-
1
-
-
30944469304
-
Mutation discovery in bacterial genomes: Metronidazole resistance in helicobacter pylori
-
Albert TJ, Dailidiene D, Dailide G, Norton JE, Kalia A, Richmond TA, Molla M, Singh J, Green RD, Berg DE (2005) Mutation discovery in bacterial genomes: metronidazole resistance in helicobacter pylori. Nat Method 2: 951-953.
-
(2005)
Nat Method
, vol.2
, pp. 951-953
-
-
Albert, T.J.1
Dailidiene, D.2
Dailide, G.3
Norton, J.E.4
Kalia, A.5
Richmond, T.A.6
Molla, M.7
Singh, J.8
Green, R.D.9
Berg, D.E.10
-
2
-
-
0029063381
-
Mini-Tn10 transposon derivatives for insertion mutagenesis and gene delivery into the chromosome of gram-negative bacteria
-
Alexeyev MF, Shokolenko IN (1995) Mini-Tn10 transposon derivatives for insertion mutagenesis and gene delivery into the chromosome of gram-negative bacteria. Gene 160: 59-62.
-
(1995)
Gene
, vol.160
, pp. 59-62
-
-
Alexeyev, M.F.1
Shokolenko, I.N.2
-
3
-
-
33847083318
-
Global transcription machinery engineering: A new approach for improving cellular phenotype
-
Alper H, Stephanopoulos G (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 9: 258-267.
-
(2007)
Metab Eng
, vol.9
, pp. 258-267
-
-
Alper, H.1
Stephanopoulos, G.2
-
4
-
-
33845442201
-
Engineering yeast transcription machinery for improved ethanol tolerance and production
-
Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314: 1565-1568.
-
(2006)
Science
, vol.314
, pp. 1565-1568
-
-
Alper, H.1
Moxley, J.2
Nevoigt, E.3
Fink, G.R.4
Stephanopoulos, G.5
-
6
-
-
78650647970
-
Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli
-
Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, Liao JC (2010) Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol 6: 449.
-
(2010)
Mol Syst Biol
, vol.6
-
-
Atsumi, S.1
Wu, T.Y.2
Machado, I.M.3
Huang, W.C.4
Chen, P.Y.5
Pellegrini, M.6
Liao, J.C.7
-
8
-
-
0037026501
-
Inverse metabolic engineering: A strategy for directed genetic engineering of useful phenotypes
-
Bailey JE, Sburlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS (2002) Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng 79: 568-579.
-
(2002)
Biotechnol Bioeng
, vol.79
, pp. 568-579
-
-
Bailey, J.E.1
Sburlati, A.2
Hatzimanikatis, V.3
Lee, K.4
Renner, W.A.5
Tsai, P.S.6
-
9
-
-
70350641005
-
Genome evolution and adaptation in a long-term experiment with Escherichia coli
-
Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243-1247.
-
(2009)
Nature
, vol.461
, pp. 1243-1247
-
-
Barrick, J.E.1
Yu, D.S.2
Yoon, S.H.3
Jeong, H.4
Oh, T.K.5
Schneider, D.6
Lenski, R.E.7
Kim, J.F.8
-
11
-
-
0242487787
-
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
Burgard AP, Pharkya P, Maranas CD (2003) Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84: 647-657.
-
(2003)
Biotechnol Bioeng
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
12
-
-
78049255973
-
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and mycobacterium tuberculosis
-
Chandrasekaran S, Price ND (2010) Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and mycobacterium tuberculosis. Proc Natl Acad Sci U S A 107: 17845-17850.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 17845-17850
-
-
Chandrasekaran, S.1
Price, N.D.2
-
13
-
-
78649694766
-
Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene
-
Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL, Xie B, Gao Y, Palsson BO (2010) Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene. PLoS Genet 6: e1001186.
-
(2010)
PLoS Genet
, vol.6
-
-
Charusanti, P.1
Conrad, T.M.2
Knight, E.M.3
Venkataraman, K.4
Fong, N.L.5
Xie, B.6
Gao, Y.7
Palsson, B.O.8
-
14
-
-
0031279273
-
Metabolic consequences of phosphotransferase (PTS) mutation in a phenylalanine-producing recombinant Escherichia coli
-
Chen R, Hatzimanikatis V, Yap WM, Postma PW, Bailey JE (1997) Metabolic consequences of phosphotransferase (PTS) mutation in a phenylalanine-producing recombinant Escherichia coli. Biotechnol Prog 13: 768-775.
-
(1997)
Biotechnol Prog
, vol.13
, pp. 768-775
-
-
Chen, R.1
Hatzimanikatis, V.2
Yap, W.M.3
Postma, P.W.4
Bailey, J.E.5
-
16
-
-
64449088698
-
Continuous base identification for single-molecule nanopore DNA sequencing
-
Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4: 265-270.
-
(2009)
Nat Nanotechnol
, vol.4
, pp. 265-270
-
-
Clarke, J.1
Wu, H.C.2
Jayasinghe, L.3
Patel, A.4
Reid, S.5
Bayley, H.6
-
17
-
-
75349114758
-
Wholegenome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media revealsflexible selection of adaptive mutations
-
Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, Palsson BO (2009) Wholegenome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media revealsflexible selection of adaptive mutations. Genome Biol 10: R118.
-
(2009)
Genome Biol
, vol.10
-
-
Conrad, T.M.1
Joyce, A.R.2
Applebee, M.K.3
Barrett, C.L.4
Xie, B.5
Gao, Y.6
Palsson, B.O.7
-
18
-
-
78650546051
-
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media
-
Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis NE, Landick R, Palsson BO (2010) RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc Natl Acad Sci U S A 107: 20500-20505.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 20500-20505
-
-
Conrad, T.M.1
Frazier, M.2
Joyce, A.R.3
Cho, B.K.4
Knight, E.M.5
Lewis, N.E.6
Landick, R.7
Palsson, B.O.8
-
19
-
-
79960104605
-
Microbial laboratory evolution in the era of genomescale science
-
Conrad TM, Lewis NE, Palsson BO (2011) Microbial laboratory evolution in the era of genomescale science. Mol Syst Biol 7: 509.
-
(2011)
Mol Syst Biol
, vol.7
-
-
Conrad, T.M.1
Lewis, N.E.2
Palsson, B.O.3
-
20
-
-
51749113592
-
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
-
Covert MW, Xiao N, Chen TJ, Karr JR (2008) Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24: 2044-2050.
-
(2008)
Bioinformatics
, vol.24
, pp. 2044-2050
-
-
Covert, M.W.1
Xiao, N.2
Chen, T.J.3
Karr, J.R.4
-
21
-
-
84862257625
-
Aptamer base: A collaborative knowledge base to describe aptamers and SELEX experiments
-
Cruz-Toledo J, McKeague M, Zhang X, Giamberardino A, McConnell E, Francis T, Derosa MC, Dumontier M (2012) Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments. Database J Biol Databases Curation 2012: 6.
-
(2012)
Database J Biol Databases Curation
, vol.2012
, pp. 6
-
-
Cruz-Toledo, J.1
McKeague, M.2
Zhang, X.3
Giamberardino, A.4
McConnell, E.5
Francis, T.6
Derosa, M.C.7
Dumontier, M.8
-
22
-
-
0006965135
-
Continuous cultivation of microorganisms
-
Dawson PSS (1985) Continuous cultivation of microorganisms. CRC Crit Rev 2: 315-372.
-
(1985)
CRC Crit Rev
, vol.2
, pp. 315-372
-
-
Dawson, P.S.S.1
-
24
-
-
84864216850
-
Life technologies promises $1, 000 genome
-
DeFraccesco L (2012) Life technologies promises $1, 000 genome. Nat Biotechnol 14: 126.
-
(2012)
Nat Biotechnol
, vol.14
-
-
DeFraccesco, L.1
-
25
-
-
23144432213
-
Optimality and evolutionary tuning of the expression level of a protein
-
Dekel E, Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588-592.
-
(2005)
Nature
, vol.436
, pp. 588-592
-
-
Dekel, E.1
Alon, U.2
-
26
-
-
0032808947
-
The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes
-
Drake JW (1999) The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes. Ann N Y Acad Sci 870: 100-107.
-
(1999)
Ann N Y Acad Sci
, vol.870
, pp. 100-107
-
-
Drake, J.W.1
-
27
-
-
0019255001
-
Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background
-
Dykhuizen D, Hartl DL (1980) Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background. Genetics 96: 801-817.
-
(1980)
Genetics
, vol.96
, pp. 801-817
-
-
Dykhuizen, D.1
Hartl, D.L.2
-
28
-
-
0025074907
-
In vitro selection of RNA molecules that bind specific ligands
-
Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
-
(1990)
Nature
, vol.346
, pp. 818-822
-
-
Ellington, A.D.1
Szostak, J.W.2
-
29
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338.
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
30
-
-
79955534060
-
A system for the continuous directed evolution of biomolecules
-
Esvelt KM, Carlson JC, Liu DR (2011) A system for the continuous directed evolution of biomolecules. Nature 472: 499-503.
-
(2011)
Nature
, vol.472
, pp. 499-503
-
-
Esvelt, K.M.1
Carlson, J.C.2
Liu, D.R.3
-
31
-
-
66149122635
-
High-throughput quantitative metabolomics: Workflow for cultivation, quenching, and analysis of yeast in a multiwell format
-
Ewald JC, Heux S, Zamboni N (2009) High-throughput quantitative metabolomics: workflow for cultivation, quenching, and analysis of yeast in a multiwell format. Anal Chem 81: 3623-3629.
-
(2009)
Anal Chem
, vol.81
, pp. 3623-3629
-
-
Ewald, J.C.1
Heux, S.2
Zamboni, N.3
-
32
-
-
77950863401
-
Modeldriven evaluation of the production potential for growth-coupled products of Escherichia coli
-
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BO (2010) Modeldriven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng 12: 173-186.
-
(2010)
Metab Eng
, vol.12
, pp. 173-186
-
-
Feist, A.M.1
Zielinski, D.C.2
Orth, J.D.3
Schellenberger, J.4
Herrgard, M.J.5
Palsson, B.O.6
-
33
-
-
0029959052
-
Pathway engineering for the production of aromatic compounds in Escherichia coli
-
Flores N, Xiao J, Berry A, Bolivar F, Valle F (1996) Pathway engineering for the production of aromatic compounds in Escherichia coli. Nat Biotechnol 14: 620-623.
-
(1996)
Nat Biotechnol
, vol.14
, pp. 620-623
-
-
Flores, N.1
Xiao, J.2
Berry, A.3
Bolivar, F.4
Valle, F.5
-
34
-
-
85063827419
-
Evolutionary engineering of industrially important microbial phenotypes
-
Fong SS (2009) Evolutionary engineering of industrially important microbial phenotypes. Metab Pathw Eng Handb 1: 1-15.
-
(2009)
Metab Pathw Eng Handb
, vol.1
, pp. 1-15
-
-
Fong, S.S.1
-
35
-
-
25144505718
-
In silico design and adaptive evolution of Escherichia coli for production of lactic acid
-
Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO (2005a) In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91: 643-648.
-
(2005)
Biotechnol Bioeng
, vol.91
, 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
-
36
-
-
25844495901
-
Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
-
Fong SS, Joyce AR, Palsson BO (2005b) Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res 15: 1365-1372.
-
(2005)
Genome Res
, vol.15
, pp. 1365-1372
-
-
Fong, S.S.1
Joyce, A.R.2
Palsson, B.O.3
-
37
-
-
33744485823
-
Genetic changes that correlate with reduced susceptibility to daptomycin in staphylococcus aureus
-
Friedman L, Alder JD, Silverman JA (2006) Genetic changes that correlate with reduced susceptibility to daptomycin in staphylococcus aureus. Antimicrob Agents Chemother 50: 2137-2145.
-
(2006)
Antimicrob Agents Chemother
, vol.50
, pp. 2137-2145
-
-
Friedman, L.1
Alder, J.D.2
Silverman, J.A.3
-
38
-
-
1642388599
-
Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli
-
Friesen ML, Saxer G, Travisano M, Doebeli M (2004) Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli. Evolution 58: 245-260.
-
(2004)
Evolution
, vol.58
, pp. 245-260
-
-
Friesen, M.L.1
Saxer, G.2
Travisano, M.3
Doebeli, M.4
-
39
-
-
33845998560
-
Global mapping of transposon location
-
Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, Dunham MJ (2006) Global mapping of transposon location. PLoS Genet 2: e212.
-
(2006)
PLoS Genet
, vol.2
-
-
Gabriel, A.1
Dapprich, J.2
Kunkel, M.3
Gresham, D.4
Pratt, S.C.5
Dunham, M.J.6
-
40
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342.
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
41
-
-
33748049119
-
Matrix formalism to describe functional states of transcriptional regulatory systems
-
Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO (2006) Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol 2: e101.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Gianchandani, E.P.1
Papin, J.A.2
Price, N.D.3
Joyce, A.R.4
Palsson, B.O.5
-
42
-
-
67349270900
-
Enzymatic assembly of DNA molecules up to several hundred kilobases
-
Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Method 6: 343-345.
-
(2009)
Nat Method
, vol.6
, pp. 343-345
-
-
Gibson, D.G.1
Young, L.2
Chuang, R.Y.3
Venter, J.C.4
Hutchison, C.A.5
Smith, H.O.6
-
43
-
-
0001359641
-
Molecular evolution over the mutational landscape
-
Gillespie JH (1984) Molecular evolution over the mutational landscape. Evolution 38: 1116-1129.
-
(1984)
Evolution
, vol.38
, pp. 1116-1129
-
-
Gillespie, J.H.1
-
45
-
-
33748100868
-
Methylglyoxal bypass identified as source of chiral contamination in l(+) and d(-)-lactate fermentations by recombinant Escherichia coli
-
Grabar TB, Zhou S, Shanmugam KT, Yomano LP, Ingram LO (2006) Methylglyoxal bypass identified as source of chiral contamination in l(+) and d(-)-lactate fermentations by recombinant Escherichia coli. Biotechnol Lett 28: 1527-1535.
-
(2006)
Biotechnol Lett
, vol.28
, pp. 1527-1535
-
-
Grabar, T.B.1
Zhou, S.2
Shanmugam, K.T.3
Yomano, L.P.4
Ingram, L.O.5
-
46
-
-
58149166731
-
The repertoire and dynamics of evolutionary adaptations to controlled nutrientlimited environments in yeast
-
Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, Ward A, DeSevo CG, Botstein D, Dunham MJ (2008) The repertoire and dynamics of evolutionary adaptations to controlled nutrientlimited environments in yeast. PLoS Genet 4: e1000303.
-
(2008)
PLoS Genet
, vol.4
-
-
Gresham, D.1
Desai, M.M.2
Tucker, C.M.3
Jenq, H.T.4
Pai, D.A.5
Ward, A.6
DeSevo, C.G.7
Botstein, D.8
Dunham, M.J.9
-
47
-
-
34248971890
-
The competitive exclusion principle
-
Hardin G (1960) The competitive exclusion principle. Science 131: 1292-1297.
-
(1960)
Science
, vol.131
, pp. 1292-1297
-
-
Hardin, G.1
-
48
-
-
84857100461
-
Sequencing set to alter clinical landscape
-
Hayden EC (2012) Sequencing set to alter clinical landscape. Nature 482(7385): 288.
-
(2012)
Nature
, vol.482
, Issue.7385
-
-
Hayden, E.C.1
-
49
-
-
0023376305
-
Evolution of Escherichia coli during growth in a constant environment
-
Helling RB, Vargas CN, Adams J (1987) Evolution of Escherichia coli during growth in a constant environment. Genetics 116: 349-358.
-
(1987)
Genetics
, vol.116
, pp. 349-358
-
-
Helling, R.B.1
Vargas, C.N.2
Adams, J.3
-
50
-
-
58049217240
-
Riboswitch RNAs: Using RNA to sense cellular metabolism
-
Henkin TM (2008) Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev 22: 3383-3390.
-
(2008)
Genes Dev
, vol.22
, pp. 3383-3390
-
-
Henkin, T.M.1
-
51
-
-
33751544539
-
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
-
Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR, Palsson BO (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38: 1406-1412.
-
(2006)
Nat Genet
, vol.38
, pp. 1406-1412
-
-
Herring, C.D.1
Raghunathan, A.2
Honisch, C.3
Patel, T.4
Applebee, M.K.5
Joyce, A.R.6
Albert, T.J.7
Blattner, F.R.8
van den Boom, D.9
Cantor, C.R.10
Palsson, B.O.11
-
52
-
-
76649104057
-
Rapid evolution of stability and productivity at the origin of a microbial mutualism
-
Hillesland KL, Stahl DA (2010) Rapid evolution of stability and productivity at the origin of a microbial mutualism. Proc Natl Acad Sci U S A 107: 2124-2129.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 2124-2129
-
-
Hillesland, K.L.1
Stahl, D.A.2
-
53
-
-
55349103743
-
The yeast metabolome addressed by electrospray ionization mass spectrometry: Initiation of a mass spectral library and its applications for metabolic footprinting by direct infusion mass spectrometry
-
Højer-Pedersen J, Smedsgaard J, Nielsen J (2008) The yeast metabolome addressed by electrospray ionization mass spectrometry: initiation of a mass spectral library and its applications for metabolic footprinting by direct infusion mass spectrometry. Metabolomics 4(4): 393-405.
-
(2008)
Metabolomics
, vol.4
, Issue.4
, pp. 393-405
-
-
Højer-Pedersen, J.1
Smedsgaard, J.2
Nielsen, J.3
-
54
-
-
3042741121
-
Engineered riboregulators enable post-transcriptional control of gene expression
-
Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 22: 841-847.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 841-847
-
-
Isaacs, F.J.1
Dwyer, D.J.2
Ding, C.3
Pervouchine, D.D.4
Cantor, C.R.5
Collins, J.J.6
-
55
-
-
34547109364
-
Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli
-
Jin YS, Stephanopoulos G (2007) Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli. Metab Eng 9: 337-347.
-
(2007)
Metab Eng
, vol.9
, pp. 337-347
-
-
Jin, Y.S.1
Stephanopoulos, G.2
-
56
-
-
0024443885
-
Amplification, mutation and selection of catalytic RNA
-
Joyce GF (1989) Amplification, mutation and selection of catalytic RNA. Gene 82: 83-87.
-
(1989)
Gene
, vol.82
, pp. 83-87
-
-
Joyce, G.F.1
-
57
-
-
0033136114
-
Functional Genomic technologies: Creating new paradigms for fundamental and applied biology
-
Kao CM (1999) Functional Genomic technologies: creating new paradigms for fundamental and applied biology. Biotechnol Prog 15: 304-311.
-
(1999)
Biotechnol Prog
, vol.15
, pp. 304-311
-
-
Kao, C.M.1
-
59
-
-
0023647382
-
Towards a general theory of adaptive walks on rugged landscapes
-
Kauffman S, Levin S (1987) Towards a general theory of adaptive walks on rugged landscapes. J Theor Biol 128: 11-45.
-
(1987)
J Theor Biol
, vol.128
, pp. 11-45
-
-
Kauffman, S.1
Levin, S.2
-
60
-
-
78449239214
-
Transition from positive to neutral in mutationfixation along with continuing risingfitness in thermal adaptive evolution
-
Kishimoto T, Iijima L, Tatsumi M, Ono N, Oyake A, Hashimoto T, Matsuo M, Okubo M, Suzuki S, Mori K, Kashiwagi A, Furusawa C, Ying BW, Yomo T (2010) Transition from positive to neutral in mutationfixation along with continuing risingfitness in thermal adaptive evolution. PLoS Genet 6: e1001164.
-
(2010)
PLoS Genet
, vol.6
-
-
Kishimoto, T.1
Iijima, L.2
Tatsumi, M.3
Ono, N.4
Oyake, A.5
Hashimoto, T.6
Matsuo, M.7
Okubo, M.8
Suzuki, S.9
Mori, K.10
Kashiwagi, A.11
Furusawa, C.12
Ying, B.W.13
Yomo, T.14
-
61
-
-
0028191743
-
All you wanted to know about SELEX
-
Klug SJ, Famulok M (1994) All you wanted to know about SELEX. Mol Biol Rep 20: 97-107.
-
(1994)
Mol Biol Rep
, vol.20
, pp. 97-107
-
-
Klug, S.J.1
Famulok, M.2
-
62
-
-
33745459776
-
Proteome analysis of yeast response to various nutrient limitations
-
Kolkman A, Daran-Lapujade P, Fullaondo A, Olsthoorn MM, Pronk JT, Slijper M, Heck AJ (2006) Proteome analysis of yeast response to various nutrient limitations. Mol Syst Biol 2: 2006. 0026.
-
(2006)
Mol Syst Biol
, vol.2
-
-
Kolkman, A.1
Daran-Lapujade, P.2
Fullaondo, A.3
Olsthoorn, M.M.4
Pronk, J.T.5
Slijper, M.6
Heck, A.J.7
-
63
-
-
77954265373
-
Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon source, L-1, 2-propanediol
-
Lee DH, Palsson BO (2010) Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon source, L-1, 2-propanediol. Appl Environ Microbiol 76: 4158-4168.
-
(2010)
Appl Environ Microbiol
, vol.76
, pp. 4158-4168
-
-
Lee, D.H.1
Palsson, B.O.2
-
64
-
-
77956328000
-
Bacterial charity work leads to population-wide resistance
-
Lee HH, Molla MN, Cantor CR, Collins JJ (2010) Bacterial charity work leads to population-wide resistance. Nature 467: 82-85.
-
(2010)
Nature
, vol.467
, pp. 82-85
-
-
Lee, H.H.1
Molla, M.N.2
Cantor, C.R.3
Collins, J.J.4
-
65
-
-
79960414910
-
Systems metabolic engineering for chemicals and materials
-
Lee JW, Kim TY, Jang YS, Choi S, Lee SY (2011) Systems metabolic engineering for chemicals and materials. Trends Biotechnol 29: 370-378.
-
(2011)
Trends Biotechnol
, vol.29
, pp. 370-378
-
-
Lee, J.W.1
Kim, T.Y.2
Jang, Y.S.3
Choi, S.4
Lee, S.Y.5
-
67
-
-
0031966353
-
Evolution of competitivefitness in experimental populations of E coli: What makes one genotype a better competitor than another?
-
Lenski RE, Mongold JA, Sniegowski PD, Travisano M, Vasi F, Gerrish PJ, Schmidt TM (1998) Evolution of competitivefitness in experimental populations of E. coli: what makes one genotype a better competitor than another? Antonie van Leeuwenhoek 73: 35-47.
-
(1998)
Antonie van Leeuwenhoek
, vol.73
, pp. 35-47
-
-
Lenski, R.E.1
Mongold, J.A.2
Sniegowski, P.D.3
Travisano, M.4
Vasi, F.5
Gerrish, P.J.6
Schmidt, T.M.7
-
68
-
-
77955141026
-
Omic data from evolved E. coli are consistent with computed optimal growth from genomescale models
-
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, Konig R, Smith RD, Palsson BO (2010) Omic data from evolved E. coli are consistent with computed optimal growth from genomescale models. Mol Syst Biol 6: 390.
-
(2010)
Mol Syst Biol
, vol.6
-
-
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
Konig, R.13
Smith, R.D.14
Palsson, B.O.15
-
69
-
-
79957700542
-
Versatile RNA-sensing transcriptional regulators for engineering genetic networks
-
Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP (2011) Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci U S A 108: 8617-8622.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 8617-8622
-
-
Lucks, J.B.1
Qi, L.2
Mutalik, V.K.3
Wang, D.4
Arkin, A.P.5
-
70
-
-
55549108089
-
Engineered enzymes for chemical production
-
Luetz S, Giver L, Lalonde J (2008) Engineered enzymes for chemical production. Biotechnol Bioeng 101: 647-653.
-
(2008)
Biotechnol Bioeng
, vol.101
, pp. 647-653
-
-
Luetz, S.1
Giver, L.2
Lalonde, J.3
-
71
-
-
0001641514
-
Mutations of bacteria from virus sensitivity to virus resistance
-
Luria SE, Delbruck M (1943) Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28: 491-511.
-
(1943)
Genetics
, vol.28
, pp. 491-511
-
-
Luria, S.E.1
Delbruck, M.2
-
73
-
-
0001224667
-
Some genetic aspects of Sex
-
Muller HJ (1932) Some genetic aspects of Sex. Am Nat 66: 118-138.
-
(1932)
Am Nat
, vol.66
, pp. 118-138
-
-
Muller, H.J.1
-
74
-
-
50549201557
-
The relation of recombination to mutational advance
-
Müller HJ (1964) The relation of recombination to mutational advance. Mutat Res 106: 2-9.
-
(1964)
Mutat Res
, vol.106
, pp. 2-9
-
-
Müller, H.J.1
-
75
-
-
0001555399
-
Description of the chemostat
-
Novick A, Szilard L (1950) Description of the chemostat. Science 112: 715-716.
-
(1950)
Science
, vol.112
, pp. 715-716
-
-
Novick, A.1
Szilard, L.2
-
76
-
-
34347344063
-
From microbial differentiation to ribosome engineering
-
Ochi K (2007) From microbial differentiation to ribosome engineering. Biosci Biotechnol Biochem 71: 1373-1386.
-
(2007)
Biosci Biotechnol Biochem
, vol.71
, pp. 1373-1386
-
-
Ochi, K.1
-
77
-
-
9644275536
-
Ribosome engineering and secondary metabolite production
-
Ochi K, Okamoto S, Tozawa Y, Inaoka T, Hosaka T, Xu J, Kurosawa K (2004) Ribosome engineering and secondary metabolite production. Adv Appl Microbiol 56: 155-184.
-
(2004)
Adv Appl Microbiol
, vol.56
, pp. 155-184
-
-
Ochi, K.1
Okamoto, S.2
Tozawa, Y.3
Inaoka, T.4
Hosaka, T.5
Xu, J.6
Kurosawa, K.7
-
79
-
-
30044437327
-
Evolutionary programming as a platform for in silico metabolic engineering
-
Patil KR, Rocha I, Forster J, Nielsen J (2005) Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinform 6: 308.
-
(2005)
BMC Bioinform
, vol.6
-
-
Patil, K.R.1
Rocha, I.2
Forster, J.3
Nielsen, J.4
-
80
-
-
3543082676
-
Dealing with complexity: Evolutionary engineering and genome shuffling
-
Petri R, Schmidt-Dannert C (2004) Dealing with complexity: evolutionary engineering and genome shuffling. Curr Opin Biotechnol 15: 298-304.
-
(2004)
Curr Opin Biotechnol
, vol.15
, pp. 298-304
-
-
Petri, R.1
Schmidt-Dannert, C.2
-
81
-
-
33846551980
-
Empiricalfitness landscapes reveal accessible evolutionary paths
-
Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ (2007) Empiricalfitness landscapes reveal accessible evolutionary paths. Nature 445: 383-386.
-
(2007)
Nature
, vol.445
, pp. 383-386
-
-
Poelwijk, F.J.1
Kiviet, D.J.2
Weinreich, D.M.3
Tans, S.J.4
-
82
-
-
84863226500
-
Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals
-
Qi L, Lucks JB, Liu CC, Mutalik VK, Arkin AP (2012) Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res 40: 5775-5786.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5775-5786
-
-
Qi, L.1
Lucks, J.B.2
Liu, C.C.3
Mutalik, V.K.4
Arkin, A.P.5
-
83
-
-
0028094645
-
Microbial evolution in a simple unstructured environment: Genetic differentiation in Escherichia coli
-
Rosenzweig RF, Sharp RR, Treves DS, Adams J (1994) Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. Genetics 137: 903-917.
-
(1994)
Genetics
, vol.137
, pp. 903-917
-
-
Rosenzweig, R.F.1
Sharp, R.R.2
Treves, D.S.3
Adams, J.4
-
84
-
-
67650713931
-
The structural and functional diversity of metabolite-binding riboswitches
-
Roth A, Breaker RR (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78: 305-334.
-
(2009)
Annu Rev Biochem
, vol.78
, pp. 305-334
-
-
Roth, A.1
Breaker, R.R.2
-
85
-
-
0010323618
-
Industrial fungal genetics and strain selection
-
Smith JE, Berry DR, Kristiansen B (eds), Edward Arnold (Publishers) Ltd, London
-
Rowlands RT (1982) Industrial fungal genetics and strain selection. In: Smith JE, Berry DR, Kristiansen B (eds) Thefilamentous fungi", volume 4 of "fungal technology". Edward Arnold (Publishers) Ltd, London, pp 346-372.
-
(1982)
Thefilamentous fungi", volume 4 of "fungal technology"
, pp. 346-372
-
-
Rowlands, R.T.1
-
86
-
-
0021197255
-
Industrial strain improvement: Mutagenesis and random screening procedures
-
Rowlands RT (1984) Industrial strain improvement: mutagenesis and random screening procedures. Enzyme Microb Technol 6: 3-10.
-
(1984)
Enzyme Microb Technol
, vol.6
, pp. 3-10
-
-
Rowlands, R.T.1
-
87
-
-
43049136820
-
Combinatorial engineering of microbes for optimizing cellular phenotype
-
Santos CNS, Stephanopoulos G (2008) Combinatorial engineering of microbes for optimizing cellular phenotype. Curr Opin Chem Biol 12: 168-176.
-
(2008)
Curr Opin Chem Biol
, vol.12
, pp. 168-176
-
-
Santos, C.N.S.1
Stephanopoulos, G.2
-
88
-
-
0035232377
-
Evolutionary engineering of industrially important microbial phenotypes
-
Sauer U (2001) Evolutionary engineering of industrially important microbial phenotypes. Adv Biochem Eng Biotechnol 73: 129-169.
-
(2001)
Adv Biochem Eng Biotechnol
, vol.73
, pp. 129-169
-
-
Sauer, U.1
-
89
-
-
0032753923
-
Metabolicflux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism
-
Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE (1999) Metabolicflux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J Bacteriol 181: 6679-6688.
-
(1999)
J Bacteriol
, vol.181
, 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
-
90
-
-
2942632968
-
Dynamics of insertion sequence elements during experimental evolution of bacteria
-
Schneider D, Lenski RE (2004) Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol 155: 319-327.
-
(2004)
Res Microbiol
, vol.155
, pp. 319-327
-
-
Schneider, D.1
Lenski, R.E.2
-
91
-
-
0036678862
-
Waddington's canalization revisited: Developmental stability and evolution
-
Siegal ML, Bergman A (2002) Waddington's canalization revisited: developmental stability and evolution. Proc Natl Acad Sci U S A 99: 10528-10532.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 10528-10532
-
-
Siegal, M.L.1
Bergman, A.2
-
92
-
-
79957467767
-
From SELEX to cell dual selections for synthetic riboswitches
-
Sinha J, Topp S, Gallivan JP (2011) From SELEX to cell dual selections for synthetic riboswitches. Methods Enzymol 497: 207-220.
-
(2011)
Methods Enzymol
, vol.497
, pp. 207-220
-
-
Sinha, J.1
Topp, S.2
Gallivan, J.P.3
-
93
-
-
0037394596
-
Evolutionary engineering of saccharomyces cerevisiae for anaerobic growth on xylose
-
Sonderegger M, Sauer U (2003) Evolutionary engineering of saccharomyces cerevisiae for anaerobic growth on xylose. Appl Environ Microbiol 69: 1990-1998.
-
(2003)
Appl Environ Microbiol
, vol.69
, pp. 1990-1998
-
-
Sonderegger, M.1
Sauer, U.2
-
95
-
-
0033059278
-
Evolutionary approaches to protein engineering
-
Steipe B (1999) Evolutionary approaches to protein engineering. Curr Top Microbiol Immunol 243: 55-86.
-
(1999)
Curr Top Microbiol Immunol
, vol.243
, pp. 55-86
-
-
Steipe, B.1
-
96
-
-
77949495880
-
Predicting metabolic engineering knockout strategies for chemical production: Accounting for competing pathways
-
Tepper N, Shlomi T (2010) Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 26: 536-543.
-
(2010)
Bioinformatics
, vol.26
, pp. 536-543
-
-
Tepper, N.1
Shlomi, T.2
-
97
-
-
77952774546
-
Functional characterization of alternate optimal solutions of Escherichia coli 's transcriptional and translational machinery
-
Thiele I, Fleming RM, Bordbar A, Schellenberger J, Palsson BO (2010) Functional characterization of alternate optimal solutions of Escherichia coli 's transcriptional and translational machinery. Biophys J 98: 2072-2081.
-
(2010)
Biophys J
, vol.98
, pp. 2072-2081
-
-
Thiele, I.1
Fleming, R.M.2
Bordbar, A.3
Schellenberger, J.4
Palsson, B.O.5
-
98
-
-
77955464045
-
Shaking up genome engineering
-
Tipton KA, Dueber J (2010) Shaking up genome engineering. Nat Biotechnol 28: 812-813.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 812-813
-
-
Tipton, K.A.1
Dueber, J.2
-
99
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
-
(1990)
Science
, vol.249
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
100
-
-
33646542650
-
High-throughput screen for poly-3-hydroxybutyrate in Escherichia coli and Synechocystis sp. Strain PCC6803
-
Tyo KE, Zhou H, Stephanopoulos GN (2006) High-throughput screen for poly-3-hydroxybutyrate in Escherichia coli and Synechocystis sp. Strain PCC6803. Appl Environ Microbiol 72: 3412-3417.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 3412-3417
-
-
Tyo, K.E.1
Zhou, H.2
Stephanopoulos, G.N.3
-
102
-
-
33744482546
-
Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor
-
Velicer GJ, Raddatz G, Keller H, Deiss S, Lanz C, Dinkelacker I, Schuster SC (2006) Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc Natl Acad Sci U S A 103: 8107-8112.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 8107-8112
-
-
Velicer, G.J.1
Raddatz, G.2
Keller, H.3
Deiss, S.4
Lanz, C.5
Dinkelacker, I.6
Schuster, S.C.7
-
103
-
-
0004060268
-
Strain improvement by non recombinant methods
-
Demain AL, Davies JE (eds), ASM Press, Washington, DC
-
Vinci VA, Byng G (1999) Strain improvement by non recombinant methods. In: Demain AL, Davies JE (eds) Manual of industrial microbiology and biotechnology, second edition. ASM Press, Washington, DC, pp 103-113.
-
(1999)
Manual of industrial microbiology and biotechnology, second edition
, pp. 103-113
-
-
Vinci, V.A.1
Byng, G.2
-
104
-
-
51149203927
-
Canalization of development and the inheritance of acquired characters
-
Waddington CH (1942) Canalization of development and the inheritance of acquired characters. Nature 150: 563-565.
-
(1942)
Nature
, vol.150
, pp. 563-565
-
-
Waddington, C.H.1
-
105
-
-
0005604172
-
Evolutionary systems; animal and human
-
Waddington CH (1959) Evolutionary systems; animal and human. Nature 183: 1634-1638.
-
(1959)
Nature
, vol.183
, pp. 1634-1638
-
-
Waddington, C.H.1
-
106
-
-
0000726183
-
Experiments in canalising selection
-
Waddington CH (1960) Experiments in canalising selection. Genet Res 1: 140-150.
-
(1960)
Genet Res
, vol.1
, pp. 140-150
-
-
Waddington, C.H.1
-
107
-
-
68949161807
-
Programming cells by multiplex genome engineering and accelerated evolution
-
Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460: 894-898.
-
(2009)
Nature
, vol.460
, pp. 894-898
-
-
Wang, H.H.1
Isaacs, F.J.2
Carr, P.A.3
Sun, Z.Z.4
Xu, G.5
Forest, C.R.6
Church, G.M.7
-
108
-
-
77955459156
-
Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides
-
Warner JR, Reeder PJ, Karimpour-Fard A, Woodruff LB, Gill RT (2010) Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat Biotechnol 28: 856-862.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 856-862
-
-
Warner, J.R.1
Reeder, P.J.2
Karimpour-Fard, A.3
Woodruff, L.B.4
Gill, R.T.5
-
109
-
-
35448990907
-
A modular and extensible RNA-based gene-regulatory platform for engineering cellular function
-
Win MN, Smolke CD (2007) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci U S A 104: 14283-14288.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 14283-14288
-
-
Win, M.N.1
Smolke, C.D.2
-
110
-
-
0017037398
-
Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli
-
Witkin EM (1976) Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli. Bacteriol Rev 40: 869-907.
-
(1976)
Bacteriol Rev
, vol.40
, pp. 869-907
-
-
Witkin, E.M.1
-
111
-
-
0001771498
-
Evolution in Mendelian populations
-
Wright S (1931) Evolution in Mendelian populations. Genetics 16: 97-159.
-
(1931)
Genetics
, vol.16
, pp. 97-159
-
-
Wright, S.1
-
112
-
-
0001416961
-
Surfaces of selective value revisited
-
Wright S (1988) Surfaces of selective value revisited. Am Nat 131: 115-123.
-
(1988)
Am Nat
, vol.131
, pp. 115-123
-
-
Wright, S.1
-
114
-
-
0037034007
-
Genome shuffling leads to rapid phenotypic improvement in bacteria
-
Zhang YX, Perry K, Vinci VA, Powell K, Stemmer WP, del Cardayre SB (2002) Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415: 644-646.
-
(2002)
Nature
, vol.415
, pp. 644-646
-
-
Zhang, Y.X.1
Perry, K.2
Vinci, V.A.3
Powell, K.4
Stemmer, W.P.5
del Cardayre, S.B.6
-
115
-
-
0031909113
-
Molecular evolution by staggered extension process (StEP) in vitro recombination
-
Zhao H, Giver L, Shao Z, Affholter JA, Arnold FH (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16: 258-261.
-
(1998)
Nat Biotechnol
, vol.16
, pp. 258-261
-
-
Zhao, H.1
Giver, L.2
Shao, Z.3
Affholter, J.A.4
Arnold, F.H.5
-
116
-
-
33646465694
-
Fermentation of 12 % (w/v) glucose to 1. 2 M lactate by Escherichia coli strain SZ194 using mineral salts medium
-
Zhou S, Shanmugam KT, Yomano LP, Grabar TB, Ingram LO (2006) Fermentation of 12 % (w/v) glucose to 1. 2 M lactate by Escherichia coli strain SZ194 using mineral salts medium. Biotechnol Lett 28: 663-670.
-
(2006)
Biotechnol Lett
, vol.28
, pp. 663-670
-
-
Zhou, S.1
Shanmugam, K.T.2
Yomano, L.P.3
Grabar, T.B.4
Ingram, L.O.5
|