-
1
-
-
0038441327
-
Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation
-
DOI 10.1038/nrg1088
-
Elena SF, Lenski RE: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet 2003,4(6):457-469. (Pubitemid 36648145)
-
(2003)
Nature Reviews Genetics
, vol.4
, Issue.6
, pp. 457-469
-
-
Elena, S.F.1
Lenski, R.E.2
-
2
-
-
79960104605
-
Microbial laboratory evolution in the era of genome-scale science
-
10.1038/msb.2011.42
-
Conrad TM, Lewis NE, Palsson BØ: Microbial laboratory evolution in the era of genome-scale science. Mol. Syst. Biol 2011, 7:509.
-
(2011)
Mol. Syst. Biol
, vol.7
, pp. 509
-
-
Conrad, T.M.1
Lewis, N.E.2
Palsson, BØ.3
-
3
-
-
0021069845
-
Long-term changes in chemostat cultures of Cytophaga johnsonae
-
Höfle MG: Long-term changes in chemostat cultures of Cytophaga johnsonae. Appl. Environ. Microbiol 1983,46(5):1045-1053. (Pubitemid 14232639)
-
(1983)
Applied and Environmental Microbiology
, vol.46
, Issue.5
, pp. 1045-1053
-
-
Hofle, M.G.1
-
4
-
-
0037079023
-
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
-
DOI 10.1038/nature01149
-
Ibarra RU, Edwards JS, Palsson BO: Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002,420(6912):186-189. (Pubitemid 35340123)
-
(2002)
Nature
, vol.420
, Issue.6912
, pp. 186-189
-
-
Ibarra, R.U.1
Edwards, J.S.2
Palsson, B.O.3
-
5
-
-
25144505718
-
In silico design and adaptive evolution of Escherichia coli for production of lactic acid
-
DOI 10.1002/bit.20542
-
Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO: In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol. Bioeng 2005,91(5):643-648. (Pubitemid 41335499)
-
(2005)
Biotechnology and Bioengineering
, vol.91
, Issue.5
, pp. 643-648
-
-
Fong, S.S.1
Burgard, A.P.2
Herring, C.D.3
Knight, E.M.4
Blattner, F.R.5
Maranas, C.D.6
Palsson, B.O.7
-
6
-
-
79960958091
-
Adaptive laboratory evolution-harnessing the power of biology for metabolic engineering
-
10.1016/j.copbio.2011.03.007
-
Portnoy VA, Bezdan D, Zengler K: Adaptive laboratory evolution-harnessing the power of biology for metabolic engineering. Curr. Opinion Biotechnol 2011,22(4):590-594.
-
(2011)
Curr. Opinion Biotechnol
, vol.22
, Issue.4
, pp. 590-594
-
-
Portnoy, V.A.1
Bezdan, D.2
Zengler, K.3
-
7
-
-
23144432213
-
Optimality and evolutionary tuning of the expression level of a protein
-
DOI 10.1038/nature03842
-
Dekel E, Alon U: Optimality and evolutionary tuning of the expression level of a protein. Nature 2005,436(7050):588-592. (Pubitemid 41112935)
-
(2005)
Nature
, vol.436
, Issue.7050
, pp. 588-592
-
-
Dekel, E.1
Alon, U.2
-
8
-
-
75349114758
-
Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
-
10.1186/gb-2009-10-10-r118
-
Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, Palsson BØ: Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol 2009,10(10):R118.
-
(2009)
Genome Biol
, vol.10
, Issue.10
, pp. 118
-
-
Conrad, T.M.1
Joyce, A.R.2
Applebee, M.K.3
Barrett, C.L.4
Xie, B.5
Gao, Y.6
Palsson, BØ.7
-
9
-
-
77953237121
-
Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. Coli
-
10.1038/msb.2010.33
-
Goodarzi H, Bennett BD, Amini S, Reaves ML, Hottes AK, Rabinowitz JD, Tavazoie S: Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol. Syst. Biol 2010, 6:378.
-
(2010)
Mol. Syst. Biol
, vol.6
, pp. 378
-
-
Goodarzi, H.1
Bennett, B.D.2
Amini, S.3
Reaves, M.L.4
Hottes, A.K.5
Rabinowitz, J.D.6
Tavazoie, S.7
-
10
-
-
48249134043
-
Evolution of evolvability in gene regulatory networks
-
2430289 10.1371/journal.pcbi.1000112
-
Crombach A, Hogeweg P: Evolution of evolvability in gene regulatory networks. PloS Comput. Biol 2008,4(7):e1000112.
-
(2008)
PloS Comput. Biol
, vol.4
, Issue.7
, pp. 1000112
-
-
Crombach, A.1
Hogeweg, P.2
-
11
-
-
79959850934
-
Towards an evolutionary model of transcription networks
-
2832110 10.1371/journal.pcbi.1002064
-
Xie D, Chen CC, He X, Cao X, Zhong S: Towards an evolutionary model of transcription networks. PloS Comput. Biol 2011,7(6):e1002064.
-
(2011)
PloS Comput. Biol
, vol.7
, Issue.6
, pp. 1002064
-
-
Xie, D.1
Chen, C.C.2
He, X.3
Cao, X.4
Zhong, S.5
-
12
-
-
77955141026
-
Omic data from evolved E.Coli are consistent with computed optimal growth from genome-scale models
-
10.1038/msb.2010.47
-
Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ: Omic data from evolved E.coli are consistent with computed optimal growth from genome-scale models. Mol. Syst. Biol 2010, 6:390.
-
(2010)
Mol. Syst. Biol
, vol.6
, pp. 390
-
-
Lewis, N.E.1
Hixson, K.K.2
Conrad, T.M.3
Lerman, J.A.4
Charusanti, P.5
Polpitiya, A.D.6
Adkins, J.N.7
Schramm, G.8
Purvine, S.O.9
Lopez-Ferrer, D.10
Weitz, K.K.11
Eils, R.12
König, R.13
Smith, R.D.14
Palsson, BØ.15
-
13
-
-
0029610838
-
Cloning of the two pyruvate kinase isoenzyme structural genes from Escherichia coli: The relative roles of these enzymes in pyruvate biosynthesis
-
Ponce E, Flores N, Martinez A, Valle F, Bolívar F: Cloning of the two pyruvate kinase isoenzyme structural genes from Escherichia coli: the relative roles of these enzymes in pyruvate biosynthesis. J. Bacteriol 1995,177(19):5719-5722. (Pubitemid 26028888)
-
(1995)
Journal of Bacteriology
, vol.177
, Issue.19
, pp. 5719-5722
-
-
Ponce, E.1
Flores, N.2
Martinez, A.3
Valle, F.4
Bolivar, F.5
-
14
-
-
33751567092
-
Experimental and computational assessment of conditionally essential genes in Escherichia coli
-
DOI 10.1128/JB.00740-06
-
Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BØ, Agarwalla S: Experimental and computational assessment of conditionally essential genes in Escherichia coli. J. Bacteriol 2006,188(23):8259-8271. (Pubitemid 44845698)
-
(2006)
Journal of Bacteriology
, vol.188
, Issue.23
, pp. 8259-8271
-
-
Joyce, A.R.1
Reed, J.L.2
White, A.3
Edwards, R.4
Osterman, A.5
Baba, T.6
Mori, H.7
Lesely, S.A.8
Palsson, B.O.9
Agarwalla, S.10
-
15
-
-
0031967783
-
Pyruvate carboxylase from Corynebacterium glutamicum: Characterization, expression and inactivation of the pyc gene
-
Peters-Wendisch PG, Kreutzer C, Kalinowski J, Pátek M, Sahm H, Eikmanns BJ: Pyruvate carboxylase from Corynebacterium glutamicum: characterization, expression, and inactivation of the pyc gene. Microbiology (Reading, England) 1998,144(Pt 4):915-927. (Pubitemid 28187917)
-
(1998)
Microbiology
, vol.144
, Issue.4
, pp. 915-927
-
-
Peters-Wendisch, P.G.1
Kreutzer, C.2
Kalinowski, J.3
Patek, M.4
Sahm, H.5
Eikmanns, B.J.6
-
16
-
-
70349306551
-
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism
-
10.1038/msb.2009.65
-
Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M: Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol. Syst. Biol 2009, 5:306.
-
(2009)
Mol. Syst. Biol
, vol.5
, pp. 306
-
-
Nakahigashi, K.1
Toya, Y.2
Ishii, N.3
Soga, T.4
Hasegawa, M.5
Watanabe, H.6
Takai, Y.7
Honma, M.8
Mori, H.9
Tomita, M.10
-
17
-
-
62549163352
-
Analyse der evolutiven adaptation am beispiel einer pyruvat-auxotrophen Escherichia coli-mutante (analysis of the evolutive adaptation of a pyruvate-auxotrophic Escherichia coli
-
10.1524/auto.2008.0704
-
Feuer R, Ederer M, Gilles ED, Sprenger GA, Sawodny O, Sauter T: Analyse der evolutiven adaptation am beispiel einer pyruvat-auxotrophen Escherichia coli-mutante (analysis of the evolutive adaptation of a pyruvate-auxotrophic Escherichia coli. mutant). at - Automatisierungstechnik 2008,56(5):257-268.
-
(2008)
Mutant). at - Automatisierungstechnik
, vol.56
, Issue.5
, pp. 257-268
-
-
Feuer, R.1
Ederer, M.2
Gilles, E.D.3
Sprenger, G.A.4
Sawodny, O.5
Sauter, T.6
-
18
-
-
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, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ: A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Systs. Biol 2007, 3:121.
-
(2007)
Mol. Systs. Biol
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, BØ.9
-
19
-
-
77749320898
-
What is flux balance analysis
-
10.1038/nbt.1614
-
Orth JD, Thiele I, Palsson BØ: What is flux balance analysis. Nat. Biotechnol 2010,28(3):245-248.
-
(2010)
Nat. Biotechnol
, vol.28
, Issue.3
, pp. 245-248
-
-
Orth, J.D.1
Thiele, I.2
Palsson, BØ.3
-
20
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
DOI 10.1016/j.ymben.2003.09.002
-
Mahadevan R, Schilling CH: The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metabolic Eng 2003,5(4):264-276. (Pubitemid 38122488)
-
(2003)
Metabolic Engineering
, vol.5
, Issue.4
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
21
-
-
13244292328
-
Computation of elementary modes: A unifying framework and the new binary approach
-
DOI 10.1186/1471-2105-5-175
-
Gagneur J, Klamt S: Computation of elementary modes: a unifying framework an dthe new binary approach. BMC Bioinf 2004, 5:175. (Pubitemid 40195334)
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 175
-
-
Gagneur, J.1
Klamt, S.2
-
22
-
-
31544438578
-
Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110
-
Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol. Systs. Biol. 2006, 2:2006.0007.
-
(2006)
Mol. Systs. Biol
, vol.2
, pp. 20060007
-
-
Hayashi, K.1
Morooka, N.2
Yamamoto, Y.3
Fujita, K.4
Isono, K.5
Choi, S.6
Ohtsubo, E.7
Baba, T.8
Wanner, B.L.9
Mori, H.10
Horiuchi, T.11
-
24
-
-
79960610255
-
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs
-
Wessely F, Bartl M, Guthke R, Li P, Schuster S, Kaleta C: Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol. Systs. Biol 2011, 7:515.
-
(2011)
Mol. Systs. Biol
, vol.7
, pp. 515
-
-
Wessely, F.1
Bartl, M.2
Guthke, R.3
Li, P.4
Schuster, S.5
Kaleta, C.6
-
25
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
DOI 10.1038/nature02456
-
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO: Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004,429(6987):92-96. (Pubitemid 38620557)
-
(2004)
Nature
, vol.429
, Issue.6987
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
Reed, J.L.3
Herrgard, M.J.4
Palsson, B.O.5
-
26
-
-
84887104093
-
Properties of a Boolean network model of Escherichia coli
-
Klotz JG, Feuer R, Gottlieb K, Sawodny O, Sprenger GA, Bossert M, Ederer M, Schober S: Properties of a Boolean network model of Escherichia coli. Proc. of the 8th International Workshop on Computational Systems Biology (WCSB) 2011 2011, 97-100.
-
(2011)
Proc. of the 8th International Workshop on Computational Systems Biology (WCSB) 2011
, pp. 97-100
-
-
Klotz, J.G.1
Feuer, R.2
Gottlieb, K.3
Sawodny, O.4
Sprenger, G.A.5
Bossert, M.6
Ederer, M.7
Schober, S.8
-
27
-
-
79953317811
-
Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
-
Haverkorn van Rijsewijk BRB, Nanchen A, Nallet S, Kleijn RJ, Sauer U: Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli. Mol. Systs. Biol 2011, 7:477.
-
(2011)
Mol. Systs. Biol
, vol.7
, pp. 477
-
-
Haverkorn Van Rijsewijk, B.R.B.1
Nanchen, A.2
Nallet, S.3
Kleijn, R.J.4
Sauer, U.5
-
28
-
-
0033877256
-
Glucose transporter mutants of Escherichia coli K-12 with changes in substrate recognition of IICB(Glc) and induction behavior of the ptsG gene
-
DOI 10.1128/JB.182.16.4443-4452.2000
-
Zeppenfeld T, Larisch C, Lengeler JW, Jahreis K: Glucose transporter mutants of Escherichia coli K-12 with changes in substrate recognition of IICB(Glc) and induction behavior of the ptsG gene. J. Bacteriol 2000,182(16):4443-4452. (Pubitemid 30599807)
-
(2000)
Journal of Bacteriology
, vol.182
, Issue.16
, pp. 4443-4452
-
-
Zeppenfeld, T.1
Larisch, C.2
Lengeler, J.W.3
Jahreis, K.4
-
29
-
-
0014055981
-
Replacement of a Phosphoenolpyruvate-dependent Phosphotransferase by a Nicotinamide Adenine Dinucleotide-linked Dehydrogenase for the Utilization of Mannitol
-
Tanaka S, Lerner SA, Lin ECC: Replacement of a Phosphoenolpyruvate- dependent Phosphotransferase by a Nicotinamide Adenine Dinucleotide-linked Dehydrogenase for the Utilization of Mannitol. J. Bacteriol 1967,93(2):642-648.
-
(1967)
J. Bacteriol
, vol.93
, Issue.2
, pp. 642-648
-
-
Tanaka, S.1
Lerner, S.A.2
Lin, E.C.C.3
-
30
-
-
0015451273
-
Pedigrees of some mutant strains of Escherichia coli K-12
-
Bachmann BJ: Pedigrees of some mutant strains of Escherichia coli K-12. Bacteriol. Rev 1972,36(4):525-557.
-
(1972)
Bacteriol. Rev
, vol.36
, Issue.4
, pp. 525-557
-
-
Bachmann, B.J.1
-
31
-
-
0004265596
-
-
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current Protocols in Molecular Biology. 1995.
-
(1995)
Current Protocols in Molecular Biology
-
-
Ausubel, F.M.1
Brent, R.2
Kingston, R.E.3
Moore, D.D.4
Seidman, J.G.5
Smith, J.A.6
Struhl, K.7
-
32
-
-
0037008673
-
Transcriptional regulation in constraints-based metabolic models of Escherichia coli
-
DOI 10.1074/jbc.M201691200
-
Covert MW, Palsson BØ: Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem 2002,277(31):28058-28064. (Pubitemid 34966757)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.31
, pp. 28058-28064
-
-
Covert, M.W.1
Palsson, B.O.2
-
33
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli (iJR904 GSM/GPR)
-
10.1186/gb-2003-4-9-r54
-
Reed JL, Vo TD, Schilling CH, Palsson BO: An expanded genome-scale model of Escherichia coli (iJR904 GSM/GPR). Genome Biol 2003,4(9):R54.
-
(2003)
Genome Biol
, vol.4
, Issue.9
, pp. 54
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.O.4
|