-
1
-
-
0030722935
-
Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome
-
Hardison, R. C.; Oeltjen, J. and Miller, W. Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome. Res., 1997, 7: 959-66.
-
(1997)
Genome. Res.
, vol.7
, pp. 959-966
-
-
Hardison, R.C.1
Oeltjen, J.2
Miller, W.3
-
2
-
-
0032923247
-
Functional genomics in Caenorhabditis elegans: An approach involving comparisons of sequences from related nematodes
-
Thacker, C., Marra, M. A., Jones, A., Baillie, D. L. and Rose, A. M. Functional genomics in Caenorhabditis elegans: An approach involving comparisons of sequences from related nematodes. Genome. Res., 1999, 9: 348-59
-
(1999)
Genome. Res.
, vol.9
, pp. 348-359
-
-
Thacker, C.1
Marra, M.A.2
Jones, A.3
Baillie, D.L.4
Rose, A.M.5
-
3
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston, R. H.; Lindblad-Toh, K.; Birney, E.; Rogers, J.; Abril, J. F.; Agarwal, P.; Agarwala, R.; Ainscough, R.; Alexandersson, M.; An, P.; Antonarakis, S. E.; Attwood, J.; Baertsch, R.; Bailey, J.; Barlow, K.; Beck, S.; Berry, E.; Birren, B.; Bloom, T.; Bork, P.; Botcherby, M.; Bray, N.; Brent, M. R.; Brown, D. G.; Brown, S. D.; Bult, C.; Burton, J.; Butler, J.; Campbell, R. D.; Carninci, P.; Cawley, S.; Chiaromonte, F.; Chinwalla, A. T.; Church, D. M.; Clamp, M.; Clee, C.; Collins, F. S.; Cook, L. L.; Copley, R. R.; Coulson, A.; Couronne, O.; Cuff, J.; Curwen, V.; Cutts, T.; Daly, M.; David, R.; Davies, J.; Delehaunty, K. D.; Deri, J., Dermitzakis, E. T.; Dewey, C.; Dickens, N. J.; Diekhans, M.; Dodge, S.; Dubchak, I.; Dunn, D. M.; Eddy, S. R.; Elnitski, L.; Emes, R. D.; Eswara, P.; Eyras, E.; Felsenfeld, A.; Fewell, G. A.; Flicek, P.; Foley, K.; Frankel, W. N.; Fulton, L. A.; Fulton, R. S.; Furey, T. S.; Gage, D.; Gibbs, R. A.; Glusman, G.; Gnerre, S.; Goldman, N.; Goodstadt, L.; Grafham, D.; Graves, T. A.; Green, E. D.; Gregory, S.; Guigo, R.; Guyer, M.; Hardison, R. C.; Haussler, D.; Hayashizaki, Y.; Hillier, L. W.; Hinrichs, A.; Hlavina, W.; Holzer, T.; Hsu, F.; Hua, A.; Hubbard, T.; Hunt, A.; Jackson, I.; Jaffe, D. B.; Johnson, L. S.; Jones, M.; Jones, T. A.; Joy, A.; Kamal, M.; et al. Initial sequencing and comparative analysis of the mouse genome. Nature, 2002, 420: 520-62.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
Agarwal, P.6
Agarwala, R.7
Ainscough, R.8
Alexandersson, M.9
An, P.10
Antonarakis, S.E.11
Attwood, J.12
Baertsch, R.13
Bailey, J.14
Barlow, K.15
Beck, S.16
Berry, E.17
Birren, B.18
Bloom, T.19
Bork, P.20
Botcherby, M.21
Bray, N.22
Brent, M.R.23
Brown, D.G.24
Brown, S.D.25
Bult, C.26
Burton, J.27
Butler, J.28
Campbell, R.D.29
Carninci, P.30
Cawley, S.31
Chiaromonte, F.32
Chinwalla, A.T.33
Church, D.M.34
Clamp, M.35
Clee, C.36
Collins, F.S.37
Cook, L.L.38
Copley, R.R.39
Coulson, A.40
Couronne, O.41
Cuff, J.42
Curwen, V.43
Cutts, T.44
Daly, M.45
David, R.46
Davies, J.47
Delehaunty, K.D.48
Deri, J.49
Dermitzakis, E.T.50
Dewey, C.51
Dickens, N.J.52
Diekhans, M.53
Dodge, S.54
Dubchak, I.55
Dunn, D.M.56
Eddy, S.R.57
Elnitski, L.58
Emes, R.D.59
Eswara, P.60
Eyras, E.61
Felsenfeld, A.62
Fewell, G.A.63
Flicek, P.64
Foley, K.65
Frankel, W.N.66
Fulton, L.A.67
Fulton, R.S.68
Furey, T.S.69
Gage, D.70
Gibbs, R.A.71
Glusman, G.72
Gnerre, S.73
Goldman, N.74
Goodstadt, L.75
Grafham, D.76
Graves, T.A.77
Green, E.D.78
Gregory, S.79
Guigo, R.80
Guyer, M.81
Hardison, R.C.82
Haussler, D.83
Hayashizaki, Y.84
Hillier, L.W.85
Hinrichs, A.86
Hlavina, W.87
Holzer, T.88
Hsu, F.89
Hua, A.90
Hubbard, T.91
Hunt, A.92
Jac93
more..
-
4
-
-
0038797803
-
Annotation of the Arabidopsis genome
-
Wortman, J. R.; Haas, B. J.; Hannick, L. I.; Smith, R. K.; Jr.; Maiti, R.; Ronning, C. M.; Chan, A. P.; Yu, C.; Ayele, M.; Whitelaw, C. A.; White, O. R. and Town, C. D. Annotation of the Arabidopsis genome. Plant Physiol., 2003, 132: 461-8.
-
(2003)
Plant Physiol.
, vol.132
, pp. 461-468
-
-
Wortman, J.R.1
Haas, B.J.2
Hannick, L.I.3
Smith Jr., R.K.4
Maiti, R.5
Ronning, C.M.6
Chan, A.P.7
Yu, C.8
Ayele, M.9
Whitelaw, C.A.10
White, O.R.11
Town, C.D.12
-
5
-
-
0034919548
-
Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis
-
Cliften, P. F.; Hillier, L. W.; Fulton, L.; Graves, T.; Miner, T.; Gish, W. R.; Waterston, R. H. and Johnston, M. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome. Res., 2001, 11: 1175-86.
-
(2001)
Genome. Res.
, vol.11
, pp. 1175-1186
-
-
Cliften, P.F.1
Hillier, L.W.2
Fulton, L.3
Graves, T.4
Miner, T.5
Gish, W.R.6
Waterston, R.H.7
Johnston, M.8
-
6
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis, M.; Patterson, N.; Endrizzi, M.; Birren, B. and Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 2003, 423: 241-54.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
7
-
-
0034783060
-
Enrichment of regulatory signals in conserved non-coding genomic sequence
-
Levy, S.; Hannenhalli, S. and Workman, C. Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics, 2001, 17: 871-7.
-
(2001)
Bioinformatics
, vol.17
, pp. 871-877
-
-
Levy, S.1
Hannenhalli, S.2
Workman, C.3
-
8
-
-
18744395183
-
Numerous potentially functional but nongenic conserved sequences on human chromosome 21
-
Dermitzakis, E. T.; Reymond, A.; Lyle, R.; Scamuffa, N.; Ucla, C.; Deutsch, S.; Stevenson, B. J.; Flegel, V.; Bucher, P.; Jongeneel, C. V. and Antonarakis, S. E. Numerous potentially functional but nongenic conserved sequences on human chromosome 21. Nature, 2002, 420: 578-82.
-
(2002)
Nature
, vol.420
, pp. 578-582
-
-
Dermitzakis, E.T.1
Reymond, A.2
Lyle, R.3
Scamuffa, N.4
Ucla, C.5
Deutsch, S.6
Stevenson, B.J.7
Flegel, V.8
Bucher, P.9
Jongeneel, C.V.10
Antonarakis, S.E.11
-
9
-
-
0002154886
-
Annotating regulatory DNA based on man-mouse genomic comparison
-
Dieterich, C.; Cusack, B.; Wang, H.; Rateitschak, K.; Krause, A. and Vingron, M. Annotating regulatory DNA based on man-mouse genomic comparison. Bioinformatics, 2002, 18: S84-90.
-
(2002)
Bioinformatics
, vol.18
-
-
Dieterich, C.1
Cusack, B.2
Wang, H.3
Rateitschak, K.4
Krause, A.5
Vingron, M.6
-
10
-
-
0037350957
-
SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model
-
Alexandersson, M.; Cawley, S. and Pachter, L. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome. Res., 2003, 13: 496-502
-
(2003)
Genome. Res.
, vol.13
, pp. 496-502
-
-
Alexandersson, M.1
Cawley, S.2
Pachter, L.3
-
11
-
-
0037311782
-
Gene finding with a hidden Markov model of genome structure and evolution
-
Pedersen, J. S. and Hein, J. Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics, 2003, 19: 219-27
-
(2003)
Bioinformatics
, vol.19
, pp. 219-227
-
-
Pedersen, J.S.1
Hein, J.2
-
12
-
-
0037264654
-
Leveraging the mouse genome for gene prediction in human: From whole-genome shotgun reads to a global synteny map
-
Flicek, P.; Keibler, E.; Hu, P.; Korf, I. and Brent, M. R. Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome. Res., 2003, 13: 46-54.
-
(2003)
Genome. Res.
, vol.13
, pp. 46-54
-
-
Flicek, P.1
Keibler, E.2
Hu, P.3
Korf, I.4
Brent, M.R.5
-
13
-
-
0037272006
-
Reevaluating human gene annotation: A second-generation analysis of chromosome 22
-
Collins, J. E.; Goward, M. E.; Cole, C. G.; Smink, L. J.; Huckle, E. J.; Knowles, S.; Bye, J. M.; Beare, D. M. and Dunham, I. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome. Res., 2003, 13: 27-36.
-
(2003)
Genome. Res.
, vol.13
, pp. 27-36
-
-
Collins, J.E.1
Goward, M.E.2
Cole, C.G.3
Smink, L.J.4
Huckle, E.J.5
Knowles, S.6
Bye, J.M.7
Beare, D.M.8
Dunham, I.9
-
14
-
-
0037246585
-
Ensembl 2002: Accommodating comparative genomics
-
Clamp, M.; Andrews, D.; Barker, D.; Bevan, P.; Cameron, G.; Chen, Y.; Clark, L.; Cox, T.; Cuff; J.; Curwen, V.; Down, T.; Durbin, R.; Eyras, E.; Gilbert, J.; Hammond, M.; Hubbard, T.; Kasprzyk, A.; Keefe, D.; Lehvaslaiho, H.; Iyer, V.; Melsopp, C.; Mongin, E.; Pettett, R.; Potter, S.; Rust, A.; Schmidt, E.; Searle, S.; Slater, G.; Smith, J.; Spooner, W.; Stabenau, A.; Stalker, J.; Stupka, E.; Ureta-Vidal, A.; Vastrik, I. and Birney, E. Ensembl 2002: accommodating comparative genomics. Nucleic. Acids Res., 2003, 31: 38-42.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 38-42
-
-
Clamp, M.1
Andrews, D.2
Barker, D.3
Bevan, P.4
Cameron, G.5
Chen, Y.6
Clark, L.7
Cox, T.8
Cuff, J.9
Curwen, V.10
Down, T.11
Durbin, R.12
Eyras, E.13
Gilbert, J.14
Hammond, M.15
Hubbard, T.16
Kasprzyk, A.17
Keefe, D.18
Lehvaslaiho, H.19
Iyer, V.20
Melsopp, C.21
Mongin, E.22
Pettett, R.23
Potter, S.24
Rust, A.25
Schmidt, E.26
Searle, S.27
Slater, G.28
Smith, J.29
Spooner, W.30
Stabenau, A.31
Stalker, J.32
Stupka, E.33
Ureta-Vidal, A.34
Vastrik, I.35
Birney, E.36
more..
-
15
-
-
0242317680
-
Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics
-
McCutcheon, J. P. and Eddy, S. R. Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic. Acids. Res., 2003, 31: 4119-28.
-
(2003)
Nucleic Acids. Res.
, vol.31
, pp. 4119-4128
-
-
McCutcheon, J.P.1
Eddy, S.R.2
-
16
-
-
0037321349
-
New microRNAs from mouse and human
-
Lagos-Quintana, M.; Rauhut, R.; Meyer, J.; Borkhardt, A. and Tuschl, T. New microRNAs from mouse and human. RNA., 2003, 9: 175-9.
-
(2003)
RNA
, vol.9
, pp. 175-179
-
-
Lagos-Quintana, M.1
Rauhut, R.2
Meyer, J.3
Borkhardt, A.4
Tuschl, T.5
-
17
-
-
0000791476
-
Lengths of chromosomal segments conserved since divergence of man and mouse
-
Nadeau, J. H. and Taylor, B. A. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl. Acad. Sci. USA, 1984, 81: 814-8.
-
(1984)
Proc. Natl. Acad. Sci. USA
, vol.81
, pp. 814-818
-
-
Nadeau, J.H.1
Taylor, B.A.2
-
18
-
-
14344273992
-
Prevalence of small versions in yeast gene order evolution
-
Seoighe, C.; Federspiel, N.; Jones, T.; Hansen, N.; Bivolarovic, V.; Surzycki, R.; Tamse, R.; Komp, C.; Huizar, L.; Davis, R. W.; Scherer, S.; Tait, E.; Shaw, D. J.; Harris, D.; Murphy, L.; Oliver, K.; Taylor, K.; Rajandream, M. A.; Barrell, B. G. and Wolfe, K. H. Prevalence of small versions in yeast gene order evolution. Proc. Natl. Acad. Sci. USA, 2000, 97: 14433-7.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 14433-14437
-
-
Seoighe, C.1
Federspiel, N.2
Jones, T.3
Hansen, N.4
Bivolarovic, V.5
Surzycki, R.6
Tamse, R.7
Komp, C.8
Huizar, L.9
Davis, R.W.10
Scherer, S.11
Tait, E.12
Shaw, D.J.13
Harris, D.14
Murphy, L.15
Oliver, K.16
Taylor, K.17
Rajandream, M.A.18
Barrell, B.G.19
Wolfe, K.H.20
more..
-
19
-
-
0033869323
-
Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions
-
Bennetzen, J. L. Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant. Cell., 2000, 12: 1021-9.
-
(2000)
Plant. Cell.
, vol.12
, pp. 1021-1029
-
-
Bennetzen, J.L.1
-
20
-
-
0035101024
-
How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila
-
Ranz, J. M.; Casals, F. and Ruiz, A. How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila. Genome. Res., 2001, 11: 230-9.
-
(2001)
Genome. Res.
, vol.11
, pp. 230-239
-
-
Ranz, J.M.1
Casals, F.2
Ruiz, A.3
-
21
-
-
0036078675
-
Fourfold faster rate of genome rearrangement in nematodes than in Drosophila
-
Coghlan, A. and Wolfe, K. H. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome. Res., 2002, 12: 857-67.
-
(2002)
Genome. Res.
, vol.12
, pp. 857-867
-
-
Coghlan, A.1
Wolfe, K.H.2
-
22
-
-
0037264074
-
Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
-
Pevzner, P. and Tesler, G. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome. Res., 2003, 13: 37-45.
-
(2003)
Genome. Res.
, vol.13
, pp. 37-45
-
-
Pevzner, P.1
Tesler, G.2
-
23
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F.; Madden, T. L.; Schaffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W. and Lipman, D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 1997, 25: 3389-402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
24
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson, W. R. and Lipman, D. J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA, 1988, 85: 2444-8.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
25
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T. F. and Waterman, M. S. Identification of common molecular subsequences. J. Mol. Biol., 1981, 147: 195-7.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
26
-
-
0029654258
-
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis
-
Sonnhammer, E. L. and Durbin, R. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene, 1995, 167: GCI-10.
-
(1995)
Gene
, vol.167
-
-
Sonnhammer, E.L.1
Durbin, R.2
-
27
-
-
0033153375
-
Alignment of whole genomes
-
Delcher, A. L.; Kasif, S.; Fleischmann, R. D.; Peterson, J.; White, O. and Salzberg, S. L. Alignment of whole genomes. Nucleic Acids Res., 1999, 27: 2369-76
-
(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
-
28
-
-
0034020416
-
PipMaker - A web server for aligning two genomic DNA sequences
-
Schwartz, S.; Zhang, Z.; Frazer, K. A.; Smit, A.; Riemer, C.; Bouck, J.; Gibbs, R.; Hardison, R. and Miller, W. PipMaker - a web server for aligning two genomic DNA sequences. Genome. Res., 2000, 10: 577-86
-
(2000)
Genome. Res.
, vol.10
, pp. 577-586
-
-
Schwartz, S.1
Zhang, Z.2
Frazer, K.A.3
Smit, A.4
Riemer, C.5
Bouck, J.6
Gibbs, R.7
Hardison, R.8
Miller, W.9
-
29
-
-
0034764307
-
SSAHA: A fast search method for large DNA databases
-
Ning, Z.; Cox, A. J. and Mullikin, J. C. SSAHA: a fast search method for large DNA databases. Genome. Res., 2001, 11: 1725-9.
-
(2001)
Genome. Res.
, vol.11
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
30
-
-
0036226603
-
BLAT - The BLAST-like alignment tool
-
Kent, W. J. BLAT - the BLAST-like alignment tool. Genome. Res., 2002, 12: 656-64
-
(2002)
Genome. Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
31
-
-
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. Human-mouse alignments with BLASTZ. Genome. Res., 2003, 13: 103-7
-
(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
-
32
-
-
0037270315
-
AVID: A global alignment program
-
Bray, N.; Dubchak, I. and Pachter, L. AVID: A global alignment program. Genome. Res., 2003, 13: 97-102.
-
(2003)
Genome. Res.
, vol.13
, pp. 97-102
-
-
Bray, N.1
Dubchak, I.2
Pachter, L.3
-
33
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno, M.; Do, C. B.; Cooper, G. M.; Kim, M. F.; Davydov, E.; Green, E. D.; Sidow, A. and Batzoglou, S. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome. Res., 2003, 13: 721-31
-
(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
-
34
-
-
0042490659
-
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences
-
Schwartz, S.; Elnitski, L.; Li, M.; Weirauch, M.; Riemer, C.; Smit, A.; Green, E. D.; Hardison, R. C. and Miller, W. MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res., 2003, 31: 3518-24.
-
(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
-
35
-
-
0030947344
-
Molecular evidence for an ancient duplication of the entire yeast genome
-
Wolfe, K. H. and Shields, D. C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 1997, 387: 708-13.
-
(1997)
Nature
, vol.387
, pp. 708-713
-
-
Wolfe, K.H.1
Shields, D.C.2
-
36
-
-
0036613237
-
Extensive genomic duplication during early chordate evolution
-
McLysaght, A.; Hokamp, K. and Wolfe, K. H. Extensive genomic duplication during early chordate evolution. Nat. Genet., 2002, 31: 200-4.
-
(2002)
Nat. Genet.
, vol.31
, pp. 200-204
-
-
McLysaght, A.1
Hokamp, K.2
Wolfe, K.H.3
-
37
-
-
0037269875
-
Detection of gene duplications and block duplications in eukaryotic genomes
-
Li, W. H.; Gu, Z.; Cavalcanti, A. R. and Nekrutenko, A. Detection of gene duplications and block duplications in eukaryotic genomes. J. Struct. Funct. Genomics, 2003, 3: 27-34
-
(2003)
J. Struct. Funct. Genomics
, vol.3
, pp. 27-34
-
-
Li, W.H.1
Gu, Z.2
Cavalcanti, A.R.3
Nekrutenko, A.4
-
38
-
-
0037313579
-
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome
-
Blanc, G.; Hokamp, K. and Wolfe, K. H. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res., 2003, 13: 137-44.
-
(2003)
Genome Res.
, vol.13
, pp. 137-144
-
-
Blanc, G.1
Hokamp, K.2
Wolfe, K.H.3
-
39
-
-
0036852286
-
The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice
-
Vandepoele, K.; Saeys, Y.; Simillion, C.; Raes, J. and Van De Peer, Y. The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice. Genome. Res., 2002a, 12: 1792-801.
-
(2002)
Genome. Res.
, vol.12
, pp. 1792-1801
-
-
Vandepoele, K.1
Saeys, Y.2
Simillion, C.3
Raes, J.4
Van De Peer, Y.5
-
40
-
-
0037109058
-
The hidden duplication past of Arabidopsis thaliana
-
Simillion, C.; Vandepoele, K.; Van Montagu, M. C.; Zabeau, M. and Van De Peer, Y. The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA, 2002, 99: 13627-32.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 13627-13632
-
-
Simillion, C.1
Vandepoele, K.2
Van Montagu, M.C.3
Zabeau, M.4
Van De Peer, Y.5
-
41
-
-
0037767267
-
LineUp: Statistical detection of chromosomal homology with application to plant comparative genomics
-
Hampson, S.; McLysaght, A.; Gaut, B. and Baldi, P. LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Res., 2003, 13: 999-1010.
-
(2003)
Genome Res.
, vol.13
, pp. 999-1010
-
-
Hampson, S.1
McLysaght, A.2
Gaut, B.3
Baldi, P.4
-
42
-
-
0035147066
-
Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses
-
Gaut, B. S. Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res., 2001, 11: 55-66.
-
(2001)
Genome Res.
, vol.11
, pp. 55-66
-
-
Gaut, B.S.1
-
43
-
-
0035179702
-
Pattern and timing of gene duplication in animal genomes
-
Friedman, R. and Hughes, A. L. Pattern and timing of gene duplication in animal genomes. Genome. Res., 2001, 11: 1842-7.
-
(2001)
Genome. Res.
, vol.11
, pp. 1842-1847
-
-
Friedman, R.1
Hughes, A.L.2
-
44
-
-
0034671866
-
The origins of genomic duplications in Arabidopsis
-
Vision, T. J.; Brown, D. G. and Tanksley, S. D. The origins of genomic duplications in Arabidopsis. Science, 2000, 290: 2114-7
-
(2000)
Science
, vol.290
, pp. 2114-2117
-
-
Vision, T.J.1
Brown, D.G.2
Tanksley, S.D.3
-
45
-
-
0037227553
-
Patterns of Gene Duplication in Saccharomyces cerevisiae and Caenorhabditis elegans
-
Cavalcanti, A. O.; Ferreira, R. O.; Gu, Z. O. and Li, W. H. Patterns of Gene Duplication in Saccharomyces cerevisiae and Caenorhabditis elegans. J. Mol. Evol., 2003, 56: 28-37.
-
(2003)
J. Mol. Evol.
, vol.56
, pp. 28-37
-
-
Cavalcanti, A.O.1
Ferreira, R.O.2
Gu, Z.O.3
Li, W.H.4
-
46
-
-
0037213551
-
Vertebrate evolution: Doubling and shuffling with a full deck
-
Durand, D. Vertebrate evolution: doubling and shuffling with a full deck. Trends Genet, 2003, 19: 2-5.
-
(2003)
Trends Genet.
, vol.19
, pp. 2-5
-
-
Durand, D.1
-
47
-
-
1042276327
-
Fast identification and statistical evaluation of segmental homologies in comparative maps
-
Calabrese, P. P.; Chakravarty, S. and Vision, T. J. Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics, 2003, 19: 174-180.
-
(2003)
Bioinformatics
, vol.19
, pp. 174-180
-
-
Calabrese, P.P.1
Chakravarty, S.2
Vision, T.J.3
-
48
-
-
2342554268
-
Building genomic profiles for uncovering segmental homology in the twilight zone
-
in press
-
Simillion, C.; Vandepoele, K.; Saeys, Y. and Van De Peer, Y. Building genomic profiles for uncovering segmental homology in the twilight zone. Genome. Res., 2004, in press.
-
(2004)
Genome Res.
-
-
Simillion, C.1
Vandepoele, K.2
Saeys, Y.3
Van De Peer, Y.4
-
49
-
-
0034893812
-
Orthologs and paralogs - We need to get it right
-
Interactions1002
-
Jensen, R. A. Orthologs and paralogs - we need to get it right. Genome. Biol., 2001, 2: Interactions1002.
-
(2001)
Genome. Biol.
, vol.2
-
-
Jensen, R.A.1
-
50
-
-
0033956060
-
The COG database: A tool for genome-scale analysis of protein functions and evolution
-
Tatusov, R. L.; Galperin, M. Y.; Natale, D. A. and Koonin, E. V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic. Acids. Res., 2000, 28: 33-6.
-
(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
-
51
-
-
0035865239
-
Evolutionary analyses of the human genome
-
Li, W. H.; Gu, Z.; Wang, H. and Nekrutenko, A. Evolutionary analyses of the human genome. Nature, 2001, 409: 847-9.
-
(2001)
Nature
, vol.409
, pp. 847-849
-
-
Li, W.H.1
Gu, Z.2
Wang, H.3
Nekrutenko, A.4
-
52
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm, M.; Storm, C. E. and Sonnhammer, E. L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 2001, 314: 1041-52.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
53
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright, A. J.; Van Dongen, S. and Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 2002, 30: 1575-84.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
54
-
-
0036889658
-
Detecting the undetectable: Uncovering duplicated segments in Arabidopsis by comparison with rice
-
Vandepoele, K.; Simillion, C. and Van de Peer, Y. Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. Trends Genet., 2002b, 18: 606-8.
-
(2002)
Trends Genet.
, vol.18
, pp. 606-608
-
-
Vandepoele, K.1
Simillion, C.2
Van de Peer, Y.3
-
55
-
-
0141564555
-
Evidence that rice, and other cereals, are ancient aneuploids
-
Vandepoele, K.; Simillion, C. and Van de Peer, Y. Evidence that rice, and other cereals, are ancient aneuploids. Plant Cell 15, 2192-2202.
-
Plant Cell
, vol.15
, pp. 2192-2202
-
-
Vandepoele, K.1
Simillion, C.2
Van de Peer, Y.3
-
56
-
-
0034255126
-
Comparing sequenced segments of the tomato and arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny
-
Ku, H. M.; Vision, T.; Liu, J. and Tanksley, S. D. Comparing sequenced segments of the tomato and arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl. Acad. Sci. USA, 2000, 97: 9121-6
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 9121-9126
-
-
Ku, H.M.1
Vision, T.2
Liu, J.3
Tanksley, S.D.4
-
57
-
-
0037047141
-
Gene order evolution and paleopolyploidy in hemiascomycete yeasts
-
Wong, S.; Butler, G. and Wolfe, K. H. Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc. Natl. Acad. Sci. USA, 2002, 99: 9272-7.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 9272-9277
-
-
Wong, S.1
Butler, G.2
Wolfe, K.H.3
-
58
-
-
0033955274
-
Evolution of genes and taxa: A primer
-
Doyle, J. J. and Gaut, B. S. Evolution of genes and taxa: a primer. Plant. Mol. Biol., 2000, 42: 1-23
-
(2000)
Plant. Mol. Biol.
, vol.42
, pp. 1-23
-
-
Doyle, J.J.1
Gaut, B.S.2
-
59
-
-
0033972072
-
The probability of duplicate gene preservation by subfunctionalization
-
Lynch, M. and Force, A. The probability of duplicate gene preservation by subfunctionalization. Genetics, 2000, 154: 459-73.
-
(2000)
Genetics
, vol.154
, pp. 459-473
-
-
Lynch, M.1
Force, A.2
-
60
-
-
0036845822
-
Splitting pairs: The diverging fates of duplicated genes
-
Prince, V. E. and Pickett, F. B., Splitting pairs: the diverging fates of duplicated genes. Nat. Rev. Genet, 2002, 3: 827-37.
-
(2002)
Nat. Rev. Genet.
, vol.3
, pp. 827-837
-
-
Prince, V.E.1
Pickett, F.B.2
-
61
-
-
0642340503
-
OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies
-
Cannon, S. B. and Young, N. D. OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies. BMC. Bioinformatics, 2003, 4: 35
-
(2003)
BMC. Bioinformatics
, vol.4
, pp. 35
-
-
Cannon, S.B.1
Young, N.D.2
-
62
-
-
0042027896
-
Structural dynamics of eukaryotic chromosome evolution
-
Eichler, E. E. and Sankoff, D. Structural dynamics of eukaryotic chromosome evolution. Science, 2003, 301: 793-7.
-
(2003)
Science
, vol.301
, pp. 793-797
-
-
Eichler, E.E.1
Sankoff, D.2
|