-
1
-
-
13444304389
-
GenBank
-
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. and Wheeler, D. L. (2005). GenBank. Nucleic Acids Res., 33, D34-D38.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
2
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner, F. R., Plunkett, G. 3rd., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B. and Shao, Y. (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 3rd, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
Riley, M.6
Collado-Vides, J.7
Glasner, J.D.8
Rode, C.K.9
Mayhew, G.F.10
Gregor, J.11
Davis, N.W.12
Kirkpatrick, H.A.13
Goeden, M.A.14
Rose, D.J.15
Mau, B.16
Shao, Y.17
-
3
-
-
0026480991
-
Chromosomal insertion sites for phages and plasmids
-
Campbell, A. M. (1992). Chromosomal insertion sites for phages and plasmids. J. Bacteriol. 174, 7495-7499.
-
(1992)
J. Bacteriol
, vol.174
, pp. 7495-7499
-
-
Campbell, A.M.1
-
4
-
-
25444520987
-
Systematic determination of the mosaic structure of bacterial genomes: Species backbone versus strain-specific loops
-
Chiapello, H., Bourgait, I., Sourivong, F., Heuclin, G., Gendrault-Jacquemard, A., Petit, M. A. and Karoui, M. E. (2005). Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. BMC Bioinformatics 6 171.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 171
-
-
Chiapello, H.1
Bourgait, I.2
Sourivong, F.3
Heuclin, G.4
Gendrault-Jacquemard, A.5
Petit, M.A.6
Karoui, M.E.7
-
5
-
-
15844364940
-
Genetic structure and chromosomal integration site of the cryptic prophage CP-1639 encoding Shiga toxin 1
-
Creuzburg, K., Kohler, B., Hempel, H., Schreier, P., Jacobs, E. and Schmidt, H. (2005). Genetic structure and chromosomal integration site of the cryptic prophage CP-1639 encoding Shiga toxin 1. Microbiology 151, 941-950.
-
(2005)
Microbiology
, vol.151
, pp. 941-950
-
-
Creuzburg, K.1
Kohler, B.2
Hempel, H.3
Schreier, P.4
Jacobs, E.5
Schmidt, H.6
-
6
-
-
2442449227
-
Genomic islands in pathogenic and environmental microorganisms
-
Dobrindt, U., Hochhut, B., Hentschel, U. and Hacker, J. (2004). Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2, 414-424.
-
(2004)
Nat. Rev. Microbiol
, vol.2
, pp. 414-424
-
-
Dobrindt, U.1
Hochhut, B.2
Hentschel, U.3
Hacker, J.4
-
7
-
-
19744383764
-
Detection and characterization of horizontal transfers in prokaryotes using genomic signature
-
Dufraigne, C., Fertil, B., Lespinats, S., Giron, A. and Deschavanne, P. (2005). Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Res. 33, e6.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Dufraigne, C.1
Fertil, B.2
Lespinats, S.3
Giron, A.4
Deschavanne, P.5
-
8
-
-
0037250391
-
HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes
-
Garcia-Vallve, S., Guzman, E., Montero, M. A. and Romeu, A. (2003). HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 31, 187-189.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 187-189
-
-
Garcia-Vallve, S.1
Guzman, E.2
Montero, M.A.3
Romeu, A.4
-
9
-
-
0037252684
-
Rfam: An RNA family database
-
Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. and Eddy, S. R. (2003). Rfam: An RNA family database. Nucleic Acids Res. 31, 439-441.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
10
-
-
13444252847
-
Rfam: Annotating non-coding RNAs in complete genomes
-
Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S. R. and Bateman, A. (2005). Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33, D121-D124.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Griffiths-Jones, S.1
Moxon, S.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
Bateman, A.6
-
11
-
-
0034978233
-
Pathogenicity islands: The tip of the iceberg
-
Hentschel, U. and Hacker, J. (2001). Pathogenicity islands: The tip of the iceberg. Microbes Infect. 3, 545-548.
-
(2001)
Microbes Infect
, vol.3
, pp. 545-548
-
-
Hentschel, U.1
Hacker, J.2
-
12
-
-
0037387973
-
A survey of small RNA-encoding genes in Escherichia coli
-
Hershberg, R., Altuvia, S. and Margalit, H. (2003). A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res. 31 1813-1820.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 1813-1820
-
-
Hershberg, R.1
Altuvia, S.2
Margalit, H.3
-
13
-
-
0345237922
-
IslandPath: Aiding detection of genomic islands in prokaryotes
-
Hsiao, W., Wan, I., Jones, S. J. and Brinkman, F. S. L. (2003). IslandPath: Aiding detection of genomic islands in prokaryotes. Bioinformatics 19, 418-420.
-
(2003)
Bioinformatics
, vol.19
, pp. 418-420
-
-
Hsiao, W.1
Wan, I.2
Jones, S.J.3
Brinkman, F.S.L.4
-
14
-
-
55449094978
-
Evidence of large novel gene pool associated with prokaryotic genomic islands
-
Hsiao, W. W., Ung, K., Aeschliman, D., Bryan, J., Finlay, B. B. and Brinkman, F. S. L. (2005). Evidence of large novel gene pool associated with prokaryotic genomic islands. PLoS Genet. 1, e62.
-
(2005)
PLoS Genet
, vol.1
-
-
Hsiao, W.W.1
Ung, K.2
Aeschliman, D.3
Bryan, J.4
Finlay, B.B.5
Brinkman, F.S.L.6
-
15
-
-
18644378721
-
-
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., Wang, J., Liu, H., Yang, J., Yang, F., Zhang, X., Zhang, J., Yang, G., Wu, H., Qu, D., Dong, J., Sun, L., Xue, Y, Zhao, A., Gao, Y., Zhu, J., Kann, B., Ding, K., Chen, S., Cheng, H., Yao. Z., He, B., Chen, R., Ma, D., Qiang, B., Wen, Y., Hou, Y. and Yu, J. (2002). Genome sequence of Shigella flexneri 2a: Insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30, 4432-4441.
-
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., Wang, J., Liu, H., Yang, J., Yang, F., Zhang, X., Zhang, J., Yang, G., Wu, H., Qu, D., Dong, J., Sun, L., Xue, Y, Zhao, A., Gao, Y., Zhu, J., Kann, B., Ding, K., Chen, S., Cheng, H., Yao. Z., He, B., Chen, R., Ma, D., Qiang, B., Wen, Y., Hou, Y. and Yu, J. (2002). Genome sequence of Shigella flexneri 2a: Insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30, 4432-4441.
-
-
-
-
16
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. and Hattori, M. (2004). The KEGG resource for deciphering the genome. Nucleic Acids Res. 32 D277-D280.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
17
-
-
0035399931
-
Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
-
Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol. 9, 335-343.
-
(2001)
Trends Microbiol
, vol.9
, pp. 335-343
-
-
Karlin, S.1
-
18
-
-
0028606501
-
Comparisons of eukaryotic genomic sequences
-
Karlin, S. and Ladunga, I. (1994). Comparisons of eukaryotic genomic sequences. Proc. Natl. Acad. Sci. USA 91, 12832-12836.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 12832-12836
-
-
Karlin, S.1
Ladunga, I.2
-
19
-
-
0030994798
-
Amelioration of bacterial genomes: Rates of change and exchange
-
Lawrence, J. G. and Ochman, H. (1997). Amelioration of bacterial genomes: Rates of change and exchange. J. Mol. Evol. 44, 383-397.
-
(1997)
J. Mol. Evol
, vol.44
, pp. 383-397
-
-
Lawrence, J.G.1
Ochman, H.2
-
20
-
-
0347126300
-
ACLAME: A CLAssification of Mobile genetic Elements
-
Leplae, R., Hebrant, A., Wodak, S. J. and Toussaint, A. (2004). ACLAME: A CLAssification of Mobile genetic Elements. Nucleic Acids Res. 32 D45-D49.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Leplae, R.1
Hebrant, A.2
Wodak, S.J.3
Toussaint, A.4
-
21
-
-
0033387903
-
Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak
-
Makino, K., Yokoyama, K., Kubota, Y., Yutsudo, C. H., Kimura,S., Kurokawa, K., Ishii, K., Hattori, M., Tatsuno, I., Abe, H., Iida, T., Yamamoto, K., Onishi, M., Hayashi, T., Yasunaga, T., Honda, T., Sasakawa, C. and Shinagawa, H. (1999). Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak. Genes Genet. Syst 74, 227-239.
-
(1999)
Genes Genet. Syst
, vol.74
, pp. 227-239
-
-
Makino, K.1
Yokoyama, K.2
Kubota, Y.3
Yutsudo, C.H.4
Kimura, S.5
Kurokawa, K.6
Ishii, K.7
Hattori, M.8
Tatsuno, I.9
Abe, H.10
Iida, T.11
Yamamoto, K.12
Onishi, M.13
Hayashi, T.14
Yasunaga, T.15
Honda, T.16
Sasakawa, C.17
Shinagawa, H.18
-
22
-
-
0347756648
-
Islander: A database of integrative islands iii prokaryotic genomes, the associated integrases and their DNA site specificities
-
Mantri, Y. and Williams, K. P. (2004). Islander: A database of integrative islands iii prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res. 32, D55-D58.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Mantri, Y.1
Williams, K.P.2
-
23
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman, H., Lawrence, J. G. and Groisman, E. A. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304.
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
24
-
-
31544472392
-
A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria
-
Ou, H.-Y., Chen, L.-L., Lonnen, J., Chaudhuri, R. R., Thani, A. B., Smith, R., Garton, N. J., Hinton, J., Pallen, M., Barer, M. R. and Rajakumar, K. (2006). A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res. 34, e3.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Ou, H.-Y.1
Chen, L.-L.2
Lonnen, J.3
Chaudhuri, R.R.4
Thani, A.B.5
Smith, R.6
Garton, N.J.7
Hinton, J.8
Pallen, M.9
Barer, M.R.10
Rajakumar, K.11
-
25
-
-
0035945586
-
Genome sequence of enterohaemorrhagic Escherichia coli O15:H7
-
Perna, N. T., Plunkett, G. 3rd., Burland, V., Mau, B., Glasner, J. D., Rose, D. J., Mayhew, G. F., Evans, P. S., Gregor, J., Kirkpatrick, H. A., Posfai, G., Hackett, J., Klink, S., Boutin, A., Shao, Y., Miller, L., Grotbeck, E. J., Davis, N. W., Lim, A., Dimalanta, E. T., Potamousis, K. D., Apodaca, J., Anantharaman, T. S., Lin, J., Yen, G. Schwartz, D. C., Welch, R. A. and Blattner, F. R. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O15:H7. Nature 409, 529-533.
-
(2001)
Nature
, vol.409
, pp. 529-533
-
-
Perna, N.T.1
Plunkett 3rd, G.2
Burland, V.3
Mau, B.4
Glasner, J.D.5
Rose, D.J.6
Mayhew, G.F.7
Evans, P.S.8
Gregor, J.9
Kirkpatrick, H.A.10
Posfai, G.11
Hackett, J.12
Klink, S.13
Boutin, A.14
Shao, Y.15
Miller, L.16
Grotbeck, E.J.17
Davis, N.W.18
Lim, A.19
Dimalanta, E.T.20
Potamousis, K.D.21
Apodaca, J.22
Anantharaman, T.S.23
Lin, J.24
Yen, G.25
Schwartz, D.C.26
Welch, R.A.27
Blattner, F.R.28
more..
-
26
-
-
0035162594
-
RefSeq and LocusLink: NCBI gene-centered resources
-
Pruitt, K. D. and Maglott, D. R. (2001). RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29, 137-140.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 137-140
-
-
Pruitt, K.D.1
Maglott, D.R.2
-
27
-
-
0024967060
-
Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements
-
Reiter, W. D., Palm, P. and Yeats, S. (1989). Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17, 1907-1914.
-
(1989)
Nucleic Acids Res
, vol.17
, pp. 1907-1914
-
-
Reiter, W.D.1
Palm, P.2
Yeats, S.3
-
28
-
-
0030915673
-
Bacteria gone native vs bacteria gone awry?: Plasmidic transfer and bacterial evolution
-
Souza, V. and Eguiarte, L. E. (1997). Bacteria gone native vs bacteria gone awry?: Plasmidic transfer and bacterial evolution. Proc. Natl. Acad. Sci. USA 94, 5501-5503.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 5501-5503
-
-
Souza, V.1
Eguiarte, L.E.2
-
29
-
-
34247194278
-
Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention
-
Sridhar, J. and Rafi, Z. A. (2007). Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention. OMICS 11, 74-99.
-
(2007)
OMICS
, vol.11
, pp. 74-99
-
-
Sridhar, J.1
Rafi, Z.A.2
-
30
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. D., Higgins, D. G. and Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
31
-
-
22244447128
-
A sensitive, support-vector-machine method for ther detection of horizontal gene transfers in viral, archaeal and bacterial genomes
-
Tsirigos, A. and Rigoutsos, I. (2005). A sensitive, support-vector-machine method for ther detection of horizontal gene transfers in viral, archaeal and bacterial genomes. Nucleic Acids Res. 33, 3699-3707.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 3699-3707
-
-
Tsirigos, A.1
Rigoutsos, I.2
-
32
-
-
21444456620
-
δp-Web, an online tool to assess composition similarity of individual nucleic acid sequences
-
van Passel, M. W. L, Luyf, A. C. M., van Kampen, A. H. C., Bart, A. and van der Ende, A. (2005a). δp-Web, an online tool to assess composition similarity of individual nucleic acid sequences. Bioinformatics 21, 3053-3055.
-
(2005)
Bioinformatics
, vol.21
, pp. 3053-3055
-
-
van Passel, M.W.L.1
Luyf, A.C.M.2
van Kampen, A.H.C.3
Bart, A.4
van der Ende, A.5
-
33
-
-
28344433019
-
An acquisition account of genomic islands based on genome signature comparisons
-
van Passel, M. W. J., Bart, A., Thygesen, H. H., Luyf, A. C. M., van Kampen, A. H. C. and van der Ende, A. (2005b). An acquisition account of genomic islands based on genome signature comparisons. BMC Genomics 6 163.
-
(2005)
BMC Genomics
, vol.6
, pp. 163
-
-
van Passel, M.W.J.1
Bart, A.2
Thygesen, H.H.3
Luyf, A.C.M.4
van Kampen, A.H.C.5
van der Ende, A.6
-
34
-
-
33745828696
-
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
-
Waack, S., Keller, O., Asper, R., Brodag, T., Damm, C., Fricke, W. F., Surovcik, K., Meinicke, P. and Merkl, R. (2006). Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7, 142.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 142
-
-
Waack, S.1
Keller, O.2
Asper, R.3
Brodag, T.4
Damm, C.5
Fricke, W.F.6
Surovcik, K.7
Meinicke, P.8
Merkl, R.9
-
35
-
-
0035395606
-
Identification of novel small RNAs using comparative genomics and microarrays
-
Wassarman, K. M., Repoila, F., Rosenow, C., Storz, G. and Gottesman, S. (2001). Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 15, 1637-1651.
-
(2001)
Genes Dev
, vol.15
, pp. 1637-1651
-
-
Wassarman, K.M.1
Repoila, F.2
Rosenow, C.3
Storz, G.4
Gottesman, S.5
-
36
-
-
0037168538
-
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
-
Welch, R. A., Burland, V., Plunkett, G. 3rd., Redford, P., Roesch, P., Rasko, D., Buckles, E. L., Liou, S. R., Boutin, A., Hackett, J., Stroud, D., Mayhew, G. F., Rose, D. J., Zhou, S., Schwartz, D. C., Perna, N. T., Mobley, H. L., Donnenberg, M. S. and Blattner, F. R. (2002). Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99 17020-17024.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 17020-17024
-
-
Welch, R.A.1
Burland, V.2
Plunkett 3rd, G.3
Redford, P.4
Roesch, P.5
Rasko, D.6
Buckles, E.L.7
Liou, S.R.8
Boutin, A.9
Hackett, J.10
Stroud, D.11
Mayhew, G.F.12
Rose, D.J.13
Zhou, S.14
Schwartz, D.C.15
Perna, N.T.16
Mobley, H.L.17
Donnenberg, M.S.18
Blattner, F.R.19
-
37
-
-
0037082414
-
Integration sites for genetic elements in prokaryotic tRNA and mRNA genes: A sublocation preference of integrase subfamilies
-
Williams, K. P. (2002). Integration sites for genetic elements in prokaryotic tRNA and mRNA genes: A sublocation preference of integrase subfamilies. Nucleic Acids Res. 30, 866-875.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 866-875
-
-
Williams, K.P.1
-
38
-
-
25444473873
-
A computational approach for identifying pathogenicity islands in prokaryotic genomes
-
Yoon, S. H., Hur, C.-G., Kang, H.-Y., Kim, Y. H., Oh, T. K. and Kim, J. F. (2005). A computational approach for identifying pathogenicity islands in prokaryotic genomes. BMC Bioinformatics 6, 184.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 184
-
-
Yoon, S.H.1
Hur, C.-G.2
Kang, H.-Y.3
Kim, Y.H.4
Oh, T.K.5
Kim, J.F.6
-
39
-
-
0036181234
-
Integrative genetic element that reverses the usual target gene orientation
-
Zhao, S. and Williams, K. P. (2002). Integrative genetic element that reverses the usual target gene orientation. J. Bacteriol. 184, 859-860.
-
(2002)
J. Bacteriol
, vol.184
, pp. 859-860
-
-
Zhao, S.1
Williams, K.P.2
|