-
3
-
-
0032425482
-
The diverse and dynamic structure of bacterial genomes
-
Casjens S. The diverse and dynamic structure of bacterial genomes. Annu Rev Genet. 1998;32:339-77.
-
(1998)
Annu Rev Genet
, vol.32
, pp. 339-377
-
-
Casjens, S.1
-
4
-
-
0025245767
-
Organization of the bacterial chromosome
-
Krawiec S, Riley M. Organization of the bacterial chromosome. Microbiol Rev. 1990;54:502-39.
-
(1990)
Microbiol Rev
, vol.54
, pp. 502-539
-
-
Krawiec, S.1
Riley, M.2
-
5
-
-
0018879196
-
Codon catalog usage and the genome hypothesis
-
Grantham R, Gautier C, Gouy M, Mercier R, Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980;8:r49-62.
-
(1980)
Nucleic Acids Res
, vol.8
-
-
Grantham, R.1
Gautier, C.2
Gouy, M.3
Mercier, R.4
Pave, A.5
-
6
-
-
0010414313
-
Evolution of gene order conservation in prokaryotes
-
research0020.1-0020.11
-
Tamames J. Evolution of gene order conservation in prokaryotes. Genome Biology. 2001;2:research0020.1-0020.11.
-
(2001)
Genome Biology
, vol.2
-
-
Tamames, J.1
-
7
-
-
37549070150
-
Evolution of genome architecture and the evolution of bacterial pathogens
-
Baquero F, Nombela C, Cassell GH, Gutierrez JA, editors, In press
-
Mira A, Pushker R. Evolution of genome architecture and the evolution of bacterial pathogens. In: Baquero F, Nombela C, Cassell GH, Gutierrez JA, editors. Introduction to evolutionary biology of bacterial and fungal pathogens. 2006. In press.
-
(2006)
Introduction to evolutionary biology of bacterial and fungal pathogens
-
-
Mira, A.1
Pushker, R.2
-
8
-
-
0033995545
-
Horizontal gene transfer of glycosyl hydrolases of the rumen fungi
-
Garcia-Vallve S, Romeu A, Palau J. Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol Biol Evol. 2000;17:352-61.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 352-361
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
-
9
-
-
0036892058
-
Simultaneous horizontal gene transfer of a gene coding for ribosomal protein l27 and operational genes in Arthrobacter sp
-
Garcia-Vallve S, Simo FX, Montero MA, Arola L, Romeu A. Simultaneous horizontal gene transfer of a gene coding for ribosomal protein l27 and operational genes in Arthrobacter sp. J Mol Evol. 2002;55:632-7.
-
(2002)
J Mol Evol
, vol.55
, pp. 632-637
-
-
Garcia-Vallve, S.1
Simo, F.X.2
Montero, M.A.3
Arola, L.4
Romeu, A.5
-
10
-
-
84983711696
-
Studies on the chemical nature of the substance inducing transformation of pneumococcal types: Induction of transformation by a deoxyribonucleic-acid fraction isolated from pneumococcus type III
-
Avery OT, MacLeod CM, McCarty M. Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a deoxyribonucleic-acid fraction isolated from pneumococcus type III. J Expl Med. 1944;79:137-58.
-
(1944)
J Expl Med
, vol.79
, pp. 137-158
-
-
Avery, O.T.1
MacLeod, C.M.2
McCarty, M.3
-
11
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
Garcia-Vallve S, Romeu A, Palau J. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 2000;10:1719-25.
-
(2000)
Genome Res
, vol.10
, pp. 1719-1725
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
-
12
-
-
0037250391
-
HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes
-
García-Vallvé S, Guzmán E, Montero MA, Romeu A. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 2003;31:187-9.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 187-189
-
-
García-Vallvé, S.1
Guzmán, E.2
Montero, M.A.3
Romeu, A.4
-
13
-
-
0035479142
-
Deletional bias and the evolution of bacterial genomes
-
Mira A, Ochman H, Moran NA. Deletional bias and the evolution of bacterial genomes. Trends Genet. 2001;17:589-96.
-
(2001)
Trends Genet
, vol.17
, pp. 589-596
-
-
Mira, A.1
Ochman, H.2
Moran, N.A.3
-
14
-
-
0001802381
-
Molecular mechanisms of bacterial pathogenicity
-
Fuchs TM. Molecular mechanisms of bacterial pathogenicity. Naturwissenchaften. 1998;85:99-108.
-
(1998)
Naturwissenchaften
, vol.85
, pp. 99-108
-
-
Fuchs, T.M.1
-
15
-
-
0030091189
-
Origins and evolution of antibiotic resistance
-
Davies J. Origins and evolution of antibiotic resistance. Microbiologia. 1996;12:9-16.
-
(1996)
Microbiologia
, vol.12
, pp. 9-16
-
-
Davies, J.1
-
16
-
-
0033758756
-
Pathogenicity islands and the evolution of microbes
-
Hacker J, Kaper JB. Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol. 2000;54:641-79.
-
(2000)
Annu Rev Microbiol
, vol.54
, pp. 641-679
-
-
Hacker, J.1
Kaper, J.B.2
-
17
-
-
27444441247
-
Common themes in the genome strategies of pathogens
-
Lawrence JG. Common themes in the genome strategies of pathogens. Curr Opin Gen Dev. 2005;15:1-5.
-
(2005)
Curr Opin Gen Dev
, vol.15
, pp. 1-5
-
-
Lawrence, J.G.1
-
18
-
-
39449122193
-
How bacterial genomes change
-
Fraser CM, Read TD, Nelson KE, editors, Totowa N.J, Humana Press;
-
Read TD, Myers GSA. How bacterial genomes change. In: Fraser CM, Read TD, Nelson KE, editors. Microbial genomes. Totowa N.J.: Humana Press; 2004. p. 155-73.
-
(2004)
Microbial genomes
, pp. 155-173
-
-
Read, T.D.1
Myers, G.S.A.2
-
19
-
-
0035931926
-
Massive gene decay in the leprosy bacillus
-
Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, et al. Massive gene decay in the leprosy bacillus. Nature. 2001;409:1007-11.
-
(2001)
Nature
, vol.409
, pp. 1007-1011
-
-
Cole, S.T.1
Eiglmeier, K.2
Parkhill, J.3
James, K.D.4
Thomson, N.R.5
Wheeler, P.R.6
-
20
-
-
4644309277
-
Order and disorder in bacterial genomes
-
Rocha EP. Order and disorder in bacterial genomes. Curr Opin Microbiol. 2004;7:519-27.
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 519-527
-
-
Rocha, E.P.1
-
21
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995;269:496-512.
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
Clayton, R.A.4
Kirkness, E.F.5
Kerlavage, A.R.6
-
22
-
-
0030775588
-
Strategies for whole microbial genome sequencing and analysis
-
Fraser CM, Fleischmann RD. Strategies for whole microbial genome sequencing and analysis. Electrophoresis. 1997;18:1207-16.
-
(1997)
Electrophoresis
, vol.18
, pp. 1207-1216
-
-
Fraser, C.M.1
Fleischmann, R.D.2
-
23
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, et al. The complete genome sequence of Escherichia coli K-12. Science. 1997;277:1453-74.
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett 3rd, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
Riley, M.6
-
24
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376-80.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
-
25
-
-
0028829125
-
The minimal gene complement of Mycoplasma genitalium
-
Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, et al. The minimal gene complement of Mycoplasma genitalium. Science. 1995;270:397-403.
-
(1995)
Science
, vol.270
, pp. 397-403
-
-
Fraser, C.M.1
Gocayne, J.D.2
White, O.3
Adams, M.D.4
Clayton, R.A.5
Fleischmann, R.D.6
-
26
-
-
39449134539
-
Bioinformatics and microbial pathogenesis
-
Fraser CM, Read TD, Nelson KE, editors, Totowa N.J, Humana Press;
-
Brinjman FSL and Fueyo JL. Bioinformatics and microbial pathogenesis. In: Fraser CM, Read TD, Nelson KE, editors. Microbial genomes. Totowa N.J.: Humana Press; 2004. p. 47-70.
-
(2004)
Microbial genomes
, pp. 47-70
-
-
Brinjman, F.S.L.1
Fueyo, J.L.2
-
28
-
-
0033552961
-
Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori
-
Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature. 1999;397:176-80.
-
(1999)
Nature
, vol.397
, pp. 176-180
-
-
Alm, R.A.1
Ling, L.S.2
Moir, D.T.3
King, B.L.4
Brown, E.D.5
Doig, P.C.6
-
29
-
-
0036791987
-
Genetic variation between Helicobacter pylori strains: Gene acquisition or loss?
-
García-Vallvé S, Janssen P, Ouzounis CA. Genetic variation between Helicobacter pylori strains: gene acquisition or loss? Trends Microbiol. 2002;10:445-7.
-
(2002)
Trends Microbiol
, vol.10
, pp. 445-447
-
-
García-Vallvé, S.1
Janssen, P.2
Ouzounis, C.A.3
-
32
-
-
3142740663
-
Comparative Genomics
-
Hardison RC. Comparative Genomics. PLoS Biol. 2003;1:e58.
-
(2003)
PLoS Biol
, vol.1
-
-
Hardison, R.C.1
-
33
-
-
0036175276
-
The past, present and future of genome-wide re-annotation. Genome Biol
-
3:COMMENT2001
-
Ouzounis CA, Karp PD. The past, present and future of genome-wide re-annotation. Genome Biol. 2002;3:COMMENT2001.
-
(2002)
-
-
Ouzounis, C.A.1
Karp, P.D.2
-
34
-
-
31644444476
-
MaGe: A microbial genome annotation system supported by synteny results
-
Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, et al. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res. 2006;34:53-65.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 53-65
-
-
Vallenet, D.1
Labarre, L.2
Rouy, Z.3
Barbe, V.4
Bocs, S.5
Cruveiller, S.6
-
35
-
-
0033119399
-
Errors in genome annotation
-
Brenner SE. Errors in genome annotation. Trends Genet. 1999;15:132-33.
-
(1999)
Trends Genet
, vol.15
, pp. 132-133
-
-
Brenner, S.E.1
-
36
-
-
33646916591
-
Shine-Dalgarno sequence locations exposes genome annotation errors
-
Starmer J, Stomp A, Vouk M, Bitzer D. Shine-Dalgarno sequence locations exposes genome annotation errors. PLoS Comput Biol. 2006;2:e57.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Starmer, J.1
Stomp, A.2
Vouk, M.3
Bitzer, D.4
-
37
-
-
28044463174
-
Genometrics as an essential tool for the assembly of whole genome sequences: The example of the chromosome of Bifidobacterium longum NCC2705
-
Guy L, Karamata D, Moreillon P, Roten CA. Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705. BMC Microbiol. 2005;5:60.
-
(2005)
BMC Microbiol
, vol.5
, pp. 60
-
-
Guy, L.1
Karamata, D.2
Moreillon, P.3
Roten, C.A.4
-
38
-
-
0035424599
-
Intrinsic errors in genome annotation
-
Devos D, Valencia A. Intrinsic errors in genome annotation. Trends Genet. 2001;17:429-31.
-
(2001)
Trends Genet
, vol.17
, pp. 429-431
-
-
Devos, D.1
Valencia, A.2
-
39
-
-
0037433717
-
Evaluation of annotation strategies using an entire genome sequence
-
Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, et al. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics. 2003;19:717-26.
-
(2003)
Bioinformatics
, vol.19
, pp. 717-726
-
-
Iliopoulos, I.1
Tsoka, S.2
Andrade, M.A.3
Enright, A.J.4
Carroll, M.5
Poullet, P.6
-
40
-
-
0035678864
-
Microbial disease in humans: A genomic perspective
-
Subramanian G, Mural R, Hoffman SL, Venter JC, Broder S. Microbial disease in humans: a genomic perspective. Mol Diagn. 2001;6:243-52.
-
(2001)
Mol Diagn
, vol.6
, pp. 243-252
-
-
Subramanian, G.1
Mural, R.2
Hoffman, S.L.3
Venter, J.C.4
Broder, S.5
-
42
-
-
33644877904
-
MetaCyc: A multiorganism database of metabolic pathways and enzymes
-
Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, et al. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2006;34:D511-16.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Caspi, R.1
Foerster, H.2
Fulcher, C.A.3
Hopkinson, R.4
Ingraham, J.5
Kaipa, P.6
-
43
-
-
33644874819
-
From genomics to chemical genomics: New developments in KEGG
-
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006;34:D354-7.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
Kawashima, S.6
-
44
-
-
33646063776
-
Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence
-
Wu G, Nie L, Zhang W. Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence. Antonie Van Leeuwenhoek. 2006;89:135-46.
-
(2006)
Antonie Van Leeuwenhoek
, vol.89
, pp. 135-146
-
-
Wu, G.1
Nie, L.2
Zhang, W.3
-
46
-
-
0034687702
-
A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains
-
Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci USA. 2000;97:14668-73.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 14668-14673
-
-
Salama, N.1
Guillemin, K.2
McDaniel, T.K.3
Sherlock, G.4
Tompkins, L.5
Falkow, S.6
-
48
-
-
29644440605
-
Antigen discovery: A postgenomic approach to leprosy diagnosis
-
Araoz R, Honore N, Cho S, Kim JP, Cho SN, Monot M, et al. Antigen discovery: a postgenomic approach to leprosy diagnosis. Infect Immun. 2006;74:175-82.
-
(2006)
Infect Immun
, vol.74
, pp. 175-182
-
-
Araoz, R.1
Honore, N.2
Cho, S.3
Kim, J.P.4
Cho, S.N.5
Monot, M.6
-
49
-
-
0035399931
-
Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
-
Karlin S. Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol. 2001;9:335-43.
-
(2001)
Trends Microbiol
, vol.9
, pp. 335-343
-
-
Karlin, S.1
-
50
-
-
28344433019
-
An acquisition account of genomic islands based on genome signature comparisons
-
van Passel MW, Bart A, Thygesen HH, Luyf AC, van Kampen AH, van der Ende A. An acquisition account of genomic islands based on genome signature comparisons. BMC Genomics. 2005;6:163.
-
(2005)
BMC Genomics
, vol.6
, pp. 163
-
-
van Passel, M.W.1
Bart, A.2
Thygesen, H.H.3
Luyf, A.C.4
van Kampen, A.H.5
van der Ende, A.6
-
51
-
-
33745659436
-
Conserved genes in a path from commensalism to pathogenicity: Comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228
-
Wei W, Cao Z, Zhu YL, Wang X, Ding G, Xu H, et al. Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228. BMC Genomics. 2006;7:112.
-
(2006)
BMC Genomics
, vol.7
, pp. 112
-
-
Wei, W.1
Cao, Z.2
Zhu, Y.L.3
Wang, X.4
Ding, G.5
Xu, H.6
-
52
-
-
17744412936
-
Comparative genomics tools applied to bioterrorism defensce
-
Slezak T, Kuczmarski T, Ott L, Torres C, Medeiros D, Smith J, et al. Comparative genomics tools applied to bioterrorism defensce. Briefings in Bioinformatics. 2003;4:133-49.
-
(2003)
Briefings in Bioinformatics
, vol.4
, pp. 133-149
-
-
Slezak, T.1
Kuczmarski, T.2
Ott, L.3
Torres, C.4
Medeiros, D.5
Smith, J.6
|