-
1
-
-
68349109625
-
Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: Current state and perspectives
-
Matsushika A, Inoue H, Kodaki T, Sawayama S (2009) Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives. Appl Microbiol Biotechnol 84: 37-53.
-
(2009)
Appl Microbiol Biotechnol
, vol.84
, pp. 37-53
-
-
Matsushika, A.1
Inoue, H.2
Kodaki, T.3
Sawayama, S.4
-
2
-
-
84863230581
-
Metabolic network modeling and simulation for drug targeting and discovery
-
Kim HU, Sohn SB, Lee SY (2012) Metabolic network modeling and simulation for drug targeting and discovery. Biotechnol J 7: 330-342.
-
(2012)
Biotechnol J
, vol.7
, pp. 330-342
-
-
Kim, H.U.1
Sohn, S.B.2
Lee, S.Y.3
-
3
-
-
84855719307
-
From cancer metabolism to new biomarkers and drug targets
-
Chiaradonna F, Moresco RM, Airoldi C, Gaglio D, Palorini R, et al. (2012) From cancer metabolism to new biomarkers and drug targets. Biotechnol Adv 30: 30-51.
-
(2012)
Biotechnol Adv
, vol.30
, pp. 30-51
-
-
Chiaradonna, F.1
Moresco, R.M.2
Airoldi, C.3
Gaglio, D.4
Palorini, R.5
-
4
-
-
80054969621
-
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
-
Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, et al. (2011) A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol 5: 180.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 180
-
-
Bordbar, A.1
Feist, A.M.2
Usaite-Black, R.3
Woodcock, J.4
Palsson, B.O.5
-
6
-
-
33846061120
-
Metabolic networks in motion: 13C-based flux analysis
-
Sauer U (2006) Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol 2: 62.
-
(2006)
Mol Syst Biol
, vol.2
, pp. 62
-
-
Sauer, U.1
-
9
-
-
84867554554
-
Predicting drug targets and biomarkers of cancer via genome-scale metabolic modeling
-
Jerby L, Ruppin E (2012) Predicting drug targets and biomarkers of cancer via genome-scale metabolic modeling. Clin Cancer Res 18: 5572-5584.
-
(2012)
Clin Cancer Res
, vol.18
, pp. 5572-5584
-
-
Jerby, L.1
Ruppin, E.2
-
10
-
-
84866487453
-
Integration of expression data in genome-scale metabolic network reconstructions
-
Blazier AS, Papin JA (2012) Integration of expression data in genome-scale metabolic network reconstructions. Front Physiol 3: 299.
-
(2012)
Front Physiol
, vol.3
, pp. 299
-
-
Blazier, A.S.1
Papin, J.A.2
-
11
-
-
6044265058
-
Integration of gene expression data into genome-scale metabolic models
-
Akesson M, Forster J, Nielsen J (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
-
12
-
-
84872093417
-
Analysis of omics data with genomescale models of metabolism
-
Hyduke DR, Lewis NE, Palsson BO (2013) Analysis of omics data with genomescale models of metabolism. Mol Biosyst 9: 167-174.
-
(2013)
Mol Biosyst
, vol.9
, pp. 167-174
-
-
Hyduke, D.R.1
Lewis, N.E.2
Palsson, B.O.3
-
13
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.
-
(2004)
Nature
, vol.429
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
Reed, J.L.3
Herrgard, M.J.4
Palsson, B.O.5
-
14
-
-
51349092391
-
Networkbased prediction of human tissue-specific metabolism
-
Shlomi T, Cabili MN, Herrgard MJ, Palsson BO, Ruppin E (2008) Networkbased prediction of human tissue-specific metabolism. Nat Biotechnol 26: 1003-1010.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1003-1010
-
-
Shlomi, T.1
Cabili, M.N.2
Herrgard, M.J.3
Palsson, B.O.4
Ruppin, E.5
-
15
-
-
84866925914
-
Modeling phenotypic metabolic adaptations of Mycobacterium tuberculosis H37Rv under hypoxia
-
Fang X, Wallqvist A, Reifman J (2012) Modeling phenotypic metabolic adaptations of Mycobacterium tuberculosis H37Rv under hypoxia. PLOS Comput Biol 8: e1002688.
-
(2012)
PLOS Comput Biol
, vol.8
, pp. e1002688
-
-
Fang, X.1
Wallqvist, A.2
Reifman, J.3
-
16
-
-
84880335117
-
Bridging the gap between gene expression and metabolic phenotype via kinetic models
-
Vital-Lopez FG, Wallqvist A, Reifman J (2013) Bridging the gap between gene expression and metabolic phenotype via kinetic models. BMC Syst Biol 7: 63.
-
(2013)
BMC Syst Biol
, vol.7
, pp. 63
-
-
Vital-Lopez, F.G.1
Wallqvist, A.2
Reifman, J.3
-
17
-
-
70049110173
-
Interpreting expression data with metabolic flux models: Predicting Mycobacterium tuberculosis mycolic acid production
-
Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, et al. (2009) Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLOS Comput Biol 5: 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
-
18
-
-
79951745716
-
IMAT: An integrative metabolic analysis tool
-
Zur H, Ruppin E, Shlomi T (2010) iMAT: an integrative metabolic analysis tool. Bioinformatics 26: 3140-3142.
-
(2010)
Bioinformatics
, vol.26
, pp. 3140-3142
-
-
Zur, H.1
Ruppin, E.2
Shlomi, T.3
-
19
-
-
84862301363
-
Improving metabolic flux predictions using absolute gene expression data
-
Lee D, Smallbone K, Dunn WB, Murabito E, Winder CL, et al. (2012) Improving metabolic flux predictions using absolute gene expression data. BMC Syst Biol 6: 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
-
20
-
-
43449132092
-
Is maximization of molar yield in metabolic networks favoured by evolution?
-
Schuster S, Pfeiffer T, Fell DA (2008) Is maximization of molar yield in metabolic networks favoured by evolution? J Theor Biol 252: 497-504.
-
(2008)
J Theor Biol
, vol.252
, pp. 497-504
-
-
Schuster, S.1
Pfeiffer, T.2
Fell, D.A.3
-
21
-
-
84858155067
-
Dynamic models of metabolism: Review of the cybernetic approach
-
Ramkrishna D, Song HS (2012) Dynamic models of metabolism: review of the cybernetic approach. AIChE J 58: 986-997.
-
(2012)
AIChE J
, vol.58
, pp. 986-997
-
-
Ramkrishna, D.1
Song, H.S.2
-
22
-
-
3242795003
-
The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks
-
Holzhutter HG (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
-
23
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
Schuetz R, Kuepfer L, Sauer U (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
-
24
-
-
84860487758
-
Multidimensional optimality of microbial metabolism
-
Schuetz R, Zamboni N, Zampieri M, Heinemann M, Sauer U (2012) Multidimensional optimality of microbial metabolism. Science 336: 601-604.
-
(2012)
Science
, vol.336
, pp. 601-604
-
-
Schuetz, R.1
Zamboni, N.2
Zampieri, M.3
Heinemann, M.4
Sauer, U.5
-
26
-
-
84875977583
-
Inferring metabolic states in uncharacterized environments using gene-expression measurements
-
Rossell S, Huynen MA, Notebaart RA (2013) Inferring metabolic states in uncharacterized environments using gene-expression measurements. PLOS Comput Biol 9: e1002988.
-
(2013)
PLOS Comput Biol
, vol.9
, pp. e1002988
-
-
Rossell, S.1
Huynen, M.A.2
Notebaart, R.A.3
-
27
-
-
44949225040
-
Context-specific metabolic networks are consistent with experiments
-
Becker SA, Palsson BO (2008) Context-specific metabolic networks are consistent with experiments. PLOS Comput Biol 4: e1000082.
-
(2008)
PLOS Comput Biol
, vol.4
, pp. e1000082
-
-
Becker, S.A.1
Palsson, B.O.2
-
28
-
-
84861744439
-
Yeast 5 - An expanded reconstruction of the Saccharomyces cerevisiae metabolic network
-
Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP (2012) Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol 6: 55.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 55
-
-
Heavner, B.D.1
Smallbone, K.2
Barker, B.3
Mendes, P.4
Walker, L.P.5
-
29
-
-
34247612307
-
Multiple highthroughput analyses monitor the response of E coli to perturbations
-
Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, et al. (2007) Multiple highthroughput analyses monitor the response of E. coli to perturbations. Science 316: 593-597.
-
(2007)
Science
, vol.316
, pp. 593-597
-
-
Ishii, N.1
Nakahigashi, K.2
Baba, T.3
Robert, M.4
Soga, T.5
-
30
-
-
84879002382
-
Basic and applied uses of genomescale metabolic network reconstructions of Escherichia coli
-
McCloskey D, Palsson BO, Feist AM (2013) Basic and applied uses of genomescale metabolic network reconstructions of Escherichia coli. Mol Syst Biol 9: 661.
-
(2013)
Mol Syst Biol
, vol.9
, pp. 661
-
-
McCloskey, D.1
Palsson, B.O.2
Feist, A.M.3
-
31
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 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
-
32
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
-
Reed JL, Vo TD, Schilling CH, Palsson BO (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4: R54.
-
(2003)
Genome Biol
, vol.4
, pp. R54
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.O.4
-
33
-
-
84866975246
-
Multiscale modeling of metabolism and macromolecular synthesis in E coli and its application to the evolution of codon usage
-
Thiele I, Fleming RM, Que R, Bordbar A, Diep D, et al. (2012) Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLOS ONE 7: e45635.
-
(2012)
PLOS ONE
, vol.7
, pp. e45635
-
-
Thiele, I.1
Fleming, R.M.2
Que, R.3
Bordbar, A.4
Diep, D.5
-
35
-
-
0037406843
-
Thirteen years of building constraint-based in silico models of Escherichia coli
-
Reed JL, Palsson BO (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
-
36
-
-
0037079023
-
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
-
Ibarra RU, Edwards JS, Palsson BO (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
-
37
-
-
84867132196
-
Scheffersomyces stipitis: A comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae
-
Papini M, Nookaew I, Uhlen M, Nielsen J (2012) Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae. Microb Cell Fact 11: 136.
-
(2012)
Microb Cell Fact
, vol.11
, pp. 136
-
-
Papini, M.1
Nookaew, I.2
Uhlen, M.3
Nielsen, J.4
-
38
-
-
77951612556
-
BiGG: A Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
-
Schellenberger J, Park JO, Conrad TM, Palsson BO (2010) BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11: 213.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson, B.O.4
-
39
-
-
80053175304
-
TIGER: Toolbox for integrating genomescale metabolic models, expression data, and transcriptional regulatory networks
-
Jensen PA, Lutz KA, Papin JA (2011) TIGER: Toolbox for integrating genomescale metabolic models, expression data, and transcriptional regulatory networks. BMC Syst Biol 5: 147.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 147
-
-
Jensen, P.A.1
Lutz, K.A.2
Papin, J.A.3
-
41
-
-
4344571581
-
Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
-
Breitling R, Armengaud P, Amtmann A, Herzyk P (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 573: 83-92.
-
(2004)
FEBS Lett
, vol.573
, pp. 83-92
-
-
Breitling, R.1
Armengaud, P.2
Amtmann, A.3
Herzyk, P.4
|