-
1
-
-
0035029472
-
Pseudogenes, junk, and the dynamics of Rickettsia genomes
-
Andersson, J.O. and Andersson, S.G. (2001) Pseudogenes, junk, and the dynamics of Rickettsia genomes. Mol. Biol. Evol., 18, 829-839.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 829-839
-
-
Andersson, J.O.1
Andersson, S.G.2
-
2
-
-
0346155809
-
Pseudogenes: Are they 'junk' or functional?
-
Balakirev, E.S. and Ayala, F.J. (2003) Pseudogenes: are they 'junk' or functional? Annu. Rev. Genet., 37, 123-151.
-
(2003)
Annu. Rev. Genet.
, vol.37
, pp. 123-151
-
-
Balakirev, E.S.1
Ayala, F.J.2
-
3
-
-
9144257886
-
The Pfam protein families database
-
Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhoummer, E.L., et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhoummer, E.L.10
-
4
-
-
0346991738
-
The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: Implications for the correlation between the synonymous substitution rate and codon usage bias
-
Bierne, N. and Eyre-Walker, A. (2003) The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias. Genetics, 165, 1587-1597.
-
(2003)
Genetics
, vol.165
, pp. 1587-1597
-
-
Bierne, N.1
Eyre-Walker, A.2
-
5
-
-
9144259164
-
Ensembl 2004
-
Birney, E., Andrews, T.D., Bevan, P., Caccarno, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T., et al. (2004) Ensembl 2004. Nucleic Acids Res., 32, D468-D470.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Birney, E.1
Andrews, T.D.2
Bevan, P.3
Caccarno, M.4
Chen, Y.5
Clarke, L.6
Coates, G.7
Cuff, J.8
Curwen, V.9
Cutts, T.10
-
6
-
-
0037446851
-
Enhanced protein domain discovery by using language modeling techniques from speech recognition
-
Coin, L., Bateman, A. and Durbin, R. (2003) Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc. Natl Acad. Sci. USA, 100, 4516-4520.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 4516-4520
-
-
Coin, L.1
Bateman, A.2
Durbin, R.3
-
7
-
-
0034894278
-
PAL: An object-oriented programming library for molecular evolution and phylogenetics
-
Drummond, A. and Strimmer, K. (2001) PAL: An object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics, 17, 662-663.
-
(2001)
Bioinformatics
, vol.17
, pp. 662-663
-
-
Drummond, A.1
Strimmer, K.2
-
8
-
-
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
-
9
-
-
0036856275
-
Novel use of equilibrium frequencies in models of sequence evolution
-
Goldman, N. and Whelan, S. (2002) Novel use of equilibrium frequencies in models of sequence evolution. Mol. Biol. Evol., 19, 1821-1831.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1821-1831
-
-
Goldman, N.1
Whelan, S.2
-
10
-
-
0028168856
-
Codon-based model of nucleotide substitution for protein-coding sequences
-
Goldman, N. and Yang, Z. (1994) Codon-based model of nucleotide substitution for protein-coding sequences. Mol. Biol. Evol., 11, 725-736.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
11
-
-
0036314772
-
Studying genomes through the aeons: Protein families, pseudogenes and proteome evolution
-
Harrison, P.M. and Gerstein, M. (2002) Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J. Mol. Biol., 318, 1155-1174.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 1155-1174
-
-
Harrison, P.M.1
Gerstein, M.2
-
12
-
-
0036180936
-
Molecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22
-
Harrison, P.M., Hegyi, H., Balasubramanian, S., Euscombe, N.M., Bertone, P., Echols, N., Johnson, T. and Gerstein, M. (2002) Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res., 12, 272-280.
-
(2002)
Genome Res.
, vol.12
, pp. 272-280
-
-
Harrison, P.M.1
Hegyi, H.2
Balasubramanian, S.3
Euscombe, N.M.4
Bertone, P.5
Echols, N.6
Johnson, T.7
Gerstein, M.8
-
13
-
-
0037327334
-
Identification of pseudogenes in the Drosophila melanogaster genome
-
Harrison, P.M., Milburn, D., Zhang, Z., Bertens, P. and Gerstein, M. (2003) Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Res., 31, 1033-1037.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1033-1037
-
-
Harrison, P.M.1
Milburn, D.2
Zhang, Z.3
Bertens, P.4
Gerstein, M.5
-
14
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondria
-
Hasegawa, M., Kishino, H. and Yano, T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondria. J. Mol. Evol., 22, 160-174.
-
(1985)
J. Mol. Evol.
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
15
-
-
0038414560
-
An expressed pseudogene regulates the messenger stability of its homologous coding gene
-
Hirotsune, S., Yoshida, N., Chen, A., Garrett, L., Sugiyama, F., Takahashi, S., Yagami, K., Wynshaw-Boris, A. and Yoshiki, A. (2003) An expressed pseudogene regulates the messenger stability of its homologous coding gene. Nature, 423, 91-96.
-
(2003)
Nature
, vol.423
, pp. 91-96
-
-
Hirotsune, S.1
Yoshida, N.2
Chen, A.3
Garrett, L.4
Sugiyama, F.5
Takahashi, S.6
Yagami, K.7
Wynshaw-Boris, A.8
Yoshiki, A.9
-
16
-
-
0032416149
-
Models of molecular evolution and phylogeny
-
Lio, P. and Goldman, N. (1998) Models of molecular evolution and phylogeny. Genome Res., 8, 1233-1244.
-
(1998)
Genome Res.
, vol.8
, pp. 1233-1244
-
-
Lio, P.1
Goldman, N.2
-
17
-
-
0033955368
-
Vertebrate pseudogenes
-
Mighell, A.J., Smith, N.R., Robinson, P.A. and Markham, A.F. (2000) Vertebrate pseudogenes. FEBS Lett., 468, 109-114.
-
(2000)
FEBS Lett.
, vol.468
, pp. 109-114
-
-
Mighell, A.J.1
Smith, N.R.2
Robinson, P.A.3
Markham, A.F.4
-
18
-
-
0033012594
-
Probabilistic treatment of phylogeny and sequence alignment
-
Mitchison, G.J. (1999) Probabilistic treatment of phylogeny and sequence alignment. J. Mol. Evol., 49, 11-22.
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 11-22
-
-
Mitchison, G.J.1
-
19
-
-
0036100124
-
Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes
-
Mounsey, A., Bauer, P. and Hope, I.A. (2002) Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes. Genome Res., 12, 770-775.
-
(2002)
Genome Res.
, vol.12
, pp. 770-775
-
-
Mounsey, A.1
Bauer, P.2
Hope, I.A.3
-
20
-
-
0242300182
-
The sequence and analysis of human chromosome 6
-
Mungall, A.J., Palmer, S.A., Sims, S.K., Edwards, C.A., Ashurst, J.L. Wilming, L., Jones, M.C., Horton, R., Hunt, S.E., Scott, C.E. et al. (2003) The sequence and analysis of human chromosome 6. Nature, 425, 805-811.
-
(2003)
Nature
, vol.425
, pp. 805-811
-
-
Mungall, A.J.1
Palmer, S.A.2
Sims, S.K.3
Edwards, C.A.4
Ashurst, J.L.5
Wilming, L.6
Jones, M.C.7
Horton, R.8
Hunt, S.E.9
Scott, C.E.10
-
21
-
-
0032509105
-
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
-
Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Huhhard, T. and Chothia, C. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol., 284, 1201-1210.
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 1201-1210
-
-
Park, J.1
Karplus, K.2
Barrett, C.3
Hughey, R.4
Haussler, D.5
Huhhard, T.6
Chothia, C.7
-
22
-
-
0036845822
-
Splitting pairs: The diverging fates of duplicated genes
-
Prince, V.E. and Pickett, F.B. (2002) Splitting pairs: The diverging fates of duplicated genes. Nat. Rev. Genet., 3, 827-837.
-
(2002)
Nat. Rev. Genet.
, vol.3
, pp. 827-837
-
-
Prince, V.E.1
Pickett, F.B.2
-
23
-
-
0041671089
-
Detecting distant homologs using phylogenetic tree-based hmms
-
Qian, B. and Goldstein, R. A. (2003) Detecting distant homologs using phylogenetic tree-based hmms. Proteins, 52, 446-453.
-
(2003)
Proteins
, vol.52
, pp. 446-453
-
-
Qian, B.1
Goldstein, R.A.2
-
24
-
-
0348013073
-
Genome-wide survey of human pseudogenes
-
Torrents, D., Suyama, M., Zdobnov, E. and Bork, P. (2003) Genome-wide survey of human pseudogenes. Genome Res., 13, 2559-2567.
-
(2003)
Genome Res.
, vol.13
, pp. 2559-2567
-
-
Torrents, D.1
Suyama, M.2
Zdobnov, E.3
Bork, P.4
-
25
-
-
0035031966
-
General empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan, S. and Goldman, N. (2001) General empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol., 18, 691-699.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
|