-
1
-
-
0034767147
-
A linear-time algorithm for computing inversion distance between signed permutations with an experimental study
-
Bader, D.A., Moret, B.M., and Yan, M. 2001. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comput. Biol. 8: 483-491.
-
(2001)
J. Comput. Biol.
, vol.8
, pp. 483-491
-
-
Bader, D.A.1
Moret, B.M.2
Yan, M.3
-
2
-
-
0033861549
-
Human and mouse gene structure: Comparative analysis and application to exon prediction
-
Batzoglou, S., Pachter, L., Mesirov, J.P., Berger, B., and Lander, E.S. 2000. Human and mouse gene structure: Comparative analysis and application to exon prediction. Genome Res. 10: 950-958.
-
(2000)
Genome Res.
, vol.10
, pp. 950-958
-
-
Batzoglou, S.1
Pachter, L.2
Mesirov, J.P.3
Berger, B.4
Lander, E.S.5
-
3
-
-
0002163159
-
Breakpoint phylogenies
-
Blanchette, M., Bourque, G., and Sankoff, D. 1997. Breakpoint phylogenies. Genome Inform Ser. Workshop Genome Inform. 8: 25-34.
-
(1997)
Genome Inform Ser. Workshop Genome Inform.
, vol.8
, pp. 25-34
-
-
Blanchette, M.1
Bourque, G.2
Sankoff, D.3
-
4
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner, F.R., Plunkett III, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474.
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett III, 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
-
5
-
-
0036143403
-
Genome-scale evolution: Reconstructing gene orders in the ancestral species
-
Bourque, G. and Pevzner, P.A. 2002. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res. 12: 26-36.
-
(2002)
Genome Res.
, vol.12
, pp. 26-36
-
-
Bourque, G.1
Pevzner, P.A.2
-
6
-
-
0042121222
-
MAVID multiple alignment server
-
Bray, N. and Pachter, L. 2003. MAVID multiple alignment server. Nucleic Acids Res. 31: 3525-3526.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3525-3526
-
-
Bray, N.1
Pachter, L.2
-
7
-
-
0037270315
-
AVID: A global alignment program
-
Bray, N., Dubchak, I., and Pachter, L. 2003. AVID: A global alignment program. Genome Res. 13: 97-102.
-
(2003)
Genome Res.
, vol.13
, pp. 97-102
-
-
Bray, N.1
Dubchak, I.2
Pachter, L.3
-
8
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
NISC Comparative Sequencing Program
-
Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., and Batzoglou, S., NISC Comparative Sequencing Program. 2003a. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13: 721-731.
-
(2003)
Genome Res.
, vol.13
, pp. 721-731
-
-
Brudno, M.1
Do, C.B.2
Cooper, G.M.3
Kim, M.F.4
Davydov, E.5
Green, E.D.6
Sidow, A.7
Batzoglou, S.8
-
9
-
-
4944262040
-
Glocal alignment: Finding rearrangements during alignment
-
Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., and Batzoglou, S. 2003b. Glocal alignment: Finding rearrangements during alignment. Bioinformatics 19 Suppl 1: 154-162.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Brudno, M.1
Malde, S.2
Poliakov, A.3
Do, C.B.4
Couronne, O.5
Dubchak, I.6
Batzoglou, S.7
-
10
-
-
1042276327
-
Fast identification and statistical evaluation of segmental homologies in comparative maps
-
Calabrese, P.P., Chakravarty, S., and Vision, T.J. 2003. Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 19 Suppl 1: i74-i80.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Calabrese, P.P.1
Chakravarty, S.2
Vision, T.J.3
-
11
-
-
0347724102
-
GRIL: Genome rearrangement and inversion locator
-
Darling, A.E., Mau, B., Blattner, F.R., and Perna, N.T. 2004. GRIL: Genome rearrangement and inversion locator. Bioinformatics 20: 122-124.
-
(2004)
Bioinformatics
, vol.20
, pp. 122-124
-
-
Darling, A.E.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
12
-
-
0033153375
-
Alignment of whole genomes
-
Delcher, A.L., Kasif, S., Fleischmann, R.D., Peterson, J., White, O., and Salzberg, S.L. 1999. Alignment of whole genomes. Nucleic Acids Res. 27: 2369-2376.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 2369-2376
-
-
Delcher, A.L.1
Kasif, S.2
Fleischmann, R.D.3
Peterson, J.4
White, O.5
Salzberg, S.L.6
-
13
-
-
0037377818
-
Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18
-
Deng, W., Liou, S.-R., Plunkett III, G., Mayhew, G.F., Rose, D.J., Burland, V., Kodoyianni, V., Schwartz, D.C., and Blattner, F.R. 2003. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J. Bacteriol. 185: 2330-2337.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 2330-2337
-
-
Deng, W.1
Liou, S.-R.2
Plunkett III, G.3
Mayhew, G.F.4
Rose, D.J.5
Burland, V.6
Kodoyianni, V.7
Schwartz, D.C.8
Blattner, F.R.9
-
14
-
-
0042027896
-
Structural dynamics of eukaryotic chromosome evolution
-
Eichler, E.E. and Sankoff, D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science 301: 793-797.
-
(2003)
Science
, vol.301
, pp. 793-797
-
-
Eichler, E.E.1
Sankoff, D.2
-
15
-
-
0034980876
-
Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes
-
Hacker, J. and Carniel, E. 2001. Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep. 2: 376-381.
-
(2001)
EMBO Rep.
, vol.2
, pp. 376-381
-
-
Hacker, J.1
Carniel, E.2
-
16
-
-
0035961748
-
Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
-
Hayashi, T., Makino, K., Ohnishi, M., Kurokawa, K., Ishii, K., Yokoyama, K., Han, C.G., Ohtsubo, E., Nakayama, K., Murata, T., et al. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8: 11-22.
-
(2001)
DNA Res.
, vol.8
, pp. 11-22
-
-
Hayashi, T.1
Makino, K.2
Ohnishi, M.3
Kurokawa, K.4
Ishii, K.5
Yokoyama, K.6
Han, C.G.7
Ohtsubo, E.8
Nakayama, K.9
Murata, T.10
-
17
-
-
0242470267
-
Efficient multiple genome alignment
-
Hohl, M., Kurtz, S., and Ohlebusch, E. 2002. Efficient multiple genome alignment. Bioinformatics 18 Suppl 1: S312-S320.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Hohl, M.1
Kurtz, S.2
Ohlebusch, E.3
-
18
-
-
18644378721
-
Genome sequence of Shigella flexneri 2a: Insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157
-
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., Wang, J., Liu, H., Yang, J., Yang, F., et al. 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.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4432-4441
-
-
Jin, Q.1
Yuan, Z.2
Xu, J.3
Wang, Y.4
Shen, Y.5
Lu, W.6
Wang, J.7
Liu, H.8
Yang, J.9
Yang, F.10
-
19
-
-
0033832676
-
Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment
-
Kent, W.J. and Zahler, A.M. 2000. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 10: 1115-1125.
-
(2000)
Genome Res.
, vol.10
, pp. 1115-1125
-
-
Kent, W.J.1
Zahler, A.M.2
-
20
-
-
0034565346
-
Computation and visualization of degenerate repeats in complete genomes
-
Kurtz, S., Ohlebusch, E., Schleiermacher, C., Stoye, J., and Giegerich, R. 2000. Computation and visualization of degenerate repeats in complete genomes. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8: 228-238.
-
(2000)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.8
, pp. 228-238
-
-
Kurtz, S.1
Ohlebusch, E.2
Schleiermacher, C.3
Stoye, J.4
Giegerich, R.5
-
21
-
-
0036434711
-
On a Bayesian approach to phylogenetic inference from animal mitochondrial genome arrangements
-
Larget, B., Simon, D.L., and Kadane, J. 2002. On a Bayesian approach to phylogenetic inference from animal mitochondrial genome arrangements. J. Roy. Stat. Soc. B 64: 681-693.
-
(2002)
J. Roy. Stat. Soc. B
, vol.64
, pp. 681-693
-
-
Larget, B.1
Simon, D.L.2
Kadane, J.3
-
22
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
Lee, C., Grasso, C., and Sharlow, M.F. 2002. Multiple sequence alignment using partial order graphs. Bioinformatics 18: 452-464.
-
(2002)
Bioinformatics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
23
-
-
0037433046
-
FORRepeats: Detects repeats on entire chromosomes and between genomes
-
Lefebvre, A., Lecroq, T., Dauchel, H., and Alexandre, J. 2003a. FORRepeats: Detects repeats on entire chromosomes and between genomes. Bioinformatics 19: 319-326.
-
(2003)
Bioinformatics
, vol.19
, pp. 319-326
-
-
Lefebvre, A.1
Lecroq, T.2
Dauchel, H.3
Alexandre, J.4
-
24
-
-
0344794389
-
Detection and validation of single gene inversions
-
Lefebvre, J.F., El-Mabrouk, N., Tillier, E., and Sankoff, D. 2003b. Detection and validation of single gene inversions. Bioinformatics 19 Suppl 1: 1190-1196.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
, pp. 1190-1196
-
-
Lefebvre, J.F.1
El-Mabrouk, N.2
Tillier, E.3
Sankoff, D.4
-
25
-
-
0013332993
-
Whole genome alignment using a multithreaded parallel implementation
-
Martins, W.S., del Cuvillo, J., Cui, W., and Gao, G.R. 2001. Whole genome alignment using a multithreaded parallel implementation. Symposium on Computer Architecture and High Performance Computing, pp. 1-8.
-
(2001)
Symposium on Computer Architecture and High Performance Computing
, pp. 1-8
-
-
Martins, W.S.1
del Cuvillo, J.2
Cui, W.3
Gao, G.R.4
-
26
-
-
0035950182
-
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
-
McClelland, M., Sanderson, K.E., Spieth, J., Clifton, S.W., Latreille, P., Courtney, L., Porwollik, S., Ali, J., Dante, M., Du, F., et al. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413: 852-826.
-
(2001)
Nature
, vol.413
, pp. 826-852
-
-
McClelland, M.1
Sanderson, K.E.2
Spieth, J.3
Clifton, S.W.4
Latreille, P.5
Courtney, L.6
Porwollik, S.7
Ali, J.8
Dante, M.9
Du, F.10
-
27
-
-
0032945593
-
DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
-
Morgenstern, B. 1999. DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15: 211-218.
-
(1999)
Bioinformatics
, vol.15
, pp. 211-218
-
-
Morgenstern, B.1
-
28
-
-
0033636013
-
A space-efficient algorithm for aligning large genomic sequences
-
Morgenstern, B. 2000. A space-efficient algorithm for aligning large genomic sequences. Bioinformatics 16: 948-949.
-
(2000)
Bioinformatics
, vol.16
, pp. 948-949
-
-
Morgenstern, B.1
-
29
-
-
0029861894
-
Multiple DNA and protein sequence alignment based on segment-to-segment comparison
-
Morgenstern, B., Dress, A., and Werner, T. 1996. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. 93: 12098-12103.
-
(1996)
Proc. Natl. Acad. Sci.
, vol.93
, pp. 12098-12103
-
-
Morgenstern, B.1
Dress, A.2
Werner, T.3
-
30
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., Higgins, D.G., and Heringa, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302: 205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
31
-
-
0035950154
-
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
-
Parkhill, J., Dougan, G., James, K.D., Thomson, N.R., Pickard, D., Wain, J., Churcher, C., Mungall, K.L., Bentley, S.D., Holden, M.T., et al. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413: 848-852.
-
(2001)
Nature
, vol.413
, pp. 848-852
-
-
Parkhill, J.1
Dougan, G.2
James, K.D.3
Thomson, N.R.4
Pickard, D.5
Wain, J.6
Churcher, C.7
Mungall, K.L.8
Bentley, S.D.9
Holden, M.T.10
-
32
-
-
0035945586
-
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
-
Perna, N.T., Plunkett III, G., Burland, V., Mau, B., Glasner, J.D., Rose, D.J., Mayhew, G.F., Evans, P.S., Gregor, J., Kirkpatrick, H.A., et al. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409: 529-533.
-
(2001)
Nature
, vol.409
, pp. 529-533
-
-
Perna, N.T.1
Plunkett III, 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
-
33
-
-
0037264074
-
Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
-
Pevzner, P. and Tesler, G. 2003a. Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes. Genome Res. 13: 37-45.
-
(2003)
Genome Res.
, vol.13
, pp. 37-45
-
-
Pevzner, P.1
Tesler, G.2
-
34
-
-
0038271921
-
Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution
-
Pevzner, P. 2003b. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc. Natl. Acad. Sci. 100: 7672-7677.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 7672-7677
-
-
Pevzner, P.1
-
35
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut, A. and Grassly, N.C. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13: 235-238.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
36
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas, A., Williams, B.L., King, N., and Carroll, S.B. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.L.2
King, N.3
Carroll, S.B.4
-
37
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
38
-
-
0042490659
-
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences
-
NISC Comparative Sequencing Consortium
-
Schwartz, S., Elnitski, L., Li, M., Weirauch, M., Riemer, C., Smit, A., Green, E.D., Hardison, R.C., and Miller, W., NISC Comparative Sequencing Consortium. 2003a. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31: 3518-3524.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3518-3524
-
-
Schwartz, S.1
Elnitski, L.2
Li, M.3
Weirauch, M.4
Riemer, C.5
Smit, A.6
Green, E.D.7
Hardison, R.C.8
Miller, W.9
-
39
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003b. Human-mouse alignments with BLASTZ. Genome Res. 13: 103-107.
-
(2003)
Genome Res.
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
Hardison, R.C.6
Haussler, D.7
Miller, W.8
-
40
-
-
0027968068
-
CLUSTALW: 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. CLUSTALW: 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
-
41
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson, J.D., Plewniak, F., and Poch, O. 1999. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 27: 2682-2690.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
42
-
-
0033776631
-
Genome rearrangement by replication-directed translocation
-
Tillier, E.R. and Collins, R.A. 2000. 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
-
43
-
-
0037380723
-
Comparative genomics: Genome-wide analysis in metazoan eukaryotes
-
Ureta-Vidal, A., Ettwiller, L., and Birney, E. 2003. Comparative genomics: Genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4: 251-262.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 251-262
-
-
Ureta-Vidal, A.1
Ettwiller, L.2
Birney, E.3
-
44
-
-
0242416999
-
Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
-
Wei, J., Goldberg, M.B., Burland, V., Venkatesan, M.M., Deng, W., Fournier, G., Mayhew, G.F., Plunkett III, G., Rose, D.J., Darling, A., et al. 2003. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71: 2775-2586.
-
(2003)
Infect. Immun.
, vol.71
, pp. 2586-2775
-
-
Wei, J.1
Goldberg, M.B.2
Burland, V.3
Venkatesan, M.M.4
Deng, W.5
Fournier, G.6
Mayhew, G.F.7
Plunkett III, G.8
Rose, D.J.9
Darling, A.10
-
45
-
-
0037168538
-
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
-
Welch, R.A., Burland, V., Plunkett III, G., Redford, P., Roesch, P., Rasko, D., Buckles, E.L., Liou, S.-R., Boutin, A., Hackett, J., et al. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. 99: 17020-17024.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 17020-17024
-
-
Welch, R.A.1
Burland, V.2
Plunkett III, 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
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