase Escherichia coli fermentations depends on the time of transition from aerobic to anaerobic conditions J Ind Microbiol Biotechnol 28 325 232
-
(2002)
J Ind Microbiol Biotechnol
, vol.28
, pp. 325-232
-
-
Vemuri, G.N.1
Eiteman, M.A.2
Altman, E.3
-
98
-
-
33751545659
-
Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production
-
Q Wang X Chen Y Yang X Zhao 2006 Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production Appl Microbiol Biotechnol 73 887 894
-
(2006)
Appl Microbiol Biotechnol
, vol.73
, pp. 887-894
-
-
Wang, Q.1
Chen, X.2
Yang, Y.3
Zhao, X.4
-
100
-
-
0034741983
-
13C metabolic flux analysis
-
13C metabolic flux analysis Metab Eng 3 195 206
-
(2001)
Metab Eng
, vol.3
, pp. 195-206
-
-
Wiechert, W.1
-
102
-
-
17144387903
-
From stationary to instationary metabolic flux analysis
-
W Wiechert K Noh 2005 From stationary to instationary metabolic flux analysis Adv Biochem Eng Biotechnol 92 145 172
-
(2005)
Adv Biochem Eng Biotechnol
, vol.92
, pp. 145-172
-
-
Wiechert, W.1
Noh, K.2
-
104
-
-
0036956758
-
Genealogy profiling through strain improvement by using metabolic network analysis: Metabolic flux genealogy of several generations of lysine-producing corynebacteria
-
C Wittmann E Heinzle 2002 Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing corynebacteria Appl Environ Microbiol 68 5843 5859
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 5843-5859
-
-
Wittmann, C.1
Heinzle, E.2
-
105
-
-
16344378267
-
13C-metabolic flux analysis with sole quantification of carbon dioxide labeling
-
13C-metabolic flux analysis with sole quantification of carbon dioxide labeling Comput Biol Chem 29 121 133
-
(2005)
Comput Biol Chem
, vol.29
, pp. 121-133
-
-
Yang, T.H.1
Heinzle, E.2
Wittmann, C.3
-
108
-
-
67649218402
-
Genetic modification of flux for flux prediction of mutants
-
Q Zhao H Kurata 2009 Genetic modification of flux for flux prediction of mutants Bioinformatics 25 1702 1708
-
(2009)
Bioinformatics
, vol.25
, pp. 1702-1708
-
-
Zhao, Q.1
Kurata, H.2
|