-
1
-
-
59249089471
-
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
-
10.1371/journal.pgen.1000344 19165319
-
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, et al. PLoS Genet 2009 5 1 1000344 10.1371/journal.pgen.1000344 19165319
-
(2009)
PLoS Genet
, vol.5
, Issue.1
, pp. 51000344
-
-
Touchon, M.1
Hoede, C.2
Tenaillon, O.3
Barbe, V.4
Baeriswyl, S.5
Bidet, P.6
Bingen, E.7
Bonacorsi, S.8
Bouchier, C.9
Bouvet, O.10
-
3
-
-
76949094947
-
The population genetics of commensal Escherichia coli
-
10.1038/nrmicro2298 20157339
-
The population genetics of commensal Escherichia coli. Tenaillon O, Skurnik D, Picard B, Denamur E, Nat Rev Microbiol 2010 8 207 217 10.1038/nrmicro2298 20157339
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 207-217
-
-
Tenaillon, O.1
Skurnik, D.2
Picard, B.3
Denamur, E.4
-
4
-
-
70449568272
-
Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli
-
10.1073/pnas.0903585106 19815525
-
Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K, Proc Natl Acad Sci USA 2009 106 42 17939 10.1073/pnas.0903585106 19815525
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.42
, pp. 17939
-
-
Ogura, Y.1
Ooka, T.2
Iguchi, A.3
Toh, H.4
Asadulghani, M.5
Oshima, K.6
Kodama, T.7
Abe, H.8
Nakayama, K.9
Kurokawa, K.10
-
5
-
-
78149470831
-
Comparison of 61 Sequenced Escherichia coli Genomes
-
10.1007/s00248-010-9717-3 20623278
-
Comparison of 61 Sequenced Escherichia coli Genomes. Lukjancenko O, Wassenaar TM, Ussery DW, Microb Ecol 2010 60 4 708 720 10.1007/s00248-010-9717-3 20623278
-
(2010)
Microb Ecol
, vol.60
, Issue.4
, pp. 708-720
-
-
Lukjancenko, O.1
Wassenaar, T.M.2
Ussery, D.W.3
-
6
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
DOI 10.1038/nrg1603
-
Phylogenomics and the reconstruction of the tree of life. Delsuc F, Brinkmann H, Philippe H, Nat Rev Genet 2005 6 5 361 375 15861208 (Pubitemid 40577180)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.5
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
7
-
-
79957787637
-
Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)
-
10.1073/pnas.1105168108 21536867
-
Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Sims GE, Kim S-H, Proc Natl Acad Sci USA 2011 108 20 8329 8334 10.1073/pnas.1105168108 21536867
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.20
, pp. 8329-8334
-
-
Sims, G.E.1
Kim, S.-H.2
-
8
-
-
70849118522
-
Operons
-
10.1007/s00018-009-0114-3 19662496
-
Operons. Osbourn AE, Field B, Cell Mol Life Sci 2009 66 23 3755 3775 10.1007/s00018-009-0114-3 19662496
-
(2009)
Cell Mol Life Sci
, vol.66
, Issue.23
, pp. 3755-3775
-
-
Osbourn, A.E.1
Field, B.2
-
9
-
-
33745712583
-
The Life-Cycle of Operons
-
10.1371/journal.pgen.0020096 16789824
-
The Life-Cycle of Operons. Price MN, Arkin AP, Alm EJ, PLoS Genet 2006 2 6 96 10.1371/journal.pgen.0020096 16789824
-
(2006)
PLoS Genet
, vol.2
, Issue.6
, pp. 596
-
-
Price, M.N.1
Arkin, A.P.2
Alm, E.J.3
-
10
-
-
0035045707
-
Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria
-
Horizontal Transfer of the Photosynthesis Gene Cluster and Operon Rearrangement in Purple Bacteria. Igarashi N, Harada J, Nagashima S, Matsuura K, Shimada K, Nagashima KV, J Mol Evol 2001 52 333 341 11343129 (Pubitemid 32368243)
-
(2001)
Journal of Molecular Evolution
, vol.52
, Issue.4
, pp. 333-341
-
-
Igarashi, N.1
Harada, J.2
Nagashima, S.3
Matsuura, K.4
Shimada, K.5
Nagashima, K.V.P.6
-
11
-
-
3543051830
-
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
-
DOI 10.1101/gr.2289704
-
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements. Darling ACE, Genome Res 2004 14 7 1394 1403 10.1101/gr.2289704 15231754 (Pubitemid 39029237)
-
(2004)
Genome Research
, vol.14
, Issue.7
, pp. 1394-1403
-
-
Darling, A.C.E.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
12
-
-
79551599525
-
Mugsy: Fast multiple alignment of closely related whole genomes
-
10.1093/bioinformatics/btq665 21148543
-
Mugsy: fast multiple alignment of closely related whole genomes. Angiuoli SV, Salzberg SL, Bioinformatics 2011 27 334 342 10.1093/bioinformatics/btq665 21148543
-
(2011)
Bioinformatics
, vol.27
, pp. 334-342
-
-
Angiuoli, S.V.1
Salzberg, S.L.2
-
13
-
-
56949097722
-
Evolution of genome architecture
-
10.1016/j.biocel.2008.09.015 18929678
-
Evolution of genome architecture. Koonin EV, Int J Biochem Cell Biol 2009 41 2 298 306 10.1016/j.biocel.2008.09.015 18929678
-
(2009)
Int J Biochem Cell Biol
, vol.41
, Issue.2
, pp. 298-306
-
-
Koonin, E.V.1
-
14
-
-
0034641731
-
Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics
-
10.1073/pnas.180094797 10954745
-
Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Pupo GM, Lan R, Reeves PR, Proc Natl Acad Sci USA 2000 97 10567 10572 10.1073/pnas.180094797 10954745
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10567-10572
-
-
Pupo, G.M.1
Lan, R.2
Reeves, P.R.3
-
15
-
-
79952393752
-
Core and Panmetabolism in Escherichia coli
-
10.1128/JB.01192-10 21239590
-
Core and Panmetabolism in Escherichia coli. Vieira G, Sabarly V, Bourguignon P-Y, Durot M, Le Fevre F, Mornico D, Vallenet D, Bouvet O, Denamur E, Schachter V, et al. J Bacteriol 2011 193 6 1461 1472 10.1128/JB.01192-10 21239590
-
(2011)
J Bacteriol
, vol.193
, Issue.6
, pp. 1461-1472
-
-
Vieira, G.1
Sabarly, V.2
Bourguignon, P.-Y.3
Durot, M.4
Le Fevre, F.5
Mornico, D.6
Vallenet, D.7
Bouvet, O.8
Denamur, E.9
Schachter, V.10
-
16
-
-
0031664320
-
Shigella and enteroinvasive Escherichia coli strains are derived from distinct ancestral strains of E. coli
-
Shigella and enteroinvasive Escherichia coli strains are derived from distinct ancestral strains of E. coli. Rolland K, Lambert-Zechovsky N, Picard B, Denamur E, Microbiology 1998 144 2667 2672 10.1099/00221287-144-9-2667 9782516 (Pubitemid 28457177)
-
(1998)
Microbiology
, vol.144
, Issue.9
, pp. 2667-2672
-
-
Rolland, K.1
Lambert-Zechovsky, N.2
Picard, B.3
Denamur, E.4
-
17
-
-
67651067964
-
Gene and genome trees conflict at many levels
-
10.1098/rstb.2009.0042 19571241
-
Gene and genome trees conflict at many levels. Haggerty LS, Martin FJ, Fitzpatrick DA, McInerney JO, Phil Trans R Soc B 2009 364 2209 2219 10.1098/rstb.2009.0042 19571241
-
(2009)
Phil Trans R Soc B
, vol.364
, pp. 2209-2219
-
-
Haggerty, L.S.1
Martin, F.J.2
Fitzpatrick, D.A.3
McInerney, J.O.4
-
18
-
-
0042386134
-
The evolutionary history of Shigella and enteroinvasive Escherichia coli revised
-
DOI 10.1007/s00239-003-2460-3
-
The evolutionary history of Shigella and enteroinvasive Escherichia coli revised. Escobar-Paramo P, Giudicelli C, Parsot C, Denamur E, J Mol Evol 2003 57 140 148 10.1007/s00239-003-2460-3 14562958 (Pubitemid 37026537)
-
(2003)
Journal of Molecular Evolution
, vol.57
, Issue.2
, pp. 140-148
-
-
Escobar-Paramo, P.1
Giudicelli, C.2
Parsot, C.3
Denamur, E.4
-
19
-
-
33846092166
-
Black holes, antivirulence genes, and gene inactivation in the evolution of bacterial pathogens
-
DOI 10.1111/j.1574-6968.2006.00526.x
-
Black holes, antivirulence genes, and gene inactivation in the evolution of bacterial pathogens. Maurelli AT, FEMS Microbiol Lett 2007 267 1 1 8 10.1111/j.1574-6968.2006.00526.x 17233672 (Pubitemid 46066532)
-
(2007)
FEMS Microbiology Letters
, vol.267
, Issue.1
, pp. 1-8
-
-
Maurelli, A.T.1
-
21
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
DOI 10.1038/35012500
-
Lateral gene transfer and the nature of bacterial innovation. Ochman H, Lawrence JG, Groisman EA, Nature 2000 405 299 304 10.1038/35012500 10830951 (Pubitemid 30337055)
-
(2000)
Nature
, vol.405
, Issue.6784
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Grolsman, E.A.3
-
22
-
-
2442667673
-
A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli
-
DOI 10.1093/molbev/msh118
-
A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Escobar-Paramo P, Clermont O, Blanc-Potard A-B, Bui H, nec CLB, Denamur E, Mol Biol Evol 2004 21 6 1085 1094 10.1093/molbev/msh118 15014151 (Pubitemid 38658217)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.6
, pp. 1085-1094
-
-
Escobar-Paramo, P.1
Clermont, O.2
Blanc-Potard, A.-B.3
Bui, H.4
Le Bouguenec, C.5
Denamur, E.6
-
23
-
-
35848958139
-
Extraintestinal virulence is a coincidental by-product of commensalism in b2 phylogenetic group Escherichia coli strains
-
DOI 10.1093/molbev/msm172
-
Gouriou Sp, Picard B, Nassif X, Denamur E, Tenaillon O: Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic groupEscherichia colistrains. Le Gall T, Clermont O, Mol Biol Evol 2007 24 11 2373 2384 10.1093/molbev/msm172 17709333 (Pubitemid 350060443)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.11
, pp. 2373-2384
-
-
Le Gall, T.1
Clermont, O.2
Gouriou, S.3
Picard, B.4
Nassif, X.5
Denamur, E.6
Tenaillon, O.7
-
24
-
-
58149518390
-
The bacterial LexA transcriptional repressor
-
10.1007/s00018-008-8378-6 18726173
-
The bacterial LexA transcriptional repressor. Butala M, gur-Bertok D, Busby SJW, Cell Mol Life Sci 2009 66 1 82 93 10.1007/s00018-008-8378-6 18726173
-
(2009)
Cell Mol Life Sci
, vol.66
, Issue.1
, pp. 82-93
-
-
Butala, M.1
Gur-Bertok, D.2
Busby, S.J.W.3
-
25
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Thompson JD, Higgins DG, Gibson TJ, Nucleic Acids Res 1994 22 4673 4680 10.1093/nar/22.22.4673 7984417 (Pubitemid 24354800)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
26
-
-
0038401982
-
Identification of additional genes belonging to the LexA regulon in Escherichia coli
-
DOI 10.1046/j.1365-2958.2000.01826.x
-
Identification of additional genes belonging to the LexA regulon in Escherichia coli. Fernández De Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R, Mol Microbiol 2000 35 6 1560 1572 10760155 (Pubitemid 30175530)
-
(2000)
Molecular Microbiology
, vol.35
, Issue.6
, pp. 1560-1572
-
-
Fernandez De Henestrosa, A.R.1
Ogi, T.2
Aoyagi, S.3
Chafin, D.4
Hayes, J.J.5
Ohmori, H.6
Woodgate, R.7
-
27
-
-
77649216223
-
The Type III Secretion Effector NleE Inhibits NF-B Activation
-
10.1371/journal.ppat.1000743 20126447
-
The Type III Secretion Effector NleE Inhibits NF-B Activation. Nadler C, Baruch K, Kobi S, Mills E, Haviv G, Farago M, Alkalay I, Bartfeld S, Meyer TF, Ben-Neriah Y, et al. PLoS Pathog 2010 6 1 1000743 10.1371/journal.ppat.1000743 20126447
-
(2010)
PLoS Pathog
, vol.6
, Issue.1
, pp. 51000743
-
-
Nadler, C.1
Baruch, K.2
Kobi, S.3
Mills, E.4
Haviv, G.5
Farago, M.6
Alkalay, I.7
Bartfeld, S.8
Meyer, T.F.9
Ben-Neriah, Y.10
-
28
-
-
0025183708
-
Basic Local Alignment Search Tool
-
2231712
-
Basic Local Alignment Search Tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, J Mol Biol 1990 215 3 403 410 2231712
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
29
-
-
33750156563
-
Overlapping genes as rare genomic markers: The phylogeny of γ-Proteobacteria as a case study
-
DOI 10.1016/j.tig.2006.08.011, PII S0168952506002939
-
Overlapping genes as rare genomic markers: the phylogeny of gamma-Proteobacteria as a case study. Luo Y, Fu C, Zhang D-Y, Lin K, Trends Genet 2006 22 11 593 596 10.1016/j.tig.2006.08.011 16973237 (Pubitemid 44602266)
-
(2006)
Trends in Genetics
, vol.22
, Issue.11
, pp. 593-596
-
-
Luo, Y.1
Fu, C.2
Zhang, D.-Y.3
Lin, K.4
-
30
-
-
0030210340
-
Gene order is not conserved in bacterial evolution
-
10.1016/0168-9525(96)20006-X 8783936
-
Gene order is not conserved in bacterial evolution. Mushegian AR, Koonin EV, Trends Genet 1996 12 289 290 10.1016/0168-9525(96)20006-X 8783936
-
(1996)
Trends Genet
, vol.12
, pp. 289-290
-
-
Mushegian, A.R.1
Koonin, E.V.2
-
31
-
-
0035085816
-
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
-
DOI 10.1101/gr.GR-1619R
-
Genome alignment, evolution of prokaryotic genome organization and prediction of gene function using genomic context. Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV, Genome Res 2001 11 356 372 10.1101/gr.GR-1619R 11230160 (Pubitemid 32243846)
-
(2001)
Genome Research
, vol.11
, Issue.3
, pp. 356-372
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Kondrashov, A.S.3
Koonin, E.V.4
-
32
-
-
84908096911
-
MicroScope: A platform for microbial genome annotation and comparative genomics
-
10.1093/database/bap021 20157493
-
MicroScope: a platform for microbial genome annotation and comparative genomics. Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, et al. Database 2009 2009 ap021 10.1093/database/bap021 20157493
-
(2009)
Database
, vol.2009
-
-
Vallenet, D.1
Engelen, S.2
Mornico, D.3
Cruveiller, S.4
Fleury, L.5
Lajus, A.6
Rouy, Z.7
Roche, D.8
Salvignol, G.9
Scarpelli, C.10
-
33
-
-
79952407065
-
Population Genetics of Pathogenic Escherichia coli
-
Hoboken: John Wiley & Sons, Inc Robinson DA, Falush D, Feil EJ
-
Population Genetics of Pathogenic Escherichia coli. Denamur E, Picard B, Tenaillon O, Bacterial Population Genetics in Infectious Disease Hoboken: John Wiley & Sons, Inc, Robinson DA, Falush D, Feil EJ, 2010
-
(2010)
Bacterial Population Genetics in Infectious Disease
-
-
Denamur, E.1
Picard, B.2
Tenaillon, O.3
-
34
-
-
84859165788
-
The Genomes OnLine Database (GOLD) v. 4: Status of genomic and metagenomic projects and their associated metadata
-
10.1093/nar/gkr1100 22135293
-
The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Pagani I, Liolios K, Jansson J, Chen I-MA, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC, Nucleic Acids Res 2012 40 571 D579 10.1093/nar/gkr1100 22135293
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Pagani, I.1
Liolios, K.2
Jansson, J.3
Chen, I.-M.4
Smirnova, T.5
Nosrat, B.6
Markowitz, V.M.7
Kyrpides, N.C.8
-
35
-
-
41049110434
-
Automated simultaneous analysis phylogenetics (ASAP): An enabling tool for phlyogenomics
-
DOI 10.1186/1471-2105-9-103
-
Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. Sarkar I, Egan MG, Coruzzi G, Lee EK, Desalle R, BMC Bioinforma 2008 9 1 103 10.1186/1471-2105-9-103 (Pubitemid 351420387)
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 103
-
-
Sarkar, I.N.1
Egan, M.G.2
Coruzzi, G.3
Lee, E.K.4
DeSalle, R.5
-
37
-
-
0031371067
-
Multiple sources of character information and the phylogeny of Hawaiian Drosophilids
-
Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Baker RH, DeSalle R, Syst Biol 1997 46 4 654 673 10.1093/sysbio/46.4.654 11975337 (Pubitemid 127366000)
-
(1997)
Systematic Biology
, vol.46
, Issue.4
, pp. 654-673
-
-
Baker, R.H.1
Desalle, R.2
|