-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 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
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0346155809
-
Pseudogenes: Are they "junk" or functional DNA?
-
Balakirev, E. S., and F. J. Ayala. 2003. Pseudogenes: are they "junk" or functional DNA? Annu. Rev. Genet. 37:123-151.
-
(2003)
Annu. Rev. Genet.
, vol.37
, pp. 123-151
-
-
Balakirev, E.S.1
Ayala, F.J.2
-
3
-
-
0032865868
-
RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements
-
Brosius, J. 1999. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115-134.
-
(1999)
Gene
, vol.238
, pp. 115-134
-
-
Brosius, J.1
-
4
-
-
0030970280
-
Evolution of anti-freeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish
-
USA
-
Chen, L., A. L. DeVries, and C. H. Cheng. 1997. Evolution of anti-freeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. Proc. Natl. Acad. Sci. USA 94:3811-3816.
-
(1997)
Proc. Natl. Acad. Sci.
, vol.94
, pp. 3811-3816
-
-
Chen, L.1
DeVries, A.L.2
Cheng, C.H.3
-
5
-
-
0036078675
-
Fourfold faster rate of genome rearrangement in nematodes than in Drosophila
-
Coghlan, A., and K. H. Wolfe. 2002. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res. 12:857-867.
-
(2002)
Genome Res.
, vol.12
, pp. 857-867
-
-
Coghlan, A.1
Wolfe, K.H.2
-
6
-
-
3843113189
-
Origins of recently gained introns in Caenorhabditis
-
USA
-
_. 2004. Origins of recently gained introns in Caenorhabditis. Proc. Natl. Acad. Sci. USA 101:11362-11367.
-
(2004)
Proc. Natl. Acad. Sci.
, vol.101
, pp. 11362-11367
-
-
-
7
-
-
33646556197
-
The rarity of gene shuffling in conserved genes
-
Conant, G. C., and A. Wagner. 2005. The rarity of gene shuffling in conserved genes. Genome Biol. 6:R50.1-R50.14.
-
(2005)
Genome Biol.
, vol.6
-
-
Conant, G.C.1
Wagner, A.2
-
8
-
-
0035895567
-
Birth of two chimeric genes in the Hominidae lineage
-
Courseaux, A., and J. L. Nahon. 2001. Birth of two chimeric genes in the Hominidae lineage. Science 291:1293-1297.
-
(2001)
Science
, vol.291
, pp. 1293-1297
-
-
Courseaux, A.1
Nahon, J.L.2
-
9
-
-
0029906594
-
Intron positions correlate with module boundaries in ancient proteins
-
USA
-
de Souza, S. J., M. Long, L. Schoenbach, S. W. Roy, and W. Gilbert. 1996. Intron positions correlate with module boundaries in ancient proteins. Proc. Natl. Acad. Sci. USA 93:14632-14636.
-
(1996)
Proc. Natl. Acad. Sci.
, vol.93
, pp. 14632-14636
-
-
De Souza, S.J.1
Long, M.2
Schoenbach, L.3
Roy, S.W.4
Gilbert, W.5
-
10
-
-
0032574738
-
Toward a resolution of the introns early/late debate: Only phase zero introns are correlated with the structure of ancient proteins
-
USA
-
de Souza, S. J., M. Long, R. J. Klein, S. Roy, S. Lin, and W. Gilbert. 1998. Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. Proc. Natl. Acad. Sci. USA 95:5094-5099.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 5094-5099
-
-
De Souza, S.J.1
Long, M.2
Klein, R.J.3
Roy, S.4
Lin, S.5
Gilbert, W.6
-
11
-
-
0029006062
-
The multiplicity of domains in proteins
-
Doolittle, R. F. 1995. The multiplicity of domains in proteins. Annu. Rev. Biochem. 64:287-314.
-
(1995)
Annu. Rev. Biochem.
, vol.64
, pp. 287-314
-
-
Doolittle, R.F.1
-
12
-
-
0038817793
-
Phylogenetically older introns strongly correlate with module boundaries in ancient proteins
-
Fedorov, A., S. Roy, X. Cao, and W. Gilbert. 2003. Phylogenetically older introns strongly correlate with module boundaries in ancient proteins. Genome Res. 13:1155-1157.
-
(2003)
Genome Res.
, vol.13
, pp. 1155-1157
-
-
Fedorov, A.1
Roy, S.2
Cao, X.3
Gilbert, W.4
-
13
-
-
0032893932
-
Preservation of duplicate genes by complementary degenerative mutations
-
Force, A., M. Lynch, F. Bryan Pickett, A. Amores, Y. Yan, and J. Postlethwait. 1999. Preservation of duplicate genes by complementary degenerative mutations. Genetics 151:1531-1545.
-
(1999)
Genetics
, vol.151
, pp. 1531-1545
-
-
Force, A.1
Lynch, M.2
Bryan Pickett, F.3
Amores, A.4
Yan, Y.5
Postlethwait, J.6
-
14
-
-
0242666278
-
Evidence for the contribution of LTR retrotransposons to C. elegans gene evolution
-
Ganko, E. W., V. Bhattacharjee, P. Schliekelman, and J. F. McDonald. 2003. Evidence for the contribution of LTR retrotransposons to C. elegans gene evolution. Mol. Biol. Evol. 20:1925-1931.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 1925-1931
-
-
Ganko, E.W.1
Bhattacharjee, V.2
Schliekelman, P.3
McDonald, J.F.4
-
15
-
-
0018263844
-
Why genes in pieces?
-
Gilbert, W. 1978. Why genes in pieces? Nature 271:501.
-
(1978)
Nature
, vol.271
, pp. 501
-
-
Gilbert, W.1
-
16
-
-
0019860994
-
Correlation of DNA exonic regions with protein structural units in haemoglobin
-
Go, M. 1981. Correlation of DNA exonic regions with protein structural units in haemoglobin. Nature 291:90-92.
-
(1981)
Nature
, vol.291
, pp. 90-92
-
-
Go, M.1
-
17
-
-
0020742670
-
Modular structural units, exons, and function in chicken lysozyme
-
USA
-
_. 1983. Modular structural units, exons, and function in chicken lysozyme. Proc. Natl. Acad. Sci. USA 80:1964-1968.
-
(1983)
Proc. Natl. Acad. Sci.
, vol.80
, pp. 1964-1968
-
-
-
18
-
-
0026605537
-
CLUSTAL V: Improved software for multiple sequence alignment
-
Higgins, D. G., A. J. Bleasby, and R. Fuchs. 1992. CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8:189-191.
-
(1992)
CABIOS
, vol.8
, pp. 189-191
-
-
Higgins, D.G.1
Bleasby, A.J.2
Fuchs, R.3
-
19
-
-
0038414560
-
An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene
-
Hirotsune, S., N. Yoshida, A. Chen, L. Garrett, F. Sugiyama, S. Takahashi, K. I. Yagami, A. Wynshaw-Boris, and A. Yoshiki. 2003. An expressed pseudogene regulates the messenger-RNA 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.I.7
Wynshaw-Boris, A.8
Yoshiki, A.9
-
20
-
-
0028342845
-
The evolution of functionally novel proteins after gene duplication
-
Hughes, A. L. 1994. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B Biol. Sci. 256:119-124.
-
(1994)
Proc. R. Soc. Lond. B Biol. Sci.
, vol.256
, pp. 119-124
-
-
Hughes, A.L.1
-
21
-
-
0346100700
-
The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome
-
Katju, V., and M. Lynch. 2003. The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Genetics 165:1793-1803.
-
(2003)
Genetics
, vol.165
, pp. 1793-1803
-
-
Katju, V.1
Lynch, M.2
-
22
-
-
0016272837
-
Probability of gene fixation in an expanding finite population
-
USA
-
Kimura, M., and T. Ohta. 1974. Probability of gene fixation in an expanding finite population. Proc. Natl. Acad. Sci. USA 71:3377-3379.
-
(1974)
Proc. Natl. Acad. Sci.
, vol.71
, pp. 3377-3379
-
-
Kimura, M.1
Ohta, T.2
-
23
-
-
0021003167
-
Rapid evolution of goat and sheep globin genes following gene duplication
-
Li, W. H., and T. Gojobori. 1983. Rapid evolution of goat and sheep globin genes following gene duplication. Mol. Biol. Evol. 1:94-108.
-
(1983)
Mol. Biol. Evol.
, vol.1
, pp. 94-108
-
-
Li, W.H.1
Gojobori, T.2
-
24
-
-
0031737389
-
The recent origins of spliceosomal introns revisited
-
Logsdon, J. M. Jr. 1998. The recent origins of spliceosomal introns revisited. Curr. Opin. Genet. Dev. 8:637-648.
-
(1998)
Curr. Opin. Genet. Dev.
, vol.8
, pp. 637-648
-
-
Logsdon Jr., J.M.1
-
25
-
-
3843106810
-
Worm genomes hold the smoking guns of intron gain
-
USA
-
_. 2004. Worm genomes hold the smoking guns of intron gain. Proc. Natl. Acad. Sci. USA 101:11195-11196.
-
(2004)
Proc. Natl. Acad. Sci.
, vol.101
, pp. 11195-11196
-
-
-
26
-
-
0242354129
-
Origin of new genes: Glimpse from young and old
-
Long, M., E. Betran, K. Thornton, and W. Wang. 2003. Origin of new genes: glimpse from young and old. Nat. Rev. Genet. 4:865-875.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 865-875
-
-
Long, M.1
Betran, E.2
Thornton, K.3
Wang, W.4
-
27
-
-
0027905006
-
Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila
-
Long, M., and C. H. Langley. 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260:91-95.
-
(1993)
Science
, vol.260
, pp. 91-95
-
-
Long, M.1
Langley, C.H.2
-
28
-
-
0034634395
-
The evolutionary fate and consequences of duplicate genes
-
Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
-
(2000)
Science
, vol.290
, pp. 1151-1155
-
-
Lynch, M.1
Conery, J.S.2
-
29
-
-
0033972072
-
The probability of duplicate gene preservation by subfunctionalization
-
Lynch, M., and A. Force. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459-473.
-
(2000)
Genetics
, vol.154
, pp. 459-473
-
-
Lynch, M.1
Force, A.2
-
30
-
-
4744343021
-
The altered evolutionary trajectories of gene duplicates
-
Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene duplicates. Trends Genet. 20:544-549.
-
(2004)
Trends Genet.
, vol.20
, pp. 544-549
-
-
Lynch, M.1
Katju, V.2
-
31
-
-
6344265850
-
Organization and evolution of a gene-rich region of the mouse genome: A 12.7-Mb region deleted in the Del(13)Svea36H mouse
-
Mallon, A. M., L. Wilming, J. Weekes et al. (16 co-authors). 2004. Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse. Genome Res. 14:1888-1901.
-
(2004)
Genome Res.
, vol.14
, pp. 1888-1901
-
-
Mallon, A.M.1
Wilming, L.2
Weekes, J.3
-
32
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
-
(1986)
Mol. Biol. Evol.
, vol.3
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
33
-
-
0035500898
-
Transposable elements are found in a large number of human protein-coding genes
-
Nekrutenko, A., and W. H. Li. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17:619-621.
-
(2001)
Trends Genet.
, vol.17
, pp. 619-621
-
-
Nekrutenko, A.1
Li, W.H.2
-
34
-
-
0032506534
-
Selective sweep of a newly evolved sperm-specific gene in Drosophila
-
Nurminsky, D. I., M. V. Nurminskaya, D. De Aguiar, and D. L. Hartl. 1998. Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396:572-575.
-
(1998)
Nature
, vol.396
, pp. 572-575
-
-
Nurminsky, D.I.1
Nurminskaya, M.V.2
De Aguiar, D.3
Hartl, D.L.4
-
36
-
-
34547408929
-
Ancient linkage groups and frozen accidents
-
_. 1973. Ancient linkage groups and frozen accidents. Nature 244:259-262.
-
(1973)
Nature
, vol.244
, pp. 259-262
-
-
-
38
-
-
0022102222
-
Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules
-
Patthy, L. 1985. Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules. Cell 41:657-663.
-
(1985)
Cell
, vol.41
, pp. 657-663
-
-
Patthy, L.1
-
39
-
-
13244292544
-
Modular exchange principles in proteins
-
_. 1991. Modular exchange principles in proteins. Curr. Opin. Struct. Biol. 1:351-361.
-
(1991)
Curr. Opin. Struct. Biol.
, vol.1
, pp. 351-361
-
-
-
40
-
-
0003838721
-
-
Blackwell Science Ltd., Oxford
-
_. 1999. Protein evolution. Blackwell Science Ltd., Oxford.
-
(1999)
Protein Evolution
-
-
-
41
-
-
0018857156
-
The evolution of genes: The chicken preproinsulin gene
-
Perler, F., A. Efstratiadis, P. Lomedico, W. Gilbert, R. Kolodner, and J. Dodgson. 1980. The evolution of genes: the chicken preproinsulin gene. Cell 20:555-566.
-
(1980)
Cell
, vol.20
, pp. 555-566
-
-
Perler, F.1
Efstratiadis, A.2
Lomedico, P.3
Gilbert, W.4
Kolodner, R.5
Dodgson, J.6
-
42
-
-
8444232039
-
Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice
-
Podlaha, O., and J. Zhang. 2004. Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice. Mol. Biol. Evol. 21:2202-2209.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 2202-2209
-
-
Podlaha, O.1
Zhang, J.2
-
43
-
-
0032544557
-
Genetic analyses of the green visual pigments of rabbit (Oryctolagus cuniculus) and rat (Rattus norvegicus)
-
Radlwimmer, F. B., and S. Yokoyama. 1998. Genetic analyses of the green visual pigments of rabbit (Oryctolagus cuniculus) and rat (Rattus norvegicus). Gene 218:103-109.
-
(1998)
Gene
, vol.218
, pp. 103-109
-
-
Radlwimmer, F.B.1
Yokoyama, S.2
-
45
-
-
0031804088
-
Two large families of chemoreceptor genes in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal extensive gene duplication, diversification, movement, and intron loss
-
Robertson, H. M. 1998. Two large families of chemoreceptor genes in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal extensive gene duplication, diversification, movement, and intron loss. Genome Res. 8:449-463.
-
(1998)
Genome Res.
, vol.8
, pp. 449-463
-
-
Robertson, H.M.1
-
46
-
-
0034049664
-
The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses
-
_. 2000. The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses. Genome Res. 10:192-203.
-
(2000)
Genome Res.
, vol.10
, pp. 192-203
-
-
-
48
-
-
0035165576
-
WormBase: Network access to the genome and biology of Caenorhabditis elegans
-
Stein, L., P. Sternberg, R. Durbin, J. Thierry-Mieg, and J. Spieth. 2001. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29:82-86.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 82-86
-
-
Stein, L.1
Sternberg, P.2
Durbin, R.3
Thierry-Mieg, J.4
Spieth, J.5
-
49
-
-
4243088097
-
The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics
-
Stein, L. D., Z. Bao, D. Blasiar et al. (33 co-authors). 2003. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1:166-192.
-
(2003)
PLoS Biol.
, vol.1
, pp. 166-192
-
-
Stein, L.D.1
Bao, Z.2
Blasiar, D.3
-
50
-
-
0028043139
-
Testing the exon theory of genes: The evidence from protein structure
-
Stoltzfus, A., D. F. Spencer, M. Zuker, J. M. Logsdon Jr., and W. F. Doolittle. 1994. Testing the exon theory of genes: the evidence from protein structure. Science 265:202-207.
-
(1994)
Science
, vol.265
, pp. 202-207
-
-
Stoltzfus, A.1
Spencer, D.F.2
Zuker, M.3
Logsdon Jr., J.M.4
Doolittle, W.F.5
-
51
-
-
0032509302
-
Genome sequence of the nematode C. elegans: A platform for investigating biology
-
The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012-2018.
-
(1998)
Science
, vol.282
, pp. 2012-2018
-
-
-
52
-
-
0033664237
-
Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene
-
Thomson, T. M., J. J. Lozano, N. Loukili et al. (11 co-authors). 2000. Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene. Genome Res. 10:1743-1756.
-
(2000)
Genome Res.
, vol.10
, pp. 1743-1756
-
-
Thomson, T.M.1
Lozano, J.J.2
Loukili, N.3
-
53
-
-
0029985821
-
Pseudogenes in ribonuclease evolution: A source of new biomacromolecular function?
-
Trabesinger-Ruef, N., T. Jermann, T. Zankel, B. Durrant, G. Frank, and S. A. Benner. 1996. Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function? FEBS Lett. 382:319-322.
-
(1996)
FEBS Lett.
, vol.382
, pp. 319-322
-
-
Trabesinger-Ruef, N.1
Jermann, T.2
Zankel, T.3
Durrant, B.4
Frank, G.5
Benner, S.A.6
-
54
-
-
0039080152
-
Do exons code for structural and functional units in proteins?
-
USA
-
Traut, T. W. 1988. Do exons code for structural and functional units in proteins? Proc. Natl. Acad. Sci. USA 85:2944-2948.
-
(1988)
Proc. Natl. Acad. Sci.
, vol.85
, pp. 2944-2948
-
-
Traut, T.W.1
-
55
-
-
0037007062
-
Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster
-
USA
-
Wang, W., F. G. Brunet, E. Nevo, and M. Long. 2002. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99:4448-4453.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 4448-4453
-
-
Wang, W.1
Brunet, F.G.2
Nevo, E.3
Long, M.4
-
56
-
-
0034255318
-
No footprints of primordial introns in a eukaryotic genome
-
Wolf, Y. I., F. A. Kondrashov, and E. V. Koonin. 2000. No footprints of primordial introns in a eukaryotic genome. Trends Genet. 16:333-334.
-
(2000)
Trends Genet.
, vol.16
, pp. 333-334
-
-
Wolf, Y.I.1
Kondrashov, F.A.2
Koonin, E.V.3
-
57
-
-
0035460444
-
Footprints of priomordial introns on the eukaryotic genome: Still no clear traces
-
_. 2001. Footprints of priomordial introns on the eukaryotic genome: still no clear traces. Trends Genet. 17:499-501.
-
(2001)
Trends Genet.
, vol.17
, pp. 499-501
-
-
-
58
-
-
0030683599
-
PAML: A computer package for phylogenetic analysis by maximum likelihood
-
Yang, Z. 1997. PAML: a computer package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
59
-
-
0001565339
-
Molecular evolution of visual pigment genes and other G-protein coupled receptor genes
-
N. Takahata and J. F. Crow, eds. Baifukan, Tokyo
-
Yokoyama, S., and R. Yokoyama. 1990. Molecular evolution of visual pigment genes and other G-protein coupled receptor genes. Pp. 307-322 in N. Takahata and J. F. Crow, eds. Population biology of genes. Baifukan, Tokyo.
-
(1990)
Population Biology of Genes
, pp. 307-322
-
-
Yokoyama, S.1
Yokoyama, R.2
-
60
-
-
0032584099
-
Positive Darwinian selection after gene duplication in primate ribonuclease genes
-
USA
-
Zhang, J., H. F. Rosenberg, and M. Nei. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 95:3708-3713.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 3708-3713
-
-
Zhang, J.1
Rosenberg, H.F.2
Nei, M.3
|