-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
ALTSCHUL, S. F., T. L. MADDEN, A. A. SCHFFER, J. ZHANG, Z. ZHANG et al., 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
2
-
-
0242353159
-
Elements for a theory of molecular evolution
-
ARBER, W., 2003 Elements for a theory of molecular evolution. Gene 317: 3-11.
-
(2003)
Gene
, vol.317
, pp. 3-11
-
-
Arber, W.1
-
3
-
-
19544374490
-
Genome rearrangement distances and gene order phylogeny in gamma-proteobacteria
-
BELDA, E., A. MOYA and F. J. SILVA, 2005 Genome rearrangement distances and gene order phylogeny in gamma-proteobacteria. Mol. Biol. Evol. 22: 1456-1467.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1456-1467
-
-
Belda, E.1
Moya, A.2
Silva, F.J.3
-
4
-
-
0036899896
-
Evolution of microbial genomes: Sequence acquisition and loss
-
BERG, O. G., and C. G. KURLAND, 2002 Evolution of microbial genomes: sequence acquisition and loss. Mol. Biol. Evol. 19: 2265-2276.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 2265-2276
-
-
Berg, O.G.1
Kurland, C.G.2
-
5
-
-
33645240284
-
Significant gene order and expression differences in Bordetella pertussis despite limited gene content variation
-
BRINIG, M. M., C. A. CUMMINGS, G. N. SANDEN, P. STEFANELLI, A. LAWRENCE et al., 2006 Significant gene order and expression differences in Bordetella pertussis despite limited gene content variation. J. Bacteriol. 188: 2375-2382.
-
(2006)
J. Bacteriol.
, vol.188
, pp. 2375-2382
-
-
Brinig, M.M.1
Cummings, C.A.2
Sanden, G.N.3
Stefanelli, P.4
Lawrence, A.5
-
6
-
-
33748041198
-
Positional homology in bacterial genomes
-
BURGETZ, I. J., S. SHARIFF, A. PANG and E. R. M. TILLIER, 2006 Positional homology in bacterial genomes. Evol. Bioinform. 2: 42-55.
-
(2006)
Evol. Bioinform.
, vol.2
, pp. 42-55
-
-
Burgetz, I.J.1
Shariff, S.2
Pang, A.3
Tillier, E.R.M.4
-
7
-
-
0036595545
-
Preferential orientation of natural lambdoid prophages and bacterial chromosome organization
-
CAMPBELL, A. M., 2002 Preferential orientation of natural lambdoid prophages and bacterial chromosome organization. Theor. Popul. Biol. 61: 503-507.
-
(2002)
Theor. Popul. Biol.
, vol.61
, pp. 503-507
-
-
Campbell, A.M.1
-
8
-
-
3142514466
-
The impact of prophages on bacterial chromosomes
-
CANCHAYA, C., G. FOURNOUS and H. BRUSSOW, 2004 The impact of prophages on bacterial chromosomes. Mol. Microbiol. 53: 9-18.
-
(2004)
Mol. Microbiol.
, vol.53
, pp. 9-18
-
-
Canchaya, C.1
Fournous, G.2
Brussow, H.3
-
9
-
-
33645232361
-
Genomic islands and the ecology and evolution of Prochlorococcus
-
COLEMAN, M. L., M. B. SULLIVAN, A. C. MARTINY, C. STEGLICH, K. BARRY et al., 2006 Genomic islands and the ecology and evolution of Prochlorococcus. Science 311: 1768-1770.
-
(2006)
Science
, vol.311
, pp. 1768-1770
-
-
Coleman, M.L.1
Sullivan, M.B.2
Martiny, A.C.3
Steglich, C.4
Barry, K.5
-
10
-
-
2442474385
-
Effects of reciprocal chromosomal translocations on the fitness of Saccharomyces cerevisiae
-
DOI 10.1038/sj.embor.7400123
-
COLSON, I., D. DELNERI and S. G. OLIVER, 2004 Effects of reciprocal chromosomal translocations on the fitness of Saccharomyces cerevisiae. EMBO Rep. 5: 392-398. (Pubitemid 38618282)
-
(2004)
EMBO Reports
, vol.5
, Issue.4
, pp. 392-398
-
-
Colson, I.1
Delneri, D.2
Oliver, S.G.3
-
11
-
-
0642312312
-
The source of laterally transferred genes in bacterial genomes
-
DAUBIN, V., E. LERAT and G. PERRIERE, 2003a The source of laterally transferred genes in bacterial genomes. Genome Biol. 4: R57.
-
(2003)
Genome Biol.
, vol.4
-
-
Daubin, V.1
Lerat, E.2
Perriere, G.3
-
12
-
-
0042027842
-
Phylogenetics and the cohesion of bacterial genomes
-
DAUBIN, V., N. A. MORAN and H. OCHMAN, 2003b Phylogenetics and the cohesion of bacterial genomes. Science 301: 829-832.
-
(2003)
Science
, vol.301
, pp. 829-832
-
-
Daubin, V.1
Moran, N.A.2
Ochman, H.3
-
13
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
DOI 10.1093/nar/gkh340
-
EDGAR, R. C., 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797. (Pubitemid 38832724)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
14
-
-
0033783996
-
Assessing evolutionary relationships among microbes from whole-genome analysis
-
EISEN, J. A., 2000 Assessing evolutionary relationships among microbes from whole-genome analysis. Curr. Opin. Microbiol. 3: 475-480.
-
(2000)
Curr. Opin. Microbiol.
, vol.3
, pp. 475-480
-
-
Eisen, J.A.1
-
15
-
-
26444558214
-
How essential are nonessential genes?
-
FANG, G., E. ROCHA and A. DANCHIN, 2005 How essential are nonessential genes? Mol. Biol. Evol. 22: 2147-2156.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 2147-2156
-
-
Fang, G.1
Rocha, E.2
Danchin, A.3
-
16
-
-
0000122573
-
PHYLIP (phylogeny inference package)
-
Version 3.2
-
FELSENSTEIN, J., 1989 PHYLIP (phylogeny inference package). Version 3.2. Cladistics 5: 164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
17
-
-
28944433798
-
Insights on biology and evolution from microbial genome sequencing
-
DOI 10.1101/gr.3724205
-
FRASER-LIGGETT, C. M., 2005 Insights on biology and evolution from microbial genome sequencing. Genome Res. 15: 1603-1610. (Pubitemid 41782228)
-
(2005)
Genome Research
, vol.15
, Issue.12
, pp. 1603-1610
-
-
Fraser-Liggett, C.M.1
-
18
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
GARCIA-VALLVÉ, S., A. ROMEU and J. PALAU, 2000 Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10: 1719-1725.
-
(2000)
Genome Res.
, vol.10
, pp. 1719-1725
-
-
Garcia-Vallvé, S.1
Romeu, A.2
Palau, J.3
-
19
-
-
15444377677
-
Integrons in Xanthomonas: A source of species genome diversity
-
GILLINGS, M. R., M. P. HOLLEY, H. W. STOKES and A. J. HOLMES, 2005 Integrons in Xanthomonas: a source of species genome diversity. Proc. Natl. Acad. Sci. USA 102: 4419-4424.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 4419-4424
-
-
Gillings, M.R.1
Holley, M.P.2
Stokes, H.W.3
Holmes, A.J.4
-
20
-
-
23944499633
-
Horizontal gene transfer, genome innovation and evolution
-
GOGARTEN, J. P., and J. P. TOWNSEND, 2005 Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3: 679-687.
-
(2005)
Nat. Rev. Microbiol.
, vol.3
, pp. 679-687
-
-
Gogarten, J.P.1
Townsend, J.P.2
-
21
-
-
0036890022
-
Rapid divergence in expression between duplicate genes inferred from microarray data
-
DOI 10.1016/S0168-9525(02)02837-8, PII S0168952502028378
-
GU, Z., D. NICOLAE, H. H. LU and W. H. LI, 2002 Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18: 609-613. (Pubitemid 35346678)
-
(2002)
Trends in Genetics
, vol.18
, Issue.12
, pp. 609-613
-
-
Gu, Z.1
Nicolae, D.2
Lu, H.H.-S.3
Li, W.-H.4
-
22
-
-
3042595153
-
Patterns of bacterial gene movement
-
HAO, W., and G. B. GOLDING, 2004 Patterns of bacterial gene movement. Mol. Biol. Evol. 21: 1294-1307.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1294-1307
-
-
Hao, W.1
Golding, G.B.2
-
23
-
-
33748115102
-
Asymmetrical evolution of cytochrome bd subunits
-
HAO, W., and G. B. GOLDING, 2006a Asymmetrical evolution of cytochrome bd subunits. J. Mol. Evol. 62: 132-142.
-
(2006)
J. Mol. Evol.
, vol.62
, pp. 132-142
-
-
Hao, W.1
Golding, G.B.2
-
24
-
-
33745172155
-
The fate of laterally transferred genes: Life in the fast lane to adaptation or death
-
HAO, W., and G. B. GOLDING, 2006b The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res. 16: 636-643.
-
(2006)
Genome Res.
, vol.16
, pp. 636-643
-
-
Hao, W.1
Golding, G.B.2
-
25
-
-
48349123911
-
High rates of lateral gene transfer are not due to false diagnosis of gene absence
-
HAO, W., and G. B. GOLDING, 2008a High rates of lateral gene transfer are not due to false diagnosis of gene absence. Gene 421: 27-31.
-
(2008)
Gene
, vol.421
, pp. 27-31
-
-
Hao, W.1
Golding, G.B.2
-
26
-
-
45249114886
-
Uncovering rate variation of lateral gene transfer during bacterial genome evolution
-
HAO, W., and G. B. GOLDING, 2008b Uncovering rate variation of lateral gene transfer during bacterial genome evolution. BMC Genomics 9: 235.
-
(2008)
BMC Genomics
, vol.9
, pp. 235
-
-
Hao, W.1
Golding, G.B.2
-
27
-
-
0035963414
-
Protein dispensability and rate of evolution
-
HIRSH, A. E., and H. B. FRASER, 2001 Protein dispensability and rate of evolution. Nature 411: 1046-1049.
-
(2001)
Nature
, vol.411
, pp. 1046-1049
-
-
Hirsh, A.E.1
Fraser, H.B.2
-
28
-
-
0038752612
-
Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis
-
DOI 10.1038/nature01582
-
IVANOVA, N., A. SOROKIN, I. ANDERSON, N. GALLERON, B. CANDELON et al., 2003 Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423: 87-91. (Pubitemid 36569587)
-
(2003)
Nature
, vol.423
, Issue.6935
, pp. 87-91
-
-
Ivanova, N.1
Sorokin, A.2
Anderson, I.3
Galleron, N.4
Candelon, B.5
Kapatral, V.6
Bhattacharyya, A.7
Reznik, G.8
Mikhailova, N.9
Lapidus, A.10
Chu, L.11
Mazur, M.12
Goltsman, E.13
Larsen, N.14
D'Souza, M.15
Walunas, T.16
Grechkin, Y.17
Pusch, G.18
Haselkorn, R.19
Fonstein, M.20
Ehrlich, S.D.21
Overbeek, R.22
Kyrpides, N.23
more..
-
29
-
-
0242371471
-
Horizontal gene transfer accelerates genome innovation and evolution
-
JAIN, R., M. C. RIVERA, J. E. MOORE and J. A. LAKE, 2003 Horizontal gene transfer accelerates genome innovation and evolution. Mol. Biol. Evol. 20: 1598-1602.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 1598-1602
-
-
Jain, R.1
Rivera, M.C.2
Moore, J.E.3
Lake, J.A.4
-
30
-
-
20144389876
-
Diversity of genome structure in Salmonella enterica serovar Typhi populations
-
DOI 10.1128/JB.187.8.2638-2650.2005
-
KOTHAPALLI, S., S. NAIR, S. ALOKAM, T. PANG, R. KHAKHRIA et al., 2005 Diversity of genome structure in Salmonella enterica serovar Typhi populations. J. Bacteriol. 187: 2638-2650. (Pubitemid 40490368)
-
(2005)
Journal of Bacteriology
, vol.187
, Issue.8
, pp. 2638-2650
-
-
Kothapalli, S.1
Nair, S.2
Alokam, S.3
Pang, T.4
Khakhria, R.5
Woodward, D.6
Johnson, W.7
Stocker, B.A.D.8
Sanderson, K.E.9
Liu, S.-L.10
-
31
-
-
0025245767
-
Organization of the bacterial chromosome
-
KRAWIEC, S., and M. RILEY, 1990 Organization of the bacterial chromosome. Microbiol. Rev. 54: 502-539.
-
(1990)
Microbiol. Rev.
, vol.54
, pp. 502-539
-
-
Krawiec, S.1
Riley, M.2
-
32
-
-
0038486918
-
The balance of driving forces during genome evolution in prokaryotes
-
KUNIN, V., and C. A. OUZOUNIS, 2003 The balance of driving forces during genome evolution in prokaryotes. Genome Res. 13: 1589-1594.
-
(2003)
Genome Res.
, vol.13
, pp. 1589-1594
-
-
Kunin, V.1
Ouzounis, C.A.2
-
33
-
-
6944225464
-
Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation
-
KUWAHARA, T., A. YAMASHITA, H. HIRAKAWA, H. NAKAYAMA, H. TOH et al., 2004 Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc. Natl. Acad. Sci. USA 101: 14919-14924.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 14919-14924
-
-
Kuwahara, T.1
Yamashita, A.2
Hirakawa, H.3
Nakayama, H.4
Toh, H.5
-
34
-
-
0035800661
-
Evolution of tuf genes: Ancient duplication, differential loss and gene conversion
-
LATHE, 3RD, W. C., and P. BORK, 2001 Evolution of tuf genes: ancient duplication, differential loss and gene conversion. FEBS Lett. 502: 113-116.
-
(2001)
FEBS Lett.
, vol.502
, pp. 113-116
-
-
Lathe III, W.C.1
Bork, P.2
-
35
-
-
0032795469
-
Palindromic DNA and genome stability. Further studies
-
LEWIS, S., E. AKGUN and M. JASIN, 1999 Palindromic DNA and genome stability. Further studies. Ann. N Y Acad. Sci. 870: 45-57.
-
(1999)
Ann. N Y Acad. Sci.
, vol.870
, pp. 45-57
-
-
Lewis, S.1
Akgun, E.2
Jasin, M.3
-
36
-
-
40749124938
-
Prophinder: A computational tool for prophage prediction in prokaryotic genomes
-
LIMA-MENDEZ, G., J. VAN HELDEN, A. TOUSSAINT and R. LEPLAE, 2008 Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 24: 863-865.
-
(2008)
Bioinformatics
, vol.24
, pp. 863-865
-
-
Lima-Mendez, G.1
Van Helden, J.2
Toussaint, A.3
Leplae, R.4
-
37
-
-
0037377848
-
Genomic diversification among archival strains of Salmonella enterica serovar typhimurium LT7
-
DOI 10.1128/JB.185.7.2131-2142.2003
-
LIU, G. R., K. EDWARDS, A. EISENSTARK, Y. M. FU, W. Q. LIU et al., 2003 Genomic diversification among archival strains of Salmonella enterica serovar typhimurium LT7. J. Bacteriol. 185: 2131-2142. (Pubitemid 36363173)
-
(2003)
Journal of Bacteriology
, vol.185
, Issue.7
, pp. 2131-2142
-
-
Liu, G.-R.1
Edwards, K.2
Eisenstark, A.3
Fu, Y.-M.4
Liu, W.-Q.5
Sanderson, K.E.6
Johnston, R.N.7
Liu, S.-L.8
-
38
-
-
30744473438
-
Genome plasticity and ori-ter rebalancing in Salmonella typhi
-
LIU, G. R., W. Q. LIU, R. N. JOHNSTON, K. E. SANDERSON, S. X. LI et al., 2006 Genome plasticity and ori-ter rebalancing in Salmonella typhi. Mol. Biol. Evol. 23: 365-371.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 365-371
-
-
Liu, G.R.1
Liu, W.Q.2
Johnston, R.N.3
Sanderson, K.E.4
Li, S.X.5
-
39
-
-
0032528311
-
Homologous recombination between rrn operons rearranges the chromosome in host-specialized species of Salmonella
-
LIU, S. L., and K. E. SANDERSON, 1998 Homologous recombination between rrn operons rearranges the chromosome in host-specialized species of Salmonella. FEMS Microbiol. Lett. 164: 275-281.
-
(1998)
FEMS Microbiol. Lett.
, vol.164
, pp. 275-281
-
-
Liu, S.L.1
Sanderson, K.E.2
-
40
-
-
0027236788
-
Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria
-
LIU, S. L., A. HESSEL and K. E. SANDERSON, 1993 Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc. Natl. Acad. Sci. USA 90: 6874-6878.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 6874-6878
-
-
Liu, S.L.1
Hessel, A.2
Sanderson, K.E.3
-
41
-
-
0029985398
-
Asymmetric substitution patterns in the two DNA strands of bacteria
-
LOBRY, J. R., 1996 Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13: 660-665.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 660-665
-
-
Lobry, J.R.1
-
42
-
-
0033972072
-
The probability of duplicate gene preservation by subfunctionalization
-
LYNCH, M., and A. FORCE, 2000 The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
-
(2000)
Genetics
, vol.154
, pp. 459-473
-
-
Lynch, M.1
Force, A.2
-
43
-
-
0035697435
-
The probability of preservation of a newly arisen gene duplicate
-
LYNCH, M., M. O'HELY, B. WALSH and A. FORCE, 2001 The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804.
-
(2001)
Genetics
, vol.159
, pp. 1789-1804
-
-
Lynch, M.1
O'Hely, M.2
Walsh, B.3
Force, A.4
-
44
-
-
33646337441
-
Structural basis for broad DNA-specificity in integron recombination
-
MACDONALD, D., G. DEMARRE, M. BOUVIER, D. MAZEL and D. N. GOPAUL, 2006 Structural basis for broad DNA-specificity in integron recombination. Nature 440: 1157-1162.
-
(2006)
Nature
, vol.440
, pp. 1157-1162
-
-
Macdonald, D.1
Demarre, G.2
Bouvier, M.3
Mazel, D.4
Gopaul, D.N.5
-
45
-
-
2942622384
-
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
-
MIRKIN, B. G., T. I. FENNER, M. Y. GALPERIN and E. V. KOONIN, 2003 Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 3: 2.
-
(2003)
BMC Evol. Biol.
, vol.3
, pp. 2
-
-
Mirkin, B.G.1
Fenner, T.I.2
Galperin, M.Y.3
Koonin, E.V.4
-
46
-
-
36849084992
-
Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes
-
MORTON, R. A., and B. R. MORTON, 2007 Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes. BMC Genomics 8: 369.
-
(2007)
BMC Genomics
, vol.8
, pp. 369
-
-
Morton, R.A.1
Morton, B.R.2
-
47
-
-
4444299868
-
Monitoring and modeling horizontal gene transfer
-
NIELSEN, K. M., and J. P. TOWNSEND, 2004 Monitoring and modeling horizontal gene transfer. Nat. Biotechnol. 22: 1110-1114.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 1110-1114
-
-
Nielsen, K.M.1
Townsend, J.P.2
-
48
-
-
25444457725
-
Mathematical modeling of evolution of horizontally transferred genes
-
NOVOZHILOV, A. S., G. P. KAREV and E. V. KOONIN, 2005 Mathematical modeling of evolution of horizontally transferred genes. Mol. Biol. Evol. 22: 1721-1732.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1721-1732
-
-
Novozhilov, A.S.1
Karev, G.P.2
Koonin, E.V.3
-
49
-
-
0034671796
-
Evolutionary dynamics of full genome content in Escherichia coli
-
OCHMAN, H., and I. B. JONES, 2000 Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19: 6637-6643.
-
(2000)
EMBO J.
, vol.19
, pp. 6637-6643
-
-
Ochman, H.1
Jones, I.B.2
-
50
-
-
0642312313
-
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
-
OMELCHENKO, M. V., K. S. MAKAROVA, Y. I. WOLF, I. B. ROGOZIN and E. V. KOONIN, 2003 Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol. 4: R55.
-
(2003)
Genome Biol.
, vol.4
-
-
Omelchenko, M.V.1
Makarova, K.S.2
Wolf, Y.I.3
Rogozin, I.B.4
Koonin, E.V.5
-
51
-
-
5344244656
-
-
R DEVELOPMENT CORE TEAM, R Foundation for Statistical Computing, Vienna
-
R DEVELOPMENT CORE TEAM, 2008 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
-
(2008)
R: a Language and Environment for Statistical Computing
-
-
-
52
-
-
28844468371
-
A relative-entropy algorithm for genomic fingerprinting captures host-phage similarities
-
ROBINS, H., M. KRASNITZ, H. BARAK and A. J. LEVINE, 2005 A relative-entropy algorithm for genomic fingerprinting captures host-phage similarities. J. Bacteriol. 187: 8370-8374.
-
(2005)
J. Bacteriol.
, vol.187
, pp. 8370-8374
-
-
Robins, H.1
Krasnitz, M.2
Barak, H.3
Levine, A.J.4
-
53
-
-
4644309277
-
Order and disorder in bacterial genomes
-
ROCHA, E. P., 2004 Order and disorder in bacterial genomes. Curr. Opin. Microbiol. 7: 519-527.
-
(2004)
Curr. Opin. Microbiol.
, vol.7
, pp. 519-527
-
-
Rocha, E.P.1
-
54
-
-
0034888796
-
Ongoing evolution of strand composition in bacterial genomes
-
ROCHA, E. P., and A. DANCHIN, 2001 Ongoing evolution of strand composition in bacterial genomes. Mol. Biol. Evol. 18: 1789-1799.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1789-1799
-
-
Rocha, E.P.1
Danchin, A.2
-
55
-
-
0344668838
-
Gene essentiality determines chromosome organisation in bacteria
-
ROCHA, E. P., and A. DANCHIN, 2003 Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res. 31: 6570-6577.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6570-6577
-
-
Rocha, E.P.1
Danchin, A.2
-
56
-
-
9144230986
-
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes
-
ROGOZIN, I. B., K. S. MAKAROVA, Y. I. WOLF and E. V. KOONIN, 2004 Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Brief. Bioinform. 5: 131-149.
-
(2004)
Brief. Bioinform.
, vol.5
, pp. 131-149
-
-
Rogozin, I.B.1
Makarova, K.S.2
Wolf, Y.I.3
Koonin, E.V.4
-
57
-
-
0033677382
-
Early eukaryote evolution based on mitochondrial gene order breakpoints
-
SANKOFF, D., D. BRYANT, M. DENEAULT, B. F. LANG and G. BURGER, 2000 Early eukaryote evolution based on mitochondrial gene order breakpoints. J. Comput. Biol. 7: 521-535.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 521-535
-
-
Sankoff, D.1
Bryant, D.2
Deneault, M.3
Lang, B.F.4
Burger, G.5
-
59
-
-
33644873699
-
ISfinder: The reference centre for bacterial insertion sequences
-
SIGUIER, P., J. PEROCHON, L. LESTRADE, J. MAHILLON and M. CHANDLER, 2006b ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34: D32-D36.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Siguier, P.1
Perochon, J.2
Lestrade, L.3
Mahillon, J.4
Chandler, M.5
-
60
-
-
34249650773
-
Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome
-
SIRAND-PUGNET, P., C. LARTIGUE, M. MARENDA, D. JACOB, A. BARRE et al., 2007 Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet. 3: e75.
-
(2007)
PLoS Genet.
, vol.3
-
-
Sirand-Pugnet, P.1
Lartigue, C.2
Marenda, M.3
Jacob, D.4
Barre, A.5
-
61
-
-
0029836454
-
Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
-
STRIMMER, K., and A. VON HAESELER, 1996 Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 964-969
-
-
Strimmer, K.1
Von Haeseler, A.2
-
62
-
-
0010414313
-
Evolution of gene order conservation in prokaryotes
-
RESEARCH0020
-
TAMAMES, J., 2001 Evolution of gene order conservation in prokaryotes. Genome Biol. 2: RESEARCH0020.
-
(2001)
Genome Biol.
, vol.2
-
-
Tamames, J.1
-
63
-
-
0033956060
-
The COG database: A tool for genome-scale analysis of protein functions and evolution
-
TATUSOV, R. L., M. Y. GALPERIN, D. A. NATALE and E. V. KOONIN, 2000 The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 33-36
-
-
Tatusov, R.L.1
Galperin, M.Y.2
Natale, D.A.3
Koonin, E.V.4
-
64
-
-
0033776631
-
Genome rearrangement by replication-directed translocation
-
TILLIER, E. R., and R. A. COLLINS, 2000a Genome rearrangement by replication-directed translocation. Nat. Genet. 26: 195-197.
-
(2000)
Nat. Genet.
, vol.26
, pp. 195-197
-
-
Tillier, E.R.1
Collins, R.A.2
-
65
-
-
0033676887
-
Replication orientation affects the rate and direction of bacterial gene evolution
-
TILLIER, E. R., and R. A. COLLINS, 2000b Replication orientation affects the rate and direction of bacterial gene evolution. J. Mol. Evol. 51: 459-463.
-
(2000)
J. Mol. Evol.
, vol.51
, pp. 459-463
-
-
Tillier, E.R.1
Collins, R.A.2
-
66
-
-
33746846488
-
Bacterial repetitive extragenic palindromic sequences are DNA targets for insertion sequence elements
-
TOBES, R., and E. PAREJA, 2006 Bacterial repetitive extragenic palindromic sequences are DNA targets for insertion sequence elements. BMC Genomics 7: 62.
-
(2006)
BMC Genomics
, vol.7
, pp. 62
-
-
Tobes, R.1
Pareja, E.2
-
67
-
-
34047240364
-
Causes of insertion sequences abundance in prokaryotic genomes
-
TOUCHON, M., and E. P. ROCHA, 2007 Causes of insertion sequences abundance in prokaryotic genomes. Mol. Biol. Evol. 24: 969-981.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 969-981
-
-
Touchon, M.1
Rocha, E.P.2
-
68
-
-
33845965715
-
Cooperation is fleeting in the world of transposable elements
-
WAGNER, A., 2006a Cooperation is fleeting in the world of transposable elements. PLoS Comput. Biol. 2: e162.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Wagner, A.1
-
69
-
-
33644899969
-
Periodic extinctions of transposable elements in bacterial lineages: Evidence from intragenomic variation in multiple genomes
-
WAGNER, A., 2006b Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes. Mol. Biol. Evol. 23: 723-733.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 723-733
-
-
Wagner, A.1
-
70
-
-
34548764905
-
A survey of bacterial insertion sequences using IScan
-
WAGNER, A., C. LEWIS and M. BICHSEL, 2007 A survey of bacterial insertion sequences using IScan. Nucleic Acids Res. 35: 5284-5293.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 5284-5293
-
-
Wagner, A.1
Lewis, C.2
Bichsel, M.3
-
71
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
YANG, Z., 2007 PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586-1591.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
72
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
YANG, Z., and R. NIELSEN, 2000 Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17: 32-43.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
73
-
-
0642373709
-
Different evolutionary patterns between young duplicate genes in the human genome
-
ZHANG, P., Z. GU and W. H. LI, 2003 Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol. 4: R56.
-
(2003)
Genome Biol.
, vol.4
-
-
Zhang, P.1
Gu, Z.2
Li, W.H.3
|