-
1
-
-
67649803191
-
Genetic suppressors and recovery of repressed biochemical memory
-
Beckwith J, (2009) Genetic suppressors and recovery of repressed biochemical memory. J Biol Chem 284: 12585-12592.
-
(2009)
J Biol Chem
, vol.284
, pp. 12585-12592
-
-
Beckwith, J.1
-
2
-
-
70350452739
-
Increased expression of Mg2+ transport proteins enhances the survival of Salmonella enterica at high temperature
-
O'Connor K, Fletcher SA, Csonka LN, (2009) Increased expression of Mg2+ transport proteins enhances the survival of Salmonella enterica at high temperature. Proc Natl Acad Sci U S A 106: 17522-17527.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 17522-17527
-
-
O'Connor, K.1
Fletcher, S.A.2
Csonka, L.N.3
-
3
-
-
77955969370
-
The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems
-
Kim K-S, Pelton JG, Inwood WB, Andersen U, Kustu S, et al. (2010) The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems. J Bacteriol 192: 4089-4102.
-
(2010)
J Bacteriol
, vol.192
, pp. 4089-4102
-
-
Kim, K.-S.1
Pelton, J.G.2
Inwood, W.B.3
Andersen, U.4
Kustu, S.5
-
4
-
-
0041335300
-
Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression
-
Soupene E, van Heeswijk WC, Plumbridge J, Stewart V, Bertenthal D, et al. (2003) Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J Bacteriol 185: 5611-5626.
-
(2003)
J Bacteriol
, vol.185
, pp. 5611-5626
-
-
Soupene, E.1
van Heeswijk, W.C.2
Plumbridge, J.3
Stewart, V.4
Bertenthal, D.5
-
5
-
-
71549159136
-
Epistatic effects of the protease/chaperone HflB on some damaged forms of the Escherichia coli ammonium channel AmtB
-
Inwood WB, Hall JA, Kim K-S, Demirkhanyan L, Wemmer D, et al. (2009) Epistatic effects of the protease/chaperone HflB on some damaged forms of the Escherichia coli ammonium channel AmtB. Genetics 183: 1327-1340.
-
(2009)
Genetics
, vol.183
, pp. 1327-1340
-
-
Inwood, W.B.1
Hall, J.A.2
Kim, K.-S.3
Demirkhanyan, L.4
Wemmer, D.5
-
6
-
-
31544450286
-
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection
-
2006.0008
-
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008.
-
(2006)
Mol Syst Biol
, vol.2
-
-
Baba, T.1
Ara, T.2
Hasegawa, M.3
Takai, Y.4
Okumura, Y.5
-
7
-
-
38949151064
-
How to usefully compare homologous plant genes and chromosomes as DNA sequences
-
Lyons E, Freeling M, (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J 53: 661-673.
-
(2008)
Plant J
, vol.53
, pp. 661-673
-
-
Lyons, E.1
Freeling, M.2
-
8
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
9
-
-
12344335569
-
DAGchainer: a tool for mining segmental genome duplications and synteny
-
Haas BJ, Delcher AL, Wortman JR, Salzberg SL, (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20: 3643-3646.
-
(2004)
Bioinformatics
, vol.20
, pp. 3643-3646
-
-
Haas, B.J.1
Delcher, A.L.2
Wortman, J.R.3
Salzberg, S.L.4
-
10
-
-
77952299957
-
Prodigal: prokaryotic gene recognition and translation initiation site identification
-
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
Chen, G.L.2
Locascio, P.F.3
Land, M.L.4
Larimer, F.W.5
-
11
-
-
0030854739
-
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR, (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
12
-
-
3543051830
-
Mauve: multiple alignment of conserved genomic sequence with rearrangements
-
Darling AC, Mau B, Blattner FR, Perna NT, (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394-1403.
-
(2004)
Genome Res
, vol.14
, pp. 1394-1403
-
-
Darling, A.C.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
13
-
-
71549140222
-
Genetic evidence for an essential oscillation of transmembrane-spanning segment 5 in the Escherichia coli ammonium channel AmtB
-
Inwood WB, Hall JA, Kim K-S, Fong R, Kustu S, (2009) Genetic evidence for an essential oscillation of transmembrane-spanning segment 5 in the Escherichia coli ammonium channel AmtB. Genetics 183: 1341-1355.
-
(2009)
Genetics
, vol.183
, pp. 1341-1355
-
-
Inwood, W.B.1
Hall, J.A.2
Kim, K.-S.3
Fong, R.4
Kustu, S.5
-
14
-
-
0035161027
-
IS186 insertion at a hot spot in the lon promoter as a basis for lon protease deficiency of Escherichia coli B: identification of a consensus target sequence for IS186 transposition
-
SaiSree L, Reddy M, Gowrishankar J, (2001) IS186 insertion at a hot spot in the lon promoter as a basis for lon protease deficiency of Escherichia coli B: identification of a consensus target sequence for IS186 transposition. J Bacteriol 183: 6943-6946.
-
(2001)
J Bacteriol
, vol.183
, pp. 6943-6946
-
-
SaiSree, L.1
Reddy, M.2
Gowrishankar, J.3
-
15
-
-
33746683240
-
Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes
-
Hughes D, (2000) Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes. Genome Biol 1: REVIEWS0006.
-
(2000)
Genome Biol
, vol.1
-
-
Hughes, D.1
-
16
-
-
0024213532
-
Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion?
-
Higgins CF, McLaren RS, Newbury SF, (1988) Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion? Gene 72: 3-14.
-
(1988)
Gene
, vol.72
, pp. 3-14
-
-
Higgins, C.F.1
McLaren, R.S.2
Newbury, S.F.3
-
17
-
-
0021669070
-
Repetitive extragenic palindromic sequences: a major component of the bacterial genome
-
Stern MJ, Ames GF, Smith NH, Robinson EC, Higgins CF, (1984) Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37: 1015-1026.
-
(1984)
Cell
, vol.37
, pp. 1015-1026
-
-
Stern, M.J.1
Ames, G.F.2
Smith, N.H.3
Robinson, E.C.4
Higgins, C.F.5
-
18
-
-
0028206349
-
Rhs elements of Escherichia coli: a family of genetic composites each encoding a large mosaic protein
-
Hill CW, Sandt CH, Vlazny DA, (1994) Rhs elements of Escherichia coli: a family of genetic composites each encoding a large mosaic protein. Mol Microbiol 12: 865-871.
-
(1994)
Mol Microbiol
, vol.12
, pp. 865-871
-
-
Hill, C.W.1
Sandt, C.H.2
Vlazny, D.A.3
-
19
-
-
0021613767
-
A repetitive DNA sequence rhs responsible for duplications within the Escherichia coli K-12 chromosome
-
Lin RJ, Capage M, Hill CW, (1984) A repetitive DNA sequence rhs responsible for duplications within the Escherichia coli K-12 chromosome. J Mol Biol 177: 1-18.
-
(1984)
J Mol Biol
, vol.177
, pp. 1-18
-
-
Lin, R.J.1
Capage, M.2
Hill, C.W.3
-
20
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2006) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
-
(2006)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
-
21
-
-
0035671034
-
Characterization of the allelic variation in the rpoS gene in thirteen K12 and six other non-pathogenic Escherichia coli strains
-
Atlung T, Nielsen HV, Hansen FG, (2002) Characterization of the allelic variation in the rpoS gene in thirteen K12 and six other non-pathogenic Escherichia coli strains. Mol Genet Genomics 266: 873-881.
-
(2002)
Mol Genet Genomics
, vol.266
, pp. 873-881
-
-
Atlung, T.1
Nielsen, H.V.2
Hansen, F.G.3
-
22
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462.
-
(1997)
Science
, vol.277
, pp. 1453-1462
-
-
Blattner, F.R.1
Plunkett III, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
-
23
-
-
0030464649
-
Bacterial polysaccharide synthesis and gene nomenclature
-
Reeves PR, Hobbs M, Valvano MA, Skurnik M, Whitfield C, et al. (1996) Bacterial polysaccharide synthesis and gene nomenclature. Trends Microbiol 4: 495-503.
-
(1996)
Trends Microbiol
, vol.4
, pp. 495-503
-
-
Reeves, P.R.1
Hobbs, M.2
Valvano, M.A.3
Skurnik, M.4
Whitfield, C.5
-
24
-
-
0036797992
-
Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea
-
Rodionov DA, Mironov AA, Gelfand MS, (2002) Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res 12: 1507-1516.
-
(2002)
Genome Res
, vol.12
, pp. 1507-1516
-
-
Rodionov, D.A.1
Mironov, A.A.2
Gelfand, M.S.3
-
25
-
-
0028023336
-
Construction of chromosomal rearrangements in Salmonella by transduction: inversions of non-permissive segments are not lethal
-
Miesel L, Segall A, Roth JR, (1994) Construction of chromosomal rearrangements in Salmonella by transduction: inversions of non-permissive segments are not lethal. Genetics 137: 919-932.
-
(1994)
Genetics
, vol.137
, pp. 919-932
-
-
Miesel, L.1
Segall, A.2
Roth, J.R.3
-
26
-
-
0014287014
-
Ultraviolet sensitivity gene of Escherichia coli B
-
Donch J, Greenberg J, (1968) Ultraviolet sensitivity gene of Escherichia coli B. J Bacteriol 95: 1555-1559.
-
(1968)
J Bacteriol
, vol.95
, pp. 1555-1559
-
-
Donch, J.1
Greenberg, J.2
-
27
-
-
70449524297
-
Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes
-
Studier FW, Daegelen P, Lenski RE, Maslov S, Kim JF, (2009) Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. J Mol Biol 11: 653-680.
-
(2009)
J Mol Biol
, vol.11
, pp. 653-680
-
-
Studier, F.W.1
Daegelen, P.2
Lenski, R.E.3
Maslov, S.4
Kim, J.F.5
-
28
-
-
39649117755
-
The impact of next-generation sequencing technology on genetics
-
Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133-141.
-
(2008)
Trends Genet
, vol.24
, pp. 133-141
-
-
Mardis, E.R.1
-
29
-
-
0033910128
-
Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli
-
Brinkkötter A, Klöss H, Alpert C, Lengeler JW, (2000) Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli. Mol Microbiol 37: 125-135.
-
(2000)
Mol Microbiol
, vol.37
, pp. 125-135
-
-
Brinkkötter, A.1
Klöss, H.2
Alpert, C.3
Lengeler, J.W.4
-
30
-
-
34547852218
-
OSLay: optimal syntenic layout of unfinished assemblies
-
Richter DC, Schuster SC, Huson DH, (2007) OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics 23: 1573-1579.
-
(2007)
Bioinformatics
, vol.23
, pp. 1573-1579
-
-
Richter, D.C.1
Schuster, S.C.2
Huson, D.H.3
-
31
-
-
0022549357
-
Target sequences for mutagenesis in Salmonella histidine-requiring mutants
-
Hartman PE, Ames BN, Roth JR, Barnes WM, Levin DE, (1986) Target sequences for mutagenesis in Salmonella histidine-requiring mutants. Environ Mutagen 8: 631-641.
-
(1986)
Environ Mutagen
, vol.8
, pp. 631-641
-
-
Hartman, P.E.1
Ames, B.N.2
Roth, J.R.3
Barnes, W.M.4
Levin, D.E.5
-
32
-
-
0016739762
-
Mutation and DNA replication in Escherichia coli treated with low concentrations of N-methyl-N′-nitro-N-nitrosoguanidine
-
Jiménez-Sánchez A, Cerdá-Olmedo E, (1975) Mutation and DNA replication in Escherichia coli treated with low concentrations of N-methyl-N′-nitro-N-nitrosoguanidine. Mutat Res 28: 337-345.
-
(1975)
Mutat Res
, vol.28
, pp. 337-345
-
-
Jiménez-Sánchez, A.1
Cerdá-Olmedo, E.2
-
33
-
-
50849126804
-
High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies
-
Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, et al. (2008) High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet 4: e1000139.
-
(2008)
PLoS Genet
, vol.4
-
-
Srivatsan, A.1
Han, Y.2
Peng, J.3
Tehranchi, A.K.4
Gibbs, R.5
-
34
-
-
58149200962
-
Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing
-
Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I, (2008) Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS One 3: e4012.
-
(2008)
PLoS One
, vol.3
-
-
Shen, Y.1
Sarin, S.2
Liu, Y.3
Hobert, O.4
Pe'er, I.5
-
35
-
-
70449533064
-
Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3)
-
Daegelen P, Studier FW, Lenski RE, Cure S, Kim JF, (2009) Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3). J Mol Biol 394: 634-643.
-
(2009)
J Mol Biol
, vol.394
, pp. 634-643
-
-
Daegelen, P.1
Studier, F.W.2
Lenski, R.E.3
Cure, S.4
Kim, J.F.5
-
36
-
-
67549090009
-
Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12
-
Ferenci T, Zhou Z, Betteridge T, Ren Y, Liu Y, et al. (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J Bacteriol 191: 4025-4029.
-
(2009)
J Bacteriol
, vol.191
, pp. 4025-4029
-
-
Ferenci, T.1
Zhou, Z.2
Betteridge, T.3
Ren, Y.4
Liu, Y.5
-
37
-
-
70350686881
-
Genome sequences of Escherichia coli B strains REL606 and BL21(DE3)
-
Jeong H, Barbe V, Lee CH, Vallenet D, Yu DS, et al. (2009) Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol 394: 644-652.
-
(2009)
J Mol Biol
, vol.394
, pp. 644-652
-
-
Jeong, H.1
Barbe, V.2
Lee, C.H.3
Vallenet, D.4
Yu, D.S.5
-
38
-
-
59949090259
-
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
-
Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, et al. (2009) De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 19: 294-305.
-
(2009)
Genome Res
, vol.19
, pp. 294-305
-
-
Reinhardt, J.A.1
Baltrus, D.A.2
Nishimura, M.T.3
Jeck, W.R.4
Jones, C.D.5
-
39
-
-
77954419450
-
The genetic basis of laboratory adaptation in Caulobacter crescentus
-
Marks ME, Castro-Rojas CM, Teiling C, Du L, Kapatral V, et al. (2010) The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol 192: 3678-3688.
-
(2010)
J Bacteriol
, vol.192
, pp. 3678-3688
-
-
Marks, M.E.1
Castro-Rojas, C.M.2
Teiling, C.3
Du, L.4
Kapatral, V.5
-
40
-
-
70350641005
-
Genome evolution and adaptation in a long-term experiment with Escherichia coli
-
Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, et al. (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
-
41
-
-
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
-
Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, et al. (2009) 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 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
-
42
-
-
33744482546
-
Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor
-
Velicer GJ, Raddatz G, Keller H, Deiss S, Lanz C, et al. (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
-
43
-
-
76749117156
-
Assembly complexity of prokaryotic genomes using short reads
-
Kingsford C, Schatz MC, Pop M, (2010) Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11: 21.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 21
-
-
Kingsford, C.1
Schatz, M.C.2
Pop, M.3
-
44
-
-
63249121217
-
Application of 'next-generation' sequencing technologies to microbial genetics
-
MacLean D, Jones JD, Studholme DJ, (2009) Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol 7: 287-296.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 287-296
-
-
MacLean, D.1
Jones, J.D.2
Studholme, D.J.3
-
45
-
-
77956279237
-
Assembly of large genomes using second-generation sequencing
-
Schatz MC, Delcher AL, Salzberg SL, (2010) Assembly of large genomes using second-generation sequencing. Genome Res 20: 1165-1173.
-
(2010)
Genome Res
, vol.20
, pp. 1165-1173
-
-
Schatz, M.C.1
Delcher, A.L.2
Salzberg, S.L.3
-
46
-
-
3142679507
-
The replication-related organization of bacterial genomes
-
Rocha EP, (2004) The replication-related organization of bacterial genomes. Microbiology 150: 1609-1627.
-
(2004)
Microbiology
, vol.150
, pp. 1609-1627
-
-
Rocha, E.P.1
|