-
1
-
-
0032600888
-
Metabolic fluxes and metabolic engineering
-
G. Stephanopoulos Metabolic fluxes and metabolic engineering Metab Eng 1 1999 1 11
-
(1999)
Metab Eng
, vol.1
, pp. 1-11
-
-
Stephanopoulos, G.1
-
2
-
-
84901321053
-
Contribution of network connectivity in determining the relationship between gene expression and metabolite concentration changes
-
A. Zelezniak, S. Sheridan, and K.R. Patil Contribution of network connectivity in determining the relationship between gene expression and metabolite concentration changes PLoS Comput Biol 10 2014 e1003572
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003572
-
-
Zelezniak, A.1
Sheridan, S.2
Patil, K.R.3
-
3
-
-
0034741983
-
13C metabolic flux analysis
-
13C metabolic flux analysis Metab Eng 3 2001 195 206
-
(2001)
Metab Eng
, vol.3
, pp. 195-206
-
-
Wiechert, W.1
-
6
-
-
0347506028
-
It is all about metabolic fluxes
-
J. Nielsen It is all about metabolic fluxes J Bacteriol 185 2003 7031 7035
-
(2003)
J Bacteriol
, vol.185
, pp. 7031-7035
-
-
Nielsen, J.1
-
8
-
-
33846061120
-
13C-based flux analysis
-
13C-based flux analysis Mol Syst Biol 2 2006 62
-
(2006)
Mol Syst Biol
, vol.2
, pp. 62
-
-
Sauer, U.1
-
9
-
-
84865574629
-
A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation
-
M. Celton, I. Sanchez, A. Goelzer, V. Fromion, C. Camarasa, and S. Dequin A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation BMC Genomics 2012 317
-
(2012)
BMC Genomics
, pp. 317
-
-
Celton, M.1
Sanchez, I.2
Goelzer, A.3
Fromion, V.4
Camarasa, C.5
Dequin, S.6
-
10
-
-
84880044091
-
Fluxomics - Connecting 'omics analysis and phenotypes
-
G. Winter, and J.O. Krömer Fluxomics - connecting 'omics analysis and phenotypes Environ Microbiol 15 2013 1901 1916
-
(2013)
Environ Microbiol
, vol.15
, pp. 1901-1916
-
-
Winter, G.1
Krömer, J.O.2
-
12
-
-
84866487453
-
Integration of expression data in genome-scale metabolic network reconstructions
-
A.S. Blazier, and J.A. Papin Integration of expression data in genome-scale metabolic network reconstructions Front Physiol 3 299 2012
-
(2012)
Front Physiol
, vol.3
, Issue.299
-
-
Blazier, A.S.1
Papin, J.A.2
-
13
-
-
84857999389
-
A metabolic network approach for the identification and prioritization of antimicrobial drug targets
-
A.K. Chavali, K.M. D'Auria, E.L. Hewlett, R.D. Pearson, and J.A. Papin A metabolic network approach for the identification and prioritization of antimicrobial drug targets Trends Microbiol 2012 113 123
-
(2012)
Trends Microbiol
, pp. 113-123
-
-
Chavali, A.K.1
D'Auria, K.M.2
Hewlett, E.L.3
Pearson, R.D.4
Papin, J.A.5
-
14
-
-
84872093417
-
Analysis of omics data with genome-scale models of metabolism
-
D.R. Hyduke, N.E. Lewis, and B.∅. Palsson Analysis of omics data with genome-scale models of metabolism Mol Biosyst 9 2013 167 174
-
(2013)
Mol Biosyst
, vol.9
, pp. 167-174
-
-
Hyduke, D.R.1
Lewis, N.E.2
Palsson, B.O.3
-
16
-
-
9544253891
-
Genome-scale models of microbial cells: Evaluating the consequences of constraints
-
N.D. Price, J.L. Reed, and B.∅. Palsson Genome-scale models of microbial cells: evaluating the consequences of constraints Nat Rev Microbiol 2 2004 886 897
-
(2004)
Nat Rev Microbiol
, vol.2
, pp. 886-897
-
-
Price, N.D.1
Reed, J.L.2
Palsson, B.O.3
-
17
-
-
70449370314
-
The transcription unit architecture of the Escherichia coli genome
-
B.-K. Cho, K. Zengler, Y. Qiu, Y.S. Park, E.M. Knight, and CL Barrett The transcription unit architecture of the Escherichia coli genome Nat Biotechnol 27 2009 1043 1049
-
(2009)
Nat Biotechnol
, vol.27
, pp. 1043-1049
-
-
Cho, B.-K.1
Zengler, K.2
Qiu, Y.3
Park, Y.S.4
Knight, E.M.5
Barrett, C.L.6
-
18
-
-
76449115656
-
Integrating multiple "omics" analysis for microbial biology: Application and methodologies
-
W. Zhang, F. Li, and L. Nie Integrating multiple "omics" analysis for microbial biology: application and methodologies Microbiology 156 2010 287 301
-
(2010)
Microbiology
, vol.156
, pp. 287-301
-
-
Zhang, W.1
Li, F.2
Nie, L.3
-
19
-
-
0035989610
-
In silico biology through "omics"
-
B. Palsson In silico biology through "omics" Nat Biotechnol 20 2002 649 650
-
(2002)
Nat Biotechnol
, vol.20
, pp. 649-650
-
-
Palsson, B.1
-
20
-
-
84858439602
-
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
-
N.E. Lewis, H. Nagarajan, and B.O. Palsson Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods Nat Rev Microbiol 10 2012 291 305
-
(2012)
Nat Rev Microbiol
, vol.10
, pp. 291-305
-
-
Lewis, N.E.1
Nagarajan, H.2
Palsson, B.O.3
-
21
-
-
33846122240
-
Lipidomics and lipid profiling in metabolomics
-
J.B. German, L.A. Gillies, J.T. Smilowitz, A.M. Zivkovic, and S.M. Watkins Lipidomics and lipid profiling in metabolomics Curr Opin Lipidol 18 2007 66 71
-
(2007)
Curr Opin Lipidol
, vol.18
, pp. 66-71
-
-
German, J.B.1
Gillies, L.A.2
Smilowitz, J.T.3
Zivkovic, A.M.4
Watkins, S.M.5
-
22
-
-
67650709732
-
Metabolomics: Ready for the prime time?
-
M. Mayr Metabolomics: ready for the prime time? Circ Cardiovasc Genet 1 2008 58 65
-
(2008)
Circ Cardiovasc Genet
, vol.1
, pp. 58-65
-
-
Mayr, M.1
-
23
-
-
84895963679
-
What mRNA abundances can tell us about metabolism
-
A. Hoppe What mRNA abundances can tell us about metabolism Metabolites 2012 614 631
-
(2012)
Metabolites
, pp. 614-631
-
-
Hoppe, A.1
-
24
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: a revolutionary tool for transcriptomics Nat Rev Genet 10 2009 57 63
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
25
-
-
79957665988
-
Microarrays, deep sequencing and the true measure of the transcriptome
-
J.H. Malone, and B. Oliver Microarrays, deep sequencing and the true measure of the transcriptome BMC Biol 9 2011 34
-
(2011)
BMC Biol
, vol.9
, pp. 34
-
-
Malone, J.H.1
Oliver, B.2
-
26
-
-
77958460555
-
The challenges of integrating multi-omic data sets
-
B. Palsson, and K. Zengler The challenges of integrating multi-omic data sets Nat Chem Biol 6 2010 787 789
-
(2010)
Nat Chem Biol
, vol.6
, pp. 787-789
-
-
Palsson, B.1
Zengler, K.2
-
27
-
-
14544268137
-
Uncovering transcriptional regulation of metabolism by using metabolic network topology
-
K.R. Patil, and J. Nielsen Uncovering transcriptional regulation of metabolism by using metabolic network topology Proc Natl Acad Sci U S A 102 2005 2685 2689
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 2685-2689
-
-
Patil, K.R.1
Nielsen, J.2
-
29
-
-
66149122278
-
Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p
-
J.F. Moxley, M.C. Jewett, M.R. Antoniewicz, S.G. Villas-Boas, H. Alper Alper, and RT Wheeler Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p Proc Natl Acad Sci U S A 106 2009 6477 6482
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 6477-6482
-
-
Moxley, J.F.1
Jewett, M.C.2
Antoniewicz, M.R.3
Villas-Boas, S.G.4
Alper Alper, H.5
Wheeler, R.T.6
-
30
-
-
84866128045
-
Shrinking the metabolic solution space using experimental datasets
-
J.L. Reed Shrinking the metabolic solution space using experimental datasets PLoS Comput Biol 2012 e1002662
-
(2012)
PLoS Comput Biol
, pp. e1002662
-
-
Reed, J.L.1
-
31
-
-
33644527950
-
The model organism as a system: Integrating 'omics' data sets
-
A.R. Joyce, and B.∅. Palsson The model organism as a system: integrating 'omics' data sets Nat Rev Mol Cell Biol 7 2006 198 210
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 198-210
-
-
Joyce, A.R.1
Palsson, B.O.2
-
32
-
-
84895986259
-
Recent advances in the reconstruction of metabolic models and integration of omics data
-
R. Saha, A. Chowdhury, and C.D. Maranas Recent advances in the reconstruction of metabolic models and integration of omics data Curr Opin Biotechnol 29C 2014 39 45
-
(2014)
Curr Opin Biotechnol
, vol.29 C
, pp. 39-45
-
-
Saha, R.1
Chowdhury, A.2
Maranas, C.D.3
-
33
-
-
84901306814
-
Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
-
D. Machado, and M. Herrgård Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism PLoS Comput Biol 10 2014 e1003580
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003580
-
-
Machado, D.1
Herrgård, M.2
-
34
-
-
84890092837
-
GIM3E: Condition-specific models of cellular metabolism developed from metabolomics and expression data
-
B.J. Schmidt, A. Ebrahim, T.O. Metz, J.N. Adkins, B. Palsson, and DR. Hyduke GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data Bioinformatics 29 2013 2900 2908
-
(2013)
Bioinformatics
, vol.29
, pp. 2900-2908
-
-
Schmidt, B.J.1
Ebrahim, A.2
Metz, T.O.3
Adkins, J.N.4
Palsson, B.5
Hyduke, D.R.6
-
35
-
-
84883808938
-
Flux-coupled genes and their use in metabolic flux analysis
-
H.U. Kim, W.J. Kim, and S.Y. Lee Flux-coupled genes and their use in metabolic flux analysis Biotechnol J 8 2013 1035 1042
-
(2013)
Biotechnol J
, vol.8
, pp. 1035-1042
-
-
Kim, H.U.1
Kim, W.J.2
Lee, S.Y.3
-
36
-
-
84866539049
-
RELATCH: Relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
-
J. Kim, and J.L. Reed RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations Genome Biol 2012 R78
-
(2012)
Genome Biol
, pp. R78
-
-
Kim, J.1
Reed, J.L.2
-
38
-
-
78049255973
-
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
-
S. Chandrasekaran, and N.D. Price Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis Proc Natl Acad Sci U S A 107 2010 17845 17850
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 17845-17850
-
-
Chandrasekaran, S.1
Price, N.D.2
-
39
-
-
79951536020
-
Functional integration of a metabolic network model and expression data without arbitrary thresholding
-
P.A. Jensen, and J.A. Papin Functional integration of a metabolic network model and expression data without arbitrary thresholding Bioinformatics 27 2011 541 547
-
(2011)
Bioinformatics
, vol.27
, pp. 541-547
-
-
Jensen, P.A.1
Papin, J.A.2
-
40
-
-
78449291015
-
Predicting metabolic fluxes using gene expression differences as constraints
-
R.J.P. Van Berlo, D. De Ridder, J.M. Daran, P.A.S. Daran-Lapujade, B. Teusink, and MJT. Reinders Predicting metabolic fluxes using gene expression differences as constraints IEEE/ACM Trans Comput Biol Bioinform 8 2011 206 216
-
(2011)
IEEE/ACM Trans Comput Biol Bioinform
, vol.8
, pp. 206-216
-
-
Van Berlo, R.J.P.1
De Ridder, D.2
Daran, J.M.3
Daran-Lapujade, P.A.S.4
Teusink, B.5
Reinders, M.J.T.6
-
41
-
-
6044265058
-
Integration of gene expression data into genome-scale metabolic models
-
M. Åkesson, J. Förster, and J. Nielsen Integration of gene expression data into genome-scale metabolic models Metab Eng 6 2004 285 293
-
(2004)
Metab Eng
, vol.6
, pp. 285-293
-
-
Åkesson, M.1
Förster, J.2
Nielsen, J.3
-
42
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
J. Förster, I. Famili, P. Fu, B.∅. Palsson, and J. Nielsen Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network Genome Res 13 2003 244 253
-
(2003)
Genome Res
, vol.13
, pp. 244-253
-
-
Förster, J.1
Famili, I.2
Fu, P.3
Palsson, B.O.4
Nielsen, J.5
-
43
-
-
44949225040
-
Context-specific metabolic networks are consistent with experiments
-
S.A. Becker, and B.O. Palsson Context-specific metabolic networks are consistent with experiments PLoS Comput Biol 4 2008 e1000082
-
(2008)
PLoS Comput Biol
, vol.4
, pp. e1000082
-
-
Becker, S.A.1
Palsson, B.O.2
-
44
-
-
79951745716
-
IMAT: An integrative metabolic analysis tool
-
H. Zur, E. Ruppin, and T. Shlomi iMAT: an integrative metabolic analysis tool Bioinformatics 26 2010 3140 3142
-
(2010)
Bioinformatics
, vol.26
, pp. 3140-3142
-
-
Zur, H.1
Ruppin, E.2
Shlomi, T.3
-
45
-
-
51349092391
-
Network-based prediction of human tissue-specific metabolism
-
T. Shlomi, M.N. Cabili, M.J. Herrgård, B.∅. Palsson, and E. Ruppin Network-based prediction of human tissue-specific metabolism Nat Biotechnol 26 2008 1003 1010
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1003-1010
-
-
Shlomi, T.1
Cabili, M.N.2
Herrgård, M.J.3
Palsson, B.O.4
Ruppin, E.5
-
46
-
-
84875977583
-
Inferring metabolic states in uncharacterized environments using gene-expression measurements
-
S. Rossell, M.A. Huynen, and R.A. Notebaart Inferring metabolic states in uncharacterized environments using gene-expression measurements PLoS Comput Biol 9 2013
-
(2013)
PLoS Comput Biol
, vol.9
-
-
Rossell, S.1
Huynen, M.A.2
Notebaart, R.A.3
-
47
-
-
70049110173
-
Interpreting expression data with metabolic flux models: Predicting Mycobacterium tuberculosis mycolic acid production
-
C. Colijn, A. Brandes, J. Zucker, D.S. Lun, B. Weiner, and MR Farhat Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production PLoS Comput Biol 5 2009 e1000489
-
(2009)
PLoS Comput Biol
, vol.5
, pp. e1000489
-
-
Colijn, C.1
Brandes, A.2
Zucker, J.3
Lun, D.S.4
Weiner, B.5
Farhat, M.R.6
-
48
-
-
84860998236
-
Inferring carbon sources from gene expression profiles using metabolic flux models
-
A. Brandes, D.S. Lun, K. Ip, J. Zucker, C. Colijn, and B Weiner Inferring carbon sources from gene expression profiles using metabolic flux models PLoS One 2012 e36947
-
(2012)
PLoS One
, pp. e36947
-
-
Brandes, A.1
Lun, D.S.2
Ip, K.3
Zucker, J.4
Colijn, C.5
Weiner, B.6
-
49
-
-
84862301363
-
Improving metabolic flux predictions using absolute gene expression data
-
D. Lee, K. Smallbone, W.B. Dunn, E. Murabito, C.L. Winder, and DB Kell Improving metabolic flux predictions using absolute gene expression data BMC Syst Biol 6 2012 73
-
(2012)
BMC Syst Biol
, vol.6
, pp. 73
-
-
Lee, D.1
Smallbone, K.2
Dunn, W.B.3
Murabito, E.4
Winder, C.L.5
Kell, D.B.6
-
50
-
-
0023709196
-
Metabolic control theory: A structural approach
-
C. Reder Metabolic control theory: a structural approach J Theor Biol 135 1988 175 201
-
(1988)
J Theor Biol
, vol.135
, pp. 175-201
-
-
Reder, C.1
-
51
-
-
84928406649
-
-
B. Barker, N. Sadagopan, Y. Wang, K. Smallbone, C.R. Myers, and H Xi A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data 2014 27
-
(2014)
A Robust and Efficient Method for Estimating Enzyme Complex Abundance and Metabolic Flux from Expression Data
, pp. 27
-
-
Barker, B.1
Sadagopan, N.2
Wang, Y.3
Smallbone, K.4
Myers, C.R.5
Xi, H.6
-
52
-
-
0343035686
-
Stoichiometric model of Escherichia coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements
-
J. Pramanik, and J.D. Keasling Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements Biotechnol Bioeng 56 1997 398 421
-
(1997)
Biotechnol Bioeng
, vol.56
, pp. 398-421
-
-
Pramanik, J.1
Keasling, J.D.2
-
53
-
-
0020687005
-
Thermodynamic efficiency of microbial growth is low but optimal for maximal growth rate
-
H.V. Westerhoff, K.J. Hellingwerf, and K. Van Dam Thermodynamic efficiency of microbial growth is low but optimal for maximal growth rate Proc Natl Acad Sci U S A 80 1983 305 309
-
(1983)
Proc Natl Acad Sci U S A
, vol.80
, pp. 305-309
-
-
Westerhoff, H.V.1
Hellingwerf, K.J.2
Van Dam, K.3
-
55
-
-
67449096729
-
Flux balance analysis of biological systems: Applications and challenges
-
K. Raman, and N. Chandra Flux balance analysis of biological systems: applications and challenges Brief Bioinform 10 2009 435 449
-
(2009)
Brief Bioinform
, vol.10
, pp. 435-449
-
-
Raman, K.1
Chandra, N.2
-
56
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
A. Mortazavi, B.A. Williams, K. McCue, L. Schaeffer, and B. Wold Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat Methods 5 2008 621 628
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
57
-
-
0027146142
-
Batch kinetics of Corynebacterium glutamicum during growth on various carbon substrates: Use of substrate mixtures to localise metabolic bottlenecks
-
M. Cocaign, C. Monnet, and N. Lindley Batch kinetics of Corynebacterium glutamicum during growth on various carbon substrates: use of substrate mixtures to localise metabolic bottlenecks Appl Microbiol Biotechnol 40 1993 526 530
-
(1993)
Appl Microbiol Biotechnol
, vol.40
, pp. 526-530
-
-
Cocaign, M.1
Monnet, C.2
Lindley, N.3
|