-
1
-
-
0028146781
-
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
-
201879, 7986045
-
Varma A, Palsson BO. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 1994, 60(10):3724-3731. 201879, 7986045.
-
(1994)
Appl Environ Microbiol
, vol.60
, Issue.10
, pp. 3724-3731
-
-
Varma, A.1
Palsson, B.O.2
-
2
-
-
0028261445
-
Temperature acclimation and competitive fitness: an experimental test of the beneficial acclimation assumption
-
10.1073/pnas.91.5.1917, 43275, 8127906
-
Leroi AM, Bennett AF, Lenski RE. Temperature acclimation and competitive fitness: an experimental test of the beneficial acclimation assumption. Proc Nat Acad Sci USA 1994, 91(5):1917-1921. 10.1073/pnas.91.5.1917, 43275, 8127906.
-
(1994)
Proc Nat Acad Sci USA
, vol.91
, Issue.5
, pp. 1917-1921
-
-
Leroi, A.M.1
Bennett, A.F.2
Lenski, R.E.3
-
3
-
-
7644238181
-
Biological robustness
-
Kitano H. Biological robustness. Nat Rev Gene 2004, 5(11):826-837.
-
(2004)
Nat Rev Gene
, vol.5
, Issue.11
, pp. 826-837
-
-
Kitano, H.1
-
4
-
-
80052416535
-
Robustness of metabolic networks: A review of existing definitions
-
Larhlimi A, Blachon S, Selbig J, Nikoloski Z. Robustness of metabolic networks: A review of existing definitions. Bio Syst 2011, 106:1-8.
-
(2011)
Bio Syst
, vol.106
, pp. 1-8
-
-
Larhlimi, A.1
Blachon, S.2
Selbig, J.3
Nikoloski, Z.4
-
5
-
-
0033552946
-
Robustness in bacterial chemotaxis
-
10.1038/16483, 9923680
-
Alon U, Surette MG, Barkai N, Leibler S. Robustness in bacterial chemotaxis. Nature 1999, 397(6715):168-171. 10.1038/16483, 9923680.
-
(1999)
Nature
, vol.397
, Issue.6715
, pp. 168-171
-
-
Alon, U.1
Surette, M.G.2
Barkai, N.3
Leibler, S.4
-
6
-
-
0030797355
-
Robustness in simple biochemical networks to transfer and process information
-
10.1038/43199, 9202124
-
Barkai N, Leibler S. Robustness in simple biochemical networks to transfer and process information. Nature 1997, 387(6636):913-917. 10.1038/43199, 9202124.
-
(1997)
Nature
, vol.387
, Issue.6636
, pp. 913-917
-
-
Barkai, N.1
Leibler, S.2
-
7
-
-
34548825690
-
Towards a theory of biological robustness
-
2013924, 17882156
-
Kitano H. Towards a theory of biological robustness. Mol Syst Biol 2007, 3:137. 2013924, 17882156.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 137
-
-
Kitano, H.1
-
8
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18(suppl 1):S233-S240.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
9
-
-
6044265058
-
Integration of gene expression data into genome-scale metabolic models
-
10.1016/j.ymben.2003.12.002, 15491858
-
Akesson M, Förster J, Nielsen J. Integration of gene expression data into genome-scale metabolic models. Metab Eng 2004, 6(4):285-293. 10.1016/j.ymben.2003.12.002, 15491858.
-
(2004)
Metab Eng
, vol.6
, Issue.4
, pp. 285-293
-
-
Akesson, M.1
Förster, J.2
Nielsen, J.3
-
10
-
-
51349092391
-
Network-based prediction of human tissue-specific metabolism
-
10.1038/nbt.1487, 18711341
-
Shlomi T, Cabili MN, Herrgård MJ, Palsson BO, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 2008, 26(9):1003-1010. 10.1038/nbt.1487, 18711341.
-
(2008)
Nat Biotechnol
, vol.26
, Issue.9
, pp. 1003-1010
-
-
Shlomi, T.1
Cabili, M.N.2
Herrgård, M.J.3
Palsson, B.O.4
Ruppin, E.5
-
11
-
-
79951536020
-
Functional integration of a metabolic network model and expression data without arbitrary thresholding
-
Jensen PA, Papin JA. Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics (Oxford, England) 2011, 27(4):541-547.
-
(2011)
Bioinformatics (Oxford, England)
, vol.27
, Issue.4
, pp. 541-547
-
-
Jensen, P.A.1
Papin, J.A.2
-
12
-
-
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(2):165-182.
-
(1994)
J Biol Syst
, vol.2
, Issue.2
, pp. 165-182
-
-
Schuster, S.1
Hilgetag, C.2
-
13
-
-
0037079050
-
Metabolic network structure determines key aspects of functionality and regulation
-
10.1038/nature01166, 12432396
-
Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002, 420(6912):190-193. 10.1038/nature01166, 12432396.
-
(2002)
Nature
, vol.420
, Issue.6912
, pp. 190-193
-
-
Stelling, J.1
Klamt, S.2
Bettenbrock, K.3
Schuster, S.4
Gilles, E.D.5
-
14
-
-
55749088074
-
Can sugars be produced from fatty acids? A test case for pathway analysis tools
-
de Figueiredo LF, Schuster S, Kaleta C, Fell DA. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics (Oxford, England) 2008, 24(22):2615-2621.
-
(2008)
Bioinformatics (Oxford, England)
, vol.24
, Issue.22
, pp. 2615-2621
-
-
de Figueiredo, L.F.1
Schuster, S.2
Kaleta, C.3
Fell, D.A.4
-
15
-
-
75849164426
-
Computing the shortest elementary flux modes in genome-scale metabolic networks
-
de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics (Oxford, England) 2009, 25(23):3158-3165.
-
(2009)
Bioinformatics (Oxford, England)
, vol.25
, Issue.23
, pp. 3158-3165
-
-
de Figueiredo, L.F.1
Podhorski, A.2
Rubio, A.3
Kaleta, C.4
Beasley, J.E.5
Schuster, S.6
Planes, F.J.7
-
16
-
-
84874020282
-
Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns - supplementary material - input-species
-
Kaleta C, de Figueiredo LF, Schuster S, Figueiredo FD, Jena D. Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns - supplementary material - input-species. Math Oper Res 2009, 19(10):1-8.
-
(2009)
Math Oper Res
, vol.19
, Issue.10
, pp. 1-8
-
-
Kaleta, C.1
de Figueiredo, L.F.2
Schuster, S.3
Figueiredo, F.D.4
Jena, D.5
-
17
-
-
84866443920
-
Random sampling of elementary flux modes in large-scale metabolic networks
-
3436828, 22962475
-
Machado D, Soons Z, Patil KR, Ferreira EC, Rocha I. Random sampling of elementary flux modes in large-scale metabolic networks. Bioinformatics 2012, 28(18):i515-i521. 3436828, 22962475.
-
(2012)
Bioinformatics
, vol.28
, Issue.18
-
-
Machado, D.1
Soons, Z.2
Patil, K.R.3
Ferreira, E.C.4
Rocha, I.5
-
18
-
-
52949098408
-
Large-scale computation of elementary flux modes with bit pattern trees
-
Terzer M, Stelling J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics (Oxford, England) 2008, 24(19):2229-2235.
-
(2008)
Bioinformatics (Oxford, England)
, vol.24
, Issue.19
, pp. 2229-2235
-
-
Terzer, M.1
Stelling, J.2
-
19
-
-
77952279419
-
Metabolomic and transcriptomic stress response of Escherichia coli
-
2890322, 20461071
-
Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, Steinhauser D, Selbig J, Willmitzer L. Metabolomic and transcriptomic stress response of Escherichia coli. Mol Syst Biol 2010, 6:364. 2890322, 20461071.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 364
-
-
Jozefczuk, S.1
Klie, S.2
Catchpole, G.3
Szymanski, J.4
Cuadros-Inostroza, A.5
Steinhauser, D.6
Selbig, J.7
Willmitzer, L.8
-
20
-
-
77952534179
-
Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes
-
10.1186/1471-2105-11-276, 2892466, 20500820
-
Hellwig B, Hengstler JG, Schmidt M, Gehrmann MC, Schormann W, Rahnenführer J. Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes. BMC Bioinformatics 2010, 11:276. 10.1186/1471-2105-11-276, 2892466, 20500820.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 276
-
-
Hellwig, B.1
Hengstler, J.G.2
Schmidt, M.3
Gehrmann, M.C.4
Schormann, W.5
Rahnenführer, J.6
-
21
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
-
10.1186/gb-2003-4-9-r54, 193654, 12952533
-
Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4(9):R54. 10.1186/gb-2003-4-9-r54, 193654, 12952533.
-
(2003)
Genome Biol
, vol.4
, Issue.9
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.O.4
-
22
-
-
70049110173
-
Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production
-
10.1371/journal.pcbi.1000489, 2726785, 19714220
-
Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol 2009, 5(8):e1000489. 10.1371/journal.pcbi.1000489, 2726785, 19714220.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.8
-
-
Colijn, C.1
Brandes, A.2
Zucker, J.3
Lun, D.S.4
Weiner, B.5
Farhat, M.R.6
Cheng, T.Y.7
Moody, D.B.8
Murray, M.9
Galagan, J.E.10
-
23
-
-
77749320898
-
What is flux balance analysis?
-
10.1038/nbt.1614, 3108565, 20212490
-
Orth JD, Thiele I, Palsson BO. What is flux balance analysis?. Nat Biotechnol 2010, 28(3):245-8. 10.1038/nbt.1614, 3108565, 20212490.
-
(2010)
Nat Biotechnol
, vol.28
, Issue.3
, pp. 245-248
-
-
Orth, J.D.1
Thiele, I.2
Palsson, B.O.3
-
24
-
-
0242487787
-
Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
10.1002/bit.10803, 14595777
-
Burgard AP, Pharkya P, Maranas CD. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003, 84(6):647-657. 10.1002/bit.10803, 14595777.
-
(2003)
Biotechnol Bioeng
, vol.84
, Issue.6
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
27
-
-
18944385541
-
On the Solution of the Bilevel Programming Formulation of the Terrorist Threat Problem
-
Arroyo J, Galiana F. On the Solution of the Bilevel Programming Formulation of the Terrorist Threat Problem. IEEE Trans Power Syst 2005, 20(2):789-797.
-
(2005)
IEEE Trans Power Syst
, vol.20
, Issue.2
, pp. 789-797
-
-
Arroyo, J.1
Galiana, F.2
-
28
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
1949037, 17625511
-
Schuetz R, Kuepfer L, Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 2007, 3:119. 1949037, 17625511.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
29
-
-
0034770083
-
Roles of thiolredox pathways in bacteria
-
Ritz D, Beckwith J. Roles of thiolredox pathways in bacteria. Microbiology 2001, 55:21-48.
-
(2001)
Microbiology
, vol.55
, pp. 21-48
-
-
Ritz, D.1
Beckwith, J.2
-
30
-
-
20144381079
-
Transcriptional response of Escherichia coli to temperature shift
-
Gadgil M, Kapur V, Hu WS. Transcriptional response of Escherichia coli to temperature shift. Biotechno Prog 21(3):689-699.
-
Biotechno Prog
, vol.21
, Issue.3
, pp. 689-699
-
-
Gadgil, M.1
Kapur, V.2
Hu, W.S.3
-
31
-
-
84856076140
-
Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress
-
10.1074/mcp.M111.009019, 3270098, 22008207
-
Kocharunchitt C, King T, Gobius K, Bowman JP, Ross T. Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress. Mol Cell Proteomics : MCP 2012, 11:M111.009019. 10.1074/mcp.M111.009019, 3270098, 22008207.
-
(2012)
Mol Cell Proteomics : MCP
, vol.11
-
-
Kocharunchitt, C.1
King, T.2
Gobius, K.3
Bowman, J.P.4
Ross, T.5
|