-
1
-
-
1842667855
-
Characterization of evolutionary rates and constraints in three mammalian genomes
-
Cooper,G.M., Brudno,M., Stone,E.A., Dubchak,I., Batzoglou,S. and Sidow,A. (2004) Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Res., 14, 539-548.
-
(2004)
Genome Res.
, vol.14
, pp. 539-548
-
-
Cooper, G.M.1
Brudno, M.2
Stone, E.A.3
Dubchak, I.4
Batzoglou, S.5
Sidow, A.6
-
2
-
-
0141815478
-
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
-
Kent,W.J., Baertsch,R., Hinrichs,A., Miller,W. and Haussler,D. (2003) Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA, 100, 11484-11489.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 11484-11489
-
-
Kent, W.J.1
Baertsch, R.2
Hinrichs, A.3
Miller, W.4
Haussler, D.5
-
3
-
-
0037264074
-
Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
-
Pevzner,P. and Tesler,G. (2003) 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
-
4
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz,S., Kent,W.J., Smit,A., Zhang,Z., Baertsch,R., Hardison,R.C., Haussler,D. and Miller,D. (2003) 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, D.8
-
5
-
-
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. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
-
(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
-
6
-
-
10644283823
-
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
-
Hillier,L.W., Miller,W., Birney,E., Warren,W., Harsison,R.C., Ponting,C.P., Bork,P., Burt,D.W. et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
-
(2004)
Nature
, vol.432
, pp. 695-716
-
-
Hillier, L.W.1
Miller, W.2
Birney, E.3
Warren, W.4
Harsison, R.C.5
Ponting, C.P.6
Bork, P.7
Burt, D.W.8
-
7
-
-
2442534964
-
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
-
San Diego, CA. ACM Press, New York, NY
-
Sharan,R., Ideker,T., Kelley,B.P., Shamir,R. and Karp,R.M. (2004) Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. In Proceedings of the Eighth Annual International Conference on Computational Molecular Biology (RECOMB), vol. 8, San Diego, CA. ACM Press, New York, NY, pp. 282-289.
-
(2004)
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology (RECOMB)
, vol.8
, pp. 282-289
-
-
Sharan, R.1
Ideker, T.2
Kelley, B.P.3
Shamir, R.4
Karp, R.M.5
-
8
-
-
29144439098
-
The ENCODE Project
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. (2004), The ENCODE Project. Science 306, 636-640.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
9
-
-
0021919480
-
Rapid and sensitive protein similarity searches
-
Lipman,D.J. and Pearson,W.R. (1985) Rapid and sensitive protein similarity searches. Science, 227, 1435-1441.
-
(1985)
Science
, vol.227
, pp. 1435-1441
-
-
Lipman, D.J.1
Pearson, W.R.2
-
10
-
-
0025183708
-
Basic local alignment search tool
-
Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
11
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schaeffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (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
Schaeffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
12
-
-
0036202921
-
PatternHunter: Faster and more sensitive homology search
-
Ma,B., Tromp,J. and Li,M. (2002) PatternHunter: Faster and more sensitive homology search. Bioinformatics, 18, 440-445.
-
(2002)
Bioinformatics
, vol.18
, pp. 440-445
-
-
Ma, B.1
Tromp, J.2
Li, M.3
-
13
-
-
0036226603
-
BLAT-The BLAST-like alignment tool
-
Kent,W.J. (2002) BLAT-The BLAST-like alignment tool. Genome Res., 12, 656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
14
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
15
-
-
24044447664
-
Automated generation of heuristics for biological sequence comparison
-
Slater,G.S. and Birney,E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 31
-
-
Slater, G.S.1
Birney, E.2
-
16
-
-
10944229056
-
A tutorial of recent developments in the seeding of local alignment
-
Brown,D.G., Li,M. and Ma,B. (2004) A tutorial of recent developments in the seeding of local alignment. J. Bioinform. Comput. Biol., 2 819-842.
-
(2004)
J. Bioinform. Comput. Biol.
, vol.2
, pp. 819-842
-
-
Brown, D.G.1
Li, M.2
Ma, B.3
-
17
-
-
0038039629
-
Designing seeds for similarity search in genomic DNA
-
Berlin, Germany. ACM Press, New York, NY
-
Buhler,J., Keich,U. and Sun,Y. (2003) Designing seeds for similarity search in genomic DNA. In Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB), vol. 7, Berlin, Germany. ACM Press, New York, NY, pp. 67-75.
-
(2003)
Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB)
, vol.7
, pp. 67-75
-
-
Buhler, J.1
Keich, U.2
Sun, Y.3
-
18
-
-
4544349273
-
PatternHunter II: Highly sensitive and fast homology search
-
Li,M., Ma,B., Kisman,D. and Tromp,J. (2003) PatternHunter II: Highly sensitive and fast homology search. J. Bioinform. Comput. Biol., 2, 417-439.
-
(2003)
J. Bioinform. Comput. Biol.
, vol.2
, pp. 417-439
-
-
Li, M.1
Ma, B.2
Kisman, D.3
Tromp, J.4
-
19
-
-
4444360116
-
Optimal spaced seeds for homologous coding regions
-
Brejova,B., Brown,D.G. and Vinar,T. (2004) Optimal spaced seeds for homologous coding regions. J. Bioinform. Comput. Biol., 1, 595-610.
-
(2004)
J. Bioinform. Comput. Biol.
, vol.1
, pp. 595-610
-
-
Brejova, B.1
Brown, D.G.2
Vinar, T.3
-
20
-
-
2442614993
-
Designing multiple simultaneous seeds for DNA similarity search
-
San Diego, CA. ACM Press, New York, NY
-
Sun,Y. and Buhler,J. (2004) Designing multiple simultaneous seeds for DNA similarity search. In Proceedings of the Eighth Annual International Conference on Computational Molecular Biology (RECOMB), vol. 8, San Diego, CA. ACM Press, New York, NY, pp. 76-84.
-
(2004)
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology (RECOMB)
, vol.8
, pp. 76-84
-
-
Sun, Y.1
Buhler, J.2
-
21
-
-
0842321997
-
Sensitivity analysis and efficient method for identifying optimal spaced seeds
-
Choi,K.P. and Zhang,L. (2004) Sensitivity analysis and efficient method for identifying optimal spaced seeds. Journal of Computer and System Sciences, 68, 22-40.
-
(2004)
Journal of Computer and System Sciences
, vol.68
, pp. 22-40
-
-
Choi, K.P.1
Zhang, L.2
-
22
-
-
35248841126
-
Vector seeds: An extension to spaced seeds allows substantial improvements in sensitivity and specificity
-
Budapest, Hungary, Springer-Verlag
-
Brejova,B., Brown,D.G. and Vinar,T. (2003) Vector seeds: An extension to spaced seeds allows substantial improvements in sensitivity and specificity. In Proceedings of WABI (Workshop on Algorithms in Bioinformatics), vol. 2812, Budapest, Hungary, Springer-Verlag, pp. 39-54.
-
(2003)
Proceedings of WABI (Workshop on Algorithms in Bioinformatics)
, vol.2812
, pp. 39-54
-
-
Brejova, B.1
Brown, D.G.2
Vinar, T.3
-
23
-
-
0037398368
-
NISC Comparative Sequencing Program. 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. NISC Comparative Sequencing Program. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res., 13, 721-731.
-
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
-
24
-
-
1542748076
-
Aligning multiple genomic sequences with the threaded blockset aligner
-
Blanchette,M., Kent,W.J., Riemer,C., Elnitski,L., Smit,A.F., Roskin,K.M., Baertsch,R.,Rosenbloom,K., Clawson,H., Green,E.D.et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res., 14, 708-715.
-
(2004)
Genome Res.
, vol.14
, pp. 708-715
-
-
Blanchette, M.1
Kent, W.J.2
Riemer, C.3
Elnitski, L.4
Smit, A.F.5
Roskin, K.M.6
Baertsch, R.7
Rosenbloom, K.8
Clawson, H.9
Green, E.D.10
-
25
-
-
1842667852
-
MAVID: Constrained ancestral alignment of multiple sequences
-
Bray,N. and Pachter,L. (2004) MAVID: Constrained ancestral alignment of multiple sequences. Genome Res., 14, 693-699.
-
(2004)
Genome Res.
, vol.14
, pp. 693-699
-
-
Bray, N.1
Pachter, L.2
-
26
-
-
8744312854
-
A novel method for multiple alignment of sequences with repeated and shuffled elements
-
Raphael,B., Zhi,D., Tang,H. and Pevzner,P. (2004) A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res., 14, 2336-2346.
-
(2004)
Genome Res.
, vol.14
, pp. 2336-2346
-
-
Raphael, B.1
Zhi, D.2
Tang, H.3
Pevzner, P.4
-
27
-
-
3242888285
-
rVista 2.0: Evolutionary analysis of transcription factor binding sites
-
Loots,G.G. and Ovcharenko,I. (2004) rVista 2.0: Evolutionary analysis of transcription factor binding sites. Nucleic Acids Res., 32, W217-W221.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Loots, G.G.1
Ovcharenko, I.2
-
28
-
-
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
-
29
-
-
17444437765
-
Integrating genomic homology into gene structure prediction
-
Korf,I., Flicek,P., Duan,D. and Brent,M.R. (2001) Integrating genomic homology into gene structure prediction. Bioinformatics, 17, S140-S148.
-
(2001)
Bioinformatics
, vol.17
-
-
Korf, I.1
Flicek, P.2
Duan, D.3
Brent, M.R.4
-
30
-
-
0037022603
-
Inference of functional regions in proteins by quantification of evolutionary constraints
-
Simon,A., Stone,E.A. and Sidow,A. (2002) Inference of functional regions in proteins by quantification of evolutionary constraints. Proc. Natl Acad. Sci. USA, 99, 2912-2917.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 2912-2917
-
-
Simon, A.1
Stone, E.A.2
Sidow, A.3
-
31
-
-
0023375315
-
Profile Analysis: Detection of distantly related proteins
-
Gribskov,M., McLachlan,A.M. and Eisenberg,D. (1987) Profile Analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA 84, 4355-4358.
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 4355-4358
-
-
Gribskov, M.1
McLachlan, A.M.2
Eisenberg, D.3
-
32
-
-
0029789461
-
Searching databases of conserved sequence regions by aligning protein multiple-alignments
-
Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24 3836-3845.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 3836-3845
-
-
Pietrokovski, S.1
-
33
-
-
0003516147
-
-
1st edn. Cambridge University Press, Cambridge,UK
-
Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis, 1st edn. Cambridge University Press, Cambridge,UK.
-
(1998)
Biological Sequence Analysis
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
-
34
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
Kimura,M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
-
(1980)
J. Mol. Evol.
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
35
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein,J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol., 17, 368-376.
-
(1981)
J. Mol. Evol.
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
36
-
-
0036375969
-
Significance of inter-species matches when evolutionary rate varies
-
Washington, DC, USA. ACM Press, New York, NY
-
Li,J. and Miller,W. (2002) Significance of inter-species matches when evolutionary rate varies. In Proceedings of the Sixth Annual International Conference on Computational Biology (RECOMB), vol. 6, Washington, DC, USA. ACM Press, New York, NY, pp. 216-224.
-
(2002)
Proceedings of the Sixth Annual International Conference on Computational Biology (RECOMB)
, vol.6
, pp. 216-224
-
-
Li, J.1
Miller, W.2
-
38
-
-
0001457509
-
Some methods for classification and analysis of multivariate observations
-
Berkeley, CA, University of California Press, Berkeley, CA
-
MacQueen,J.B. (1967) Some methods for classification and analysis of multivariate observations. In Berkeley Symposium on Mathematical Statistics and Probability, vol. 1, Berkeley, CA, University of California Press, Berkeley, CA, pp. 281-297.
-
(1967)
Berkeley Symposium on Mathematical Statistics and Probability
, vol.1
, pp. 281-297
-
-
MacQueen, J.B.1
-
40
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
41
-
-
0036606576
-
Fast algorithms for large-scale genome alignment and comparison
-
Delcher,A.L., Phillippy,A., Carlton,J. and Salzberg,S.L. (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res., 30, 2478-2483.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2478-2483
-
-
Delcher, A.L.1
Phillippy, A.2
Carlton, J.3
Salzberg, S.L.4
-
42
-
-
0041465867
-
Comparative analyses of multi-species sequencing from targeted genomic regions
-
Thomas,J.W., Touchman,J.W., Blakesley,R.W., Bouffard,G.G., Beckstrom-Sternberg,S.M., Margulies,E.H., Blanchette,M., Siepel,A.C., Thomas,P.J., McDowell,J.C. et al. (2003) Comparative analyses of multi-species sequencing from targeted genomic regions. Nature, 424, 788-793.
-
(2003)
Nature
, vol.424
, pp. 788-793
-
-
Thomas, J.W.1
Touchman, J.W.2
Blakesley, R.W.3
Bouffard, G.G.4
Beckstrom-Sternberg, S.M.5
Margulies, E.H.6
Blanchette, M.7
Siepel, A.C.8
Thomas, P.J.9
McDowell, J.C.10
-
43
-
-
0025259313
-
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
-
Karlin,A. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 2264-2268
-
-
Karlin, A.1
Altschul, S.F.2
|