-
1
-
-
0036205874
-
Ab initio gene identification: Prokaryote genome annotation with GeneScan and GLIMMER
-
Aggarwal, G. and Ramaswamy, R. 2002. Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER. J. Biosci., 27:7-14.
-
(2002)
J. Biosci
, vol.27
, pp. 7-14
-
-
Aggarwal, G.1
Ramaswamy, R.2
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schäffer, A.A. et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25:3389-402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
-
3
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M., Ball, C.A., Blake, J.A. et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium: Nat. Genet., 25:25-29.
-
(2000)
Nat. Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
4
-
-
33745373606
-
Primate segmental duplications: Crucibles of evolution, diversity and disease
-
Bailey, J.A. and Eichler, E.E. 2006. Primate segmental duplications: Crucibles of evolution, diversity and disease. Nat. Rev. Genet., 7:552-64.
-
(2006)
Nat. Rev. Genet
, vol.7
, pp. 552-564
-
-
Bailey, J.A.1
Eichler, E.E.2
-
5
-
-
22544457599
-
vALId: Validation of protein sequence quality based on multiple alignment data
-
Bianchetti, L., Thompson, J.D., Lecompte, O. et al. 2005. vALId: validation of protein sequence quality based on multiple alignment data. J. Bioinforin. Comput. Biol., 3:929-47.
-
(2005)
J. Bioinforin. Comput. Biol
, vol.3
, pp. 929-947
-
-
Bianchetti, L.1
Thompson, J.D.2
Lecompte, O.3
-
6
-
-
33746237567
-
Genomic insights into positive selection
-
Biswas, S. and Akey, J.M. 2006. Genomic insights into positive selection. Trends Genet., 22:437-46.
-
(2006)
Trends Genet
, vol.22
, pp. 437-446
-
-
Biswas, S.1
Akey, J.M.2
-
7
-
-
0041589546
-
Foot Printer: A program designed for phylogenetic foot printing
-
Blanchette, M. and Tompa, M. 2003. Foot Printer: A program designed for phylogenetic foot printing. Nucleic Acids Res., 31:3840-2.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3840-3842
-
-
Blanchette, M.1
Tompa, M.2
-
8
-
-
10944228197
-
Reconstructing large regions of an ancestral mammalian genome in silico
-
Blanchette, M., Green, E.D., Miller, W. et al. 2004. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res., 14:2412-23.
-
(2004)
Genome Res
, vol.14
, pp. 2412-2423
-
-
Blanchette, M.1
Green, E.D.2
Miller, W.3
-
9
-
-
33745067419
-
The gain and loss of genes during 600 million years of vertebrate evolution
-
Blomme, T., Vandepoele, K., De Bodt, S. et al. 2006. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol., 7:R43.
-
(2006)
Genome Biol
, vol.7
-
-
Blomme, T.1
Vandepoele, K.2
De Bodt, S.3
-
10
-
-
0037440008
-
Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information
-
Blouin, C., Boucher, Y. and Roger, A.J. 2003. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res., 31:790-7.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 790-797
-
-
Blouin, C.1
Boucher, Y.2
Roger, A.J.3
-
11
-
-
16444378220
-
Natural selection during functional divergence to LMP7 and proteasome subunit X (PSMB5) following gene duplication
-
Bos. D.H. 2005. Natural selection during functional divergence to LMP7 and proteasome subunit X (PSMB5) following gene duplication. J. Mol. Evol., 60:221-228.
-
(2005)
J. Mol. Evol
, vol.60
, pp. 221-228
-
-
Bos, D.H.1
-
12
-
-
1842768393
-
Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes
-
Bourque, G. and Pevzner, P.A. 2004. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res., 14:507-16.
-
(2004)
Genome Res
, vol.14
, pp. 507-516
-
-
Bourque, G.1
Pevzner, P.A.2
-
13
-
-
12744263078
-
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
-
Bourque, G., Zdobnov, E.M., Bork, P. et al. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res., 15:98-110.
-
(2005)
Genome Res
, vol.15
, pp. 98-110
-
-
Bourque, G.1
Zdobnov, E.M.2
Bork, P.3
-
14
-
-
0037270315
-
AVID: A Global Alignment Program
-
Bray, N., Dubchak, I. and Pachter, L. 2003. AVID: A Global Alignment Program. Genome Research, 13:97-102.
-
(2003)
Genome Research
, vol.13
, pp. 97-102
-
-
Bray, N.1
Dubchak, I.2
Pachter, L.3
-
15
-
-
0035201828
-
Phylogenetic inferences from molecular sequences: Review and critique
-
Brocchieri, L. 2001. Phylogenetic inferences from molecular sequences: review and critique. Theor. Popul. Biol., 59:27-40.
-
(2001)
Theor. Popul. Biol
, vol.59
, pp. 27-40
-
-
Brocchieri, L.1
-
16
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno, M., Do, C.B., Cooper, G.M. et al. 2003. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res., 13:721-31.
-
(2003)
Genome Res
, vol.13
, pp. 721-731
-
-
Brudno, M.1
Do, C.B.2
Cooper, G.M.3
-
17
-
-
0000303438
-
The Multiple Sequence Alignment Problem in Biology
-
Carrillo, H. and Lipman, D. 1988. The Multiple Sequence Alignment Problem in Biology. SIAM Appl. Math., 48:1073-82.
-
(1988)
SIAM Appl. Math
, vol.48
, pp. 1073-1082
-
-
Carrillo, H.1
Lipman, D.2
-
18
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna, R., Sugawara, H., Koike, T. et al. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31:3497-500.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
-
19
-
-
2942604504
-
Bioinformatics tools for single nucleotide polymorphism discovery and analysis
-
Clifford, R.J., Edmonson, M.N., Nguyen, C. et al. 2004. Bioinformatics tools for single nucleotide polymorphism discovery and analysis, Ann. N. Y. Acad. Sci., 1020:101-9.
-
(2004)
Ann. N. Y. Acad. Sci
, vol.1020
, pp. 101-109
-
-
Clifford, R.J.1
Edmonson, M.N.2
Nguyen, C.3
-
20
-
-
0038305140
-
A co-evolution perspective of the TNFSF and TNFRSF families in the immune system
-
Collette, Y., Gilles, A., Pontarotti, P. et al. 2003. A co-evolution perspective of the TNFSF and TNFRSF families in the immune system. Trends Immunol., 24:387-94.
-
(2003)
Trends Immunol
, vol.24
, pp. 387-394
-
-
Collette, Y.1
Gilles, A.2
Pontarotti, P.3
-
21
-
-
0344898488
-
GIMS: An integrated data storage and analysis environment for genomic and functional data
-
Cornell, M., Paton, N.W., Hedeler, C. et al. 2003. GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast, 20:1291-306.
-
(2003)
Yeast
, vol.20
, pp. 1291-1306
-
-
Cornell, M.1
Paton, N.W.2
Hedeler, C.3
-
22
-
-
33846476262
-
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
-
Dagan, T. and Martin, W. 2007. Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc. Natl. Acad. Sci. U.S.A., 104:870-5.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, pp. 870-875
-
-
Dagan, T.1
Martin, W.2
-
23
-
-
33644557410
-
Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals
-
Danchin, E.G., Gouret, P. and Pontarotti, P. 2006. Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals. BMC Evol. Biol., 6:5.
-
(2006)
BMC Evol. Biol
, vol.6
, pp. 5
-
-
Danchin, E.G.1
Gouret, P.2
Pontarotti, P.3
-
24
-
-
44249100806
-
-
Danchin, E.G., Gaucher, E.A. and Pontarotti, P. 2007. Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters In Liberles D, ed. Ancestral Sequence Reconstruction. Oxfond University Press.
-
Danchin, E.G., Gaucher, E.A. and Pontarotti, P. 2007. Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters In Liberles D, ed. Ancestral Sequence Reconstruction. Oxfond University Press.
-
-
-
-
25
-
-
0036061865
-
A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
-
Daubin, V., Gouy, M. and Perrière, G. 2002. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res., 12:1080-90.
-
(2002)
Genome Res
, vol.12
, pp. 1080-1090
-
-
Daubin, V.1
Gouy, M.2
Perrière, G.3
-
26
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsue, F., Brinkmann, H. and Philippe, H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev Genet., 6:361-75.
-
(2005)
Nat. Rev Genet
, vol.6
, pp. 361-375
-
-
Delsue, F.1
Brinkmann, H.2
Philippe, H.3
-
27
-
-
44249110160
-
The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species
-
in press
-
Descorps-Declere, S., Lemoine, F., Sculo, Q. et al. 2007. The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species. Biochimie (in press).
-
(2007)
Biochimie
-
-
Descorps-Declere, S.1
Lemoine, F.2
Sculo, Q.3
-
28
-
-
0035424599
-
Intrinsic errors in genome annotation
-
Devos, D. and Valencia, A. 2001. Intrinsic errors in genome annotation. Trends Genet., 17:429-31.
-
(2001)
Trends Genet
, vol.17
, pp. 429-431
-
-
Devos, D.1
Valencia, A.2
-
29
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do, C.B., Mahabhashyam, M.S., Brudno, M. et al. 2005. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15:330-40.
-
(2005)
Genome Res
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.2
Brudno, M.3
-
30
-
-
3242677815
-
Cytogenetics and cladistics
-
Dobigny, G., Ducroz, J.F., Robinson, T.J. et al. 2004. Cytogenetics and cladistics. Syst. Biol., 53:470-84.
-
(2004)
Syst. Biol
, vol.53
, pp. 470-484
-
-
Dobigny, G.1
Ducroz, J.F.2
Robinson, T.J.3
-
31
-
-
20444500847
-
Evolutionary aspects of whole-genome biology
-
Doolittle, R.F. 2005. Evolutionary aspects of whole-genome biology. Curr. Opin. Struct. Biol., 15:248-53.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 248-253
-
-
Doolittle, R.F.1
-
32
-
-
20744436518
-
Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases
-
Dufayard, J.F., Duret, L., Penel, S. et al. 2005. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics, 21:2596-603.
-
(2005)
Bioinformatics
, vol.21
, pp. 2596-2603
-
-
Dufayard, J.F.1
Duret, L.2
Penel, S.3
-
33
-
-
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., 32:1792-7.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
34
-
-
22044443709
-
-
Eilbeck, K, Lewis, S.E., Mungall, C.J. et al. 2005. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol., 6:R.44.
-
Eilbeck, K, Lewis, S.E., Mungall, C.J. et al. 2005. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol., 6:R.44.
-
-
-
-
35
-
-
0031976258
-
Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
-
Eisen, J.A. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res., 8:163-7.
-
(1998)
Genome Res
, vol.8
, pp. 163-167
-
-
Eisen, J.A.1
-
36
-
-
0036595632
-
Phylogenetic analysis and gene functional predictions: Phylogenomics in action
-
Eisen, J.A. and Wu, M. 2002. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor. Popul. Biol., 61:481-7.
-
(2002)
Theor. Popul. Biol
, vol.61
, pp. 481-487
-
-
Eisen, J.A.1
Wu, M.2
-
37
-
-
33645310990
-
Protein molecular function prediction by Bayesian phylogenomics
-
Engelhardt, B.E., Jordan, M.I., Muratore, K.E. et al. 2005. Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput. Biol., 1:e45.
-
(2005)
PLoS Comput. Biol
, vol.1
-
-
Engelhardt, B.E.1
Jordan, M.I.2
Muratore, K.E.3
-
38
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright, A.J., Iliopoulos, I., Kyrpides, N.C. et al. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature, 402:86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
-
39
-
-
33747844623
-
FootPrinter3: Phylogenetic footprinting in partially alignable sequences
-
Fang, F. and Blanchette, M. 2006. FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res., 34: W617-20.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Fang, F.1
Blanchette, M.2
-
40
-
-
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., 17:368-76.
-
(1981)
J. Mol. Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
41
-
-
0023084055
-
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
-
Feng, D.F. and Doolittle, R.F. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25:351-60
-
(1987)
J. Mol. Evol
, vol.25
, pp. 351-360
-
-
Feng, D.F.1
Doolittle, R.F.2
-
42
-
-
33846266906
-
Modeling the evolution of protein domain architectures using maximum parsimony
-
Fong, J.H., Geer, L.Y., Panchenko, A.R. et al. 2007. Modeling the evolution of protein domain architectures using maximum parsimony. J. Mol. Biol., 366:307-15.
-
(2007)
J. Mol. Biol
, vol.366
, pp. 307-315
-
-
Fong, J.H.1
Geer, L.Y.2
Panchenko, A.R.3
-
43
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
Force, A., Lynch, M., Pickett, F.B. et al. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics, 151:1531-45.
-
(1999)
Genetics
, vol.151
, pp. 1531-1545
-
-
Force, A.1
Lynch, M.2
Pickett, F.B.3
-
44
-
-
0032229196
-
Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
-
Galperin, M.Y. and Koonin, E.V. 1998. Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol., 1:55-67.
-
(1998)
In Silico Biol
, vol.1
, pp. 55-67
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
45
-
-
17844386108
-
A benchmark of multiple sequence alignment programs upon structural RNAs
-
Gardner, P.P.; Wilm, A. and Washietl, S. 2005. A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res., 33:2433-9.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2433-2439
-
-
Gardner, P.P.1
Wilm, A.2
Washietl, S.3
-
46
-
-
0036606898
-
Predicting functional divergence in protein evolution by site-specific rate shifts
-
Gaucher, E.A., Gu, X., Miyamoto, M.M. et al. 2002. Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci., 27:315-21.
-
(2002)
Trends Biochem Sci
, vol.27
, pp. 315-321
-
-
Gaucher, E.A.1
Gu, X.2
Miyamoto, M.M.3
-
47
-
-
0034923923
-
Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
-
Gerlt, J.A. and Babbitt, P.C. 2001. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem., 70:209-46.
-
(2001)
Annu. Rev. Biochem
, vol.70
, pp. 209-246
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
48
-
-
33746684967
-
Phylogeny based discovery of regulatory elements
-
Gertz, J., Fay, J. and Cohen, B. 2006. Phylogeny based discovery of regulatory elements. BMC Bioinformatics, 7:266.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 266
-
-
Gertz, J.1
Fay, J.2
Cohen, B.3
-
49
-
-
12244283680
-
Modeling the percolation of annotation errors in a database of protein sequences
-
Gilks, W.R., Audit, B., De Angelis, D. et al. 2002. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics, 18:1641-9.
-
(2002)
Bioinformatics
, vol.18
, pp. 1641-1649
-
-
Gilks, W.R.1
Audit, B.2
De Angelis, D.3
-
50
-
-
30344483214
-
Nexplorer: Phylogeny-based exploration of sequence family data
-
Gopalan, V., Qiu, W.G., Chen, M.Z. et al. 2006. Nexplorer: phylogeny-based exploration of sequence family data. Bioinformatics, 22:120-1.
-
(2006)
Bioinformatics
, vol.22
, pp. 120-121
-
-
Gopalan, V.1
Qiu, W.G.2
Chen, M.Z.3
-
51
-
-
25444473119
-
FIGENIX: Intelligent automation of genomic annotation expertise integration in a new software platform
-
Gouret, P., Vitiello, V., Balandraud, N. et al. 2005. FIGENIX: intelligent automation of genomic annotation expertise integration in a new software platform. BMC Bioinformatics, 6:198.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 198
-
-
Gouret, P.1
Vitiello, V.2
Balandraud, N.3
-
52
-
-
0037968852
-
Functional Divergence in Protein (Family) Sequence Evolution
-
Gu, X. 2003. Functional Divergence in Protein (Family) Sequence Evolution. Genetica, 118:133-41.
-
(2003)
Genetica
, vol.118
, pp. 133-141
-
-
Gu, X.1
-
54
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
Hertz, G.Z. and Stormo, G.D. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15:563-577.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
55
-
-
33847324470
-
Imputing supertrees and supernetworks from quartets
-
Holland, B., Conner, G., Huber, K. et al. 2007. Imputing supertrees and supernetworks from quartets. Syst. Biol., 56:57-67.
-
(2007)
Syst. Biol
, vol.56
, pp. 57-67
-
-
Holland, B.1
Conner, G.2
Huber, K.3
-
56
-
-
7244259101
-
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate protokaryotype
-
Jaillon, O., Aury, J.M., Brunet, F. et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate protokaryotype. Nature, 431:946-57.
-
(2004)
Nature
, vol.431
, pp. 946-957
-
-
Jaillon, O.1
Aury, J.M.2
Brunet, F.3
-
57
-
-
33750298722
-
Prediction of genomic functional elements
-
Jones, S.J. 2006. Prediction of genomic functional elements. Annu. Rev. Genomics Hum. Genet., 7:315-38.
-
(2006)
Annu. Rev. Genomics Hum. Genet
, vol.7
, pp. 315-338
-
-
Jones, S.J.1
-
58
-
-
0037370478
-
Bioinformatics in the post-sequence era
-
Kanehisa, M. and Bork, P. 2003. Bioinformatics in the post-sequence era. Nat. Genet., 33:305-10.
-
(2003)
Nat. Genet
, vol.33
, pp. 305-310
-
-
Kanehisa, M.1
Bork, P.2
-
59
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplas, K., Barrett, C. and Hughey, R. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14:846-56.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplas, K.1
Barrett, C.2
Hughey, R.3
-
60
-
-
0037100671
-
MAFFT. a novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh, K., Misawa, K., Kuma, K. et al. 2002. MAFFT. a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30:3059-3066.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
-
61
-
-
0036226603
-
BLAT - the BLAST-like alignment tool
-
Kent, W.J. 2002. BLAT - the BLAST-like alignment tool. Genome Res., 12:656-64.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
62
-
-
34248153777
-
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
-
Kikuta, H., Laplante, M., Navratilova, P. et al. 2007. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res., 17:545-55.
-
(2007)
Genome Res
, vol.17
, pp. 545-555
-
-
Kikuta, H.1
Laplante, M.2
Navratilova, P.3
-
63
-
-
33644845048
-
Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships
-
Kim, Y. and Subramaniam, S. 2006. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins, 62:1115-24.
-
(2006)
Proteins
, vol.62
, pp. 1115-1124
-
-
Kim, Y.1
Subramaniam, S.2
-
64
-
-
0024307824
-
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
-
Kishino, H. and Hasegawa, M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol., 29:170-9.
-
(1989)
J. Mol. Evol
, vol.29
, pp. 170-179
-
-
Kishino, H.1
Hasegawa, M.2
-
65
-
-
33645865251
-
Reconstruction of a 450-My-old ancestral vertebrate protokaryotype
-
Kohn, M., Höogel, J., Vogel, W. et al. 2006. Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. Trends Genet., 22:203-10.
-
(2006)
Trends Genet
, vol.22
, pp. 203-210
-
-
Kohn, M.1
Höogel, J.2
Vogel, W.3
-
66
-
-
16444381885
-
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
-
Koonin, E.V., Federova, N.D., Jackson, J.D. et al. 2004. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol., 5:R-7.
-
(2004)
Genome Biol
, vol.5
-
-
Koonin, E.V.1
Federova, N.D.2
Jackson, J.D.3
-
67
-
-
27644472372
-
Orthologs, paralogs, and evolutionary genomics
-
Koonin, E.V. 2005. Orthologs, paralogs, and evolutionary genomics. Annu Rev. Genet., 39:309-38.
-
(2005)
Annu Rev. Genet
, vol.39
, pp. 309-338
-
-
Koonin, E.V.1
-
68
-
-
33748980210
-
Evolutionary systems biology: Links between gene evolution and function
-
Koonin, E.V. and Wolf, Y.I. 2006. Evolutionary systems biology: links between gene evolution and function. Curr. Opin. Biotechnol., 17:481-7.
-
(2006)
Curr. Opin. Biotechnol
, vol.17
, pp. 481-487
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
69
-
-
31144442881
-
Automatic assessment of alignment quality
-
Lassmann, T. and Sonnhammer, E.L. 2005. Automatic assessment of alignment quality. Nucleic Acids Res., 33:7120-8.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 7120-7128
-
-
Lassmann, T.1
Sonnhammer, E.L.2
-
70
-
-
33646468497
-
Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters
-
Lee, A.P., Koh, E.G., Tay, A. et al. 2006. Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters. Proc. Natl. Acad. Sci., U.S.A., 103:6994-9.
-
(2006)
Proc. Natl. Acad. Sci., U.S.A
, vol.103
, pp. 6994-6999
-
-
Lee, A.P.1
Koh, E.G.2
Tay, A.3
-
71
-
-
33751414256
-
Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family
-
Levasseur, A, Gouret, P., Lesage-Meessen, L. et al. 2006. Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family. BMC Evol. Biol., 8:6:92.
-
(2006)
BMC Evol. Biol
, vol.8
, Issue.6
, pp. 92
-
-
Levasseur, A.1
Gouret, P.2
Lesage-Meessen, L.3
-
72
-
-
35349010004
-
Conceptual bases for quantifying the role of the environment on gene evolution: The participation of positive selection and neutral evolution
-
Levasseur, A., Orlando, L., Bailly, X. et al. 2007. Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution. Biol. Rev. Camb. Philos. Soc., 82:551-72.
-
(2007)
Biol. Rev. Camb. Philos. Soc
, vol.82
, pp. 551-572
-
-
Levasseur, A.1
Orlando, L.2
Bailly, X.3
-
73
-
-
28044457401
-
Reliable prediction of transcription factor binding sites by phylogenetic verification
-
Li, X., Zhong, S. and Wong, W.H. 2005. Reliable prediction of transcription factor binding sites by phylogenetic verification. Proc. Natl. Acad. Sci., U.S.A., 102:16945-50.
-
(2005)
Proc. Natl. Acad. Sci., U.S.A
, vol.102
, pp. 16945-16950
-
-
Li, X.1
Zhong, S.2
Wong, W.H.3
-
74
-
-
33244455951
-
Evolutionary conservation of expression profiles between human and mouse orthologous genes
-
Liao, B.Y. and Zhang, J.Z. 2006. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Molecular Biology and Evolution, 23:530-40.
-
(2006)
Molecular Biology and Evolution
, vol.23
, pp. 530-540
-
-
Liao, B.Y.1
Zhang, J.Z.2
-
75
-
-
0036075245
-
Tracking adaptive evolutionary events in genomic sequences
-
3:REVIEWS1018
-
Liberles, D.A. and Wayne, M.L. 2002. Tracking adaptive evolutionary events in genomic sequences. Genome Biol., 3:REVIEWS1018.
-
(2002)
Genome Biol
-
-
Liberles, D.A.1
Wayne, M.L.2
-
76
-
-
0027764344
-
Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
-
Livingstone, C.D. and Barton, G.J. 1993. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci., 9:745-56.
-
(1993)
Comput. Appl. Biosci
, vol.9
, pp. 745-756
-
-
Livingstone, C.D.1
Barton, G.J.2
-
77
-
-
0036134757
-
Heterotachy, an important process of protein evolution
-
Lopez, P., Casane, D. and Philippe, H. 2002. Heterotachy, an important process of protein evolution. Mol. Biol. Evol., 19:1-7.
-
(2002)
Mol. Biol. Evol
, vol.19
, pp. 1-7
-
-
Lopez, P.1
Casane, D.2
Philippe, H.3
-
78
-
-
34547664096
-
Genomic disorders: Molecular mechanisms for rearrangements and conveyed phenotypes
-
Lupski, J.R. and Stankiewicz, P. 2005. Genomic disorders: Molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet., 1:e49.
-
(2005)
PLoS Genet
, vol.1
-
-
Lupski, J.R.1
Stankiewicz, P.2
-
79
-
-
0036202921
-
PatternHunter: Faster and more sensitive homology search
-
Ma, B., Tromp, J. and Li, M. 2002. PatternHunter: faster and more sensitive homology search. Bioinformatics, 18:440-5.
-
(2002)
Bioinformatics
, vol.18
, pp. 440-445
-
-
Ma, B.1
Tromp, J.2
Li, M.3
-
80
-
-
33750386912
-
Reconstructing contiguous regions of an ancestial genome
-
Ma, J., Zhang, L., Suh, B.B. et al. 2006. Reconstructing contiguous regions of an ancestial genome. Genome Res., 16:1557-65.
-
(2006)
Genome Res
, vol.16
, pp. 1557-1565
-
-
Ma, J.1
Zhang, L.2
Suh, B.B.3
-
81
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte, E.M., Pellegrini, M., Ho-Leung, N. et al. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science, 30:751-3.
-
(1999)
Science
, vol.30
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ho-Leung, N.3
-
82
-
-
0036796369
-
Current methods of gene prediction, their strengths and weaknesses
-
Mathe, C., Sagot, M.F., Schiex, T. et al. 2002. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res., 30:4103-17.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4103-4117
-
-
Mathe, C.1
Sagot, M.F.2
Schiex, T.3
-
83
-
-
0038634975
-
Improvement of the GenTHREADER. method for genomic fold recognition
-
McGuffin, L.J. and Jones, D.T. 2003. Improvement of the GenTHREADER. method for genomic fold recognition. Bioinformatics, 19:874-81.
-
(2003)
Bioinformatics
, vol.19
, pp. 874-881
-
-
McGuffin, L.J.1
Jones, D.T.2
-
84
-
-
2942622384
-
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
-
Mirkin, B.G., Fenner, T.I., Galperin, M.Y. et al. 2003. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol., 3:2.
-
(2003)
BMC Evol. Biol
, vol.3
, pp. 2
-
-
Mirkin, B.G.1
Fenner, T.I.2
Galperin, M.Y.3
-
85
-
-
0019134329
-
Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application
-
Miyata, T. and Yasunaga, T. 1980. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J. Mol. Evol., 16:23-36.
-
(1980)
J. Mol. Evol
, vol.16
, pp. 23-36
-
-
Miyata, T.1
Yasunaga, T.2
-
86
-
-
0642368358
-
Position specific variation in the rate of evolutibn in trancription factor binding sites
-
Moses, A.M., Chiang, D.Y., Kellis, M. et a. 2003. Position specific variation in the rate of evolutibn in trancription factor binding sites. BMC Evol. Biol., 3:19.
-
(2003)
BMC Evol. Biol
, vol.3
, pp. 19
-
-
Moses, A.M.1
Chiang, D.Y.2
Kellis, M.3
et a4
-
87
-
-
22744440499
-
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
-
Murphy, W.J., Larkin, D.M., Everts-van der Wind, A. et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science, 309:613-617.
-
(2005)
Science
, vol.309
, pp. 613-617
-
-
Murphy, W.J.1
Larkin, D.M.2
Everts-van der Wind, A.3
-
88
-
-
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
-
89
-
-
0031110886
-
From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem
-
Page, R.D. and Charleston, M.A. 1997. From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem. Mol. Phylogenet. Evol., 7:231-40.
-
(1997)
Mol. Phylogenet. Evol
, vol.7
, pp. 231-240
-
-
Page, R.D.1
Charleston, M.A.2
-
90
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos, F., Helmer-Citterich, M., Ausiello, G. et al. 1997. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271:511-23.
-
(1997)
J. Mol. Biol
, vol.271
, pp. 511-523
-
-
Pazos, F.1
Helmer-Citterich, M.2
Ausiello, G.3
-
91
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
Pazos, F. and Valencia, A. 2001. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng., 14:609-14.
-
(2001)
Protein Eng
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
92
-
-
0036568319
-
In silico two-hybrid system for the selection of physically interacting protein pairs
-
Pazos, F. and Valencia, A. 2002. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins, 47:219-27.
-
(2002)
Proteins
, vol.47
, pp. 219-227
-
-
Pazos, F.1
Valencia, A.2
-
93
-
-
0034843597
-
AL2CO: Calcilation of positional conservation in a protein sequence alignment
-
Pei, J. and Grishin, N.V. 2001. AL2CO: calcilation of positional conservation in a protein sequence alignment. Bioinformatics, 17:700-712.
-
(2001)
Bioinformatics
, vol.17
, pp. 700-712
-
-
Pei, J.1
Grishin, N.V.2
-
94
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini, M., Marcotte, E.M., Thompson, M.J. et al. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci., U.S.A., 96:4285-8.
-
(1999)
Proc. Natl. Acad. Sci., U.S.A
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
-
95
-
-
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
-
96
-
-
34648825194
-
Ancestral animal genomes reconstruction
-
Rascol, V.L., Pontarotti, P. and Levasseur, A. 2007. Ancestral animal genomes reconstruction. Curr. Opin. Immunol., 19:542-6.
-
(2007)
Curr. Opin. Immunol
, vol.19
, pp. 542-546
-
-
Rascol, V.L.1
Pontarotti, P.2
Levasseur, A.3
-
97
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm, M., Storm, C.E. and Sonnhammer, E.L. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 314:1041-52.
-
(2001)
J. Mol. Biol
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
98
-
-
12344324765
-
DIVAA: Analysis of amino acid diversity in multiple aligned protein sequences
-
Rodi, D.J., Mandava, S. and Makowski, L. 2004. DIVAA: analysis of amino acid diversity in multiple aligned protein sequences. Bioinformatics, 20:3481-9.
-
(2004)
Bioinformatics
, vol.20
, pp. 3481-3489
-
-
Rodi, D.J.1
Mandava, S.2
Makowski, L.3
-
99
-
-
0344824014
-
Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene
-
Rodriguez-Trelles, F., Tarrío, R. and Ayala, F.J. 2003. Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene. Proc. Natl. Acad. Sci., U.SA., 100:13413-7.
-
(2003)
Proc. Natl. Acad. Sci., U.SA
, vol.100
, pp. 13413-13417
-
-
Rodriguez-Trelles, F.1
Tarrío, R.2
Ayala, F.J.3
-
100
-
-
33645470450
-
Genome-wide scans for loci under selection in humans
-
Ronald, J. and Akey, J.M. 2005. Genome-wide scans for loci under selection in humans. Hum. Genomics, 2:113-25.
-
(2005)
Hum. Genomics
, vol.2
, pp. 113-125
-
-
Ronald, J.1
Akey, J.M.2
-
101
-
-
23944525773
-
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data
-
Rossnes, R., Eidhammer, I. and Liberles, D.A. 2005. Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data. BMC Bioinformatics, 6:127.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 127
-
-
Rossnes, R.1
Eidhammer, I.2
Liberles, D.A.3
-
102
-
-
0030045281
-
Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny
-
Russo, C.A., Takezaki, N. and Nei, M. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol., 13:525-36.
-
(1996)
Mol. Biol. Evol
, vol.13
, pp. 525-536
-
-
Russo, C.A.1
Takezaki, N.2
Nei, M.3
-
103
-
-
3242891274
-
ConSite: Web-based prediction of regulatory elements using cross-species comparison
-
Sandelin, A., Wasserman, W.W. and Lenhard, B. 2004. ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Reg., 32:W249-52.
-
(2004)
Nucleic Acids Reg
, vol.32
-
-
Sandelin, A.1
Wasserman, W.W.2
Lenhard, B.3
-
104
-
-
0042695888
-
The challenge of constructing large phylogenetic trees
-
Sanderson, M.J. and Driskell, A.C. 2003. The challenge of constructing large phylogenetic trees. Trends Plant Sci., 8:374-9.
-
(2003)
Trends Plant Sci
, vol.8
, pp. 374-379
-
-
Sanderson, M.J.1
Driskell, A.C.2
-
105
-
-
33847741060
-
The origins of polypeptide domains
-
Schmidt, E.E. and Davies, C.J. 2007. The origins of polypeptide domains. Bioessays, 29:262-70.
-
(2007)
Bioessays
, vol.29
, pp. 262-270
-
-
Schmidt, E.E.1
Davies, C.J.2
-
106
-
-
1842507574
-
Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments
-
Shah, N., Couronne, O., Pennacchio, L.A. et al. 2004. Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics, 20:636-43.
-
(2004)
Bioinformatics
, vol.20
, pp. 636-643
-
-
Shah, N.1
Couronne, O.2
Pennacchio, L.A.3
-
107
-
-
28944450584
-
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
-
Shapiro, B., Rambaut, A. and Drummond, A.J. 2006. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol., 23:7-9.
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 7-9
-
-
Shapiro, B.1
Rambaut, A.2
Drummond, A.J.3
-
108
-
-
0035863767
-
A phylogenomic approach to microbial evolution
-
Sicheritz-Pontén, T. and Andersson, S.G. 2001. A phylogenomic approach to microbial evolution. Nucleic Acids Res., 29:545-52.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 545-552
-
-
Sicheritz-Pontén, T.1
Andersson, S.G.2
-
109
-
-
33750218960
-
PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny
-
Siddharthan, R., Siggia, E.D. and van Nimwegen, E. 2005. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput. Biol., 1:e67.
-
(2005)
PLoS Comput. Biol
, vol.1
-
-
Siddharthan, R.1
Siggia, E.D.2
van Nimwegen, E.3
-
110
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel, A., Bejerano, G., Pedersen, J.S. et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15:1034-50.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
-
111
-
-
13244260826
-
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
-
Sinha, S., Blanchette, M. and Tompa, M. 2004. PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics, 5:170.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 170
-
-
Sinha, S.1
Blanchette, M.2
Tompa, M.3
-
112
-
-
0037267806
-
Human-Mouse Alignments with BLASTZ
-
Schwartz, S., Kent, W.J., Smith, A. et al. 2003. Human-Mouse Alignments with BLASTZ. Genome Research, 13:103-7.
-
(2003)
Genome Research
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smith, A.3
-
113
-
-
1042280957
-
Phylogenomic inference of protein molecular function: Advances and challenges
-
Sjölander, K. 2004. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics, 20:170-9.
-
(2004)
Bioinformatics
, vol.20
, pp. 170-179
-
-
Sjölander, K.1
-
114
-
-
28944438378
-
ConFind: A robust tool for conserved sequence identification
-
Smagala, J.A., Dawson, E.D., Mehlmann, M. et al. 2005. ConFind: a robust tool for conserved sequence identification. Bioinformatics, 21:4420-2.
-
(2005)
Bioinformatics
, vol.21
, pp. 4420-4422
-
-
Smagala, J.A.1
Dawson, E.D.2
Mehlmann, M.3
-
115
-
-
27144493223
-
Genome trees and the nature of genome evolution
-
Snel, B., Huynen, M.A. and Dutilh, B.E. 2005. Genome trees and the nature of genome evolution. Annu Rev. Microbiol., 59:191-209.
-
(2005)
Annu Rev. Microbiol
, vol.59
, pp. 191-209
-
-
Snel, B.1
Huynen, M.A.2
Dutilh, B.E.3
-
116
-
-
0038658640
-
Efficient algorithms for multichromosomal genome rearrangements
-
Tesler, G. 2002a. Efficient algorithms for multichromosomal genome rearrangements. J. Comp. Sys. Sci., 65:587-609.
-
(2002)
J. Comp. Sys. Sci
, vol.65
, pp. 587-609
-
-
Tesler, G.1
-
117
-
-
0036211065
-
GRIMM: Genome rearrangements web server
-
Tesler, G. 2002b. GRIMM: genome rearrangements web server. Bioinformatics, 18:492-3.
-
(2002)
Bioinformatics
, vol.18
, pp. 492-493
-
-
Tesler, G.1
-
118
-
-
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., 27:2682-90.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
119
-
-
0034255358
-
DbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches
-
Thompson, J.D., Plewniak, F., Thierry, J.C. et al. 2000. DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res., 28:2919-26.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 2919-2926
-
-
Thompson, J.D.1
Plewniak, F.2
Thierry, J.C.3
-
120
-
-
0035824873
-
Towards a reliable objective function for multiple sequence alignments
-
Thompson, J.D., Plewniak, F., Ripp, R. et al. 2001. Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol., 314:937-51.
-
(2001)
J. Mol. Biol
, vol.314
, pp. 937-951
-
-
Thompson, J.D.1
Plewniak, F.2
Ripp, R.3
-
121
-
-
24644457706
-
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
-
Thompson, J.D., Koehl, P., Ripp, R. et al. 2005a. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins, 61:127-36.
-
(2005)
Proteins
, vol.61
, pp. 127-136
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
-
122
-
-
23444442072
-
b. MAO: A Multiple Alignment Ontology for nucleic acid and protein sequences
-
Thompson, J.D., Holbrook, S.R., Katoh, K. et al. 2005b. MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res., 33:4164-71.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4164-4171
-
-
Thompson, J.D.1
Holbrook, S.R.2
Katoh, K.3
-
123
-
-
33847138105
-
MACSIMS: Multiple alignment of complete sequences information management system
-
Thompson, J.D., Muller, A., Waterhouse, A. et al. 2006. MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics, 7:318.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 318
-
-
Thompson, J.D.1
Muller, A.2
Waterhouse, A.3
-
124
-
-
0033674329
-
Models of protein sequence evolution and their applications
-
Thorne, J.L. 2000. Models of protein sequence evolution and their applications. Curr. Opin. Genet. Dev., 10:602-5.
-
(2000)
Curr. Opin. Genet. Dev
, vol.10
, pp. 602-605
-
-
Thorne, J.L.1
-
125
-
-
0043074672
-
Systematic phylogenomic evidence of en bloc duplication of the ancestral 8p11.21-8p21.3-like region
-
Vienne, A., Rasmussen, J., Abi-Rached, L. et al. 2003. Systematic phylogenomic evidence of en bloc duplication of the ancestral 8p11.21-8p21.3-like region. Mol. Biol, Evol., 20:1290-8.
-
(2003)
Mol. Biol, Evol
, vol.20
, pp. 1290-1298
-
-
Vienne, A.1
Rasmussen, J.2
Abi-Rached, L.3
-
126
-
-
0037250152
-
A database of predicted functional associations between proteins
-
STRING
-
von Mering, C., Huynen, M., Jaeggi, D. et al. 2003. STRING: A database of predicted functional associations between proteins. Nucleic Acids Res., 31:258-61.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 258-261
-
-
von Mering, C.1
Huynen, M.2
Jaeggi, D.3
-
127
-
-
14044272835
-
Fast and reliable prediction of noncoding RNAs
-
Washietl, S., Hofacker, I.L. and Stadler, P.F. 2005. Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci., U.S.A., 192:2454-9.
-
(2005)
Proc. Natl. Acad. Sci., U.S.A
, vol.192
, pp. 2454-2459
-
-
Washietl, S.1
Hofacker, I.L.2
Stadler, P.F.3
-
128
-
-
0036719929
-
Genome trees and the tree of life
-
Wolf, Y.I., Rogozin, I.B., Grishin, N.V. et al. 2002. Genome trees and the tree of life. Trends Genet., 18:472-9.
-
(2002)
Trends Genet
, vol.18
, pp. 472-479
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
-
129
-
-
0037370306
-
Molecular evolution meets the genomics revolution
-
Wolfe, K.H. and Li, W.H. 2003. Molecular evolution meets the genomics revolution. Nat. Genet., 33:255-65.
-
(2003)
Nat. Genet
, vol.33
, pp. 255-265
-
-
Wolfe, K.H.1
Li, W.H.2
-
130
-
-
20044366725
-
Highly Conserved Non Coding Sequences Are Associated with Vertebrate Development
-
Woolfe, A., Goodson, M., Goode, D.K. et al. 2005. Highly Conserved Non Coding Sequences Are Associated with Vertebrate Development. PLoS Biol., 3:e7.
-
(2005)
PLoS Biol
, vol.3
-
-
Woolfe, A.1
Goodson, M.2
Goode, D.K.3
-
131
-
-
0030451420
-
Among-site rate variation and its impact on phylogenetic analyses
-
Yang, Z.H. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol., 11:367-72.
-
(1996)
Trends Ecol. Evol
, vol.11
, pp. 367-372
-
-
Yang, Z.H.1
-
132
-
-
14744275703
-
The power of phylogenetic comparison in revealing protein function
-
Yang, Z. 2005. The power of phylogenetic comparison in revealing protein function. Proc. Natl. Acad. Sci., U.S.A., 102:3179-80.
-
(2005)
Proc. Natl. Acad. Sci., U.S.A
, vol.102
, pp. 3179-3180
-
-
Yang, Z.1
-
133
-
-
0036733640
-
Computational prediction of eukaryotic protein-coding genes
-
Zhang, M.Q. 2002. Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet., 3:698-709.
-
(2002)
Nat. Rev. Genet
, vol.3
, pp. 698-709
-
-
Zhang, M.Q.1
-
134
-
-
0013017592
-
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
-
Zmasek, C.M. and Eddy, S.R. 2002. RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics, 3:14.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 14
-
-
Zmasek, C.M.1
Eddy, S.R.2
|