-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 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
-
2
-
-
0036272936
-
Accuracy and power of Bayes prediction of amino acid sites under positive selection
-
Anisimova M, Bielawski J, Yang Z. 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol Biol Evol. 19:950-958.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 950-958
-
-
Anisimova, M.1
Bielawski, J.2
Yang, Z.3
-
3
-
-
33645241471
-
Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags
-
Begun DJ, Lindfors HA, Thompson ME, Holloway AK. 2006. Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics. 172:1675-1681.
-
(2006)
Genetics
, vol.172
, pp. 1675-1681
-
-
Begun, D.J.1
Lindfors, H.A.2
Thompson, M.E.3
Holloway, A.K.4
-
5
-
-
0037270595
-
Maximum likelihood methods for detecting adaptive evolution after gene duplication
-
Bielawski J, Yang Z. 2003. Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics. 3:201-212.
-
(2003)
J Struct Funct Genomics
, vol.3
, pp. 201-212
-
-
Bielawski, J.1
Yang, Z.2
-
6
-
-
33748043354
-
Identification and comparative analysis of accessory gland proteins in orthoptera
-
Braswell W, Andres J, Maroja L, Harrison R, Howard D, Swanson W. 2006. Identification and comparative analysis of accessory gland proteins in orthoptera. Genome. 49:1069-1080.
-
(2006)
Genome
, vol.49
, pp. 1069-1080
-
-
Braswell, W.1
Andres, J.2
Maroja, L.3
Harrison, R.4
Howard, D.5
Swanson, W.6
-
7
-
-
27144539145
-
-
Bustamante C, Fledel-Alon A, Williamson S. (11 co-authors). 2005. Natural selection on protein-coding genes in the human genome. Nature. 437:1153-1157.
-
Bustamante C, Fledel-Alon A, Williamson S. (11 co-authors). 2005. Natural selection on protein-coding genes in the human genome. Nature. 437:1153-1157.
-
-
-
-
8
-
-
15944403214
-
Molecular phylogeny of the genus Mus (Rodentia: Murinae) based on mitochondrial and nuclear data
-
Chevret P, Veyrunes F, Britton-Davidian J. 2005. Molecular phylogeny of the genus Mus (Rodentia: Murinae) based on mitochondrial and nuclear data. Biol J Linn Soc Lond. 84:417-427.
-
(2005)
Biol J Linn Soc Lond
, vol.84
, pp. 417-427
-
-
Chevret, P.1
Veyrunes, F.2
Britton-Davidian, J.3
-
9
-
-
32544445408
-
Evolution of reproductive proteins from animals and plants
-
Clark N, Aagard J, Swanson W. 2006. Evolution of reproductive proteins from animals and plants. Reproduction. 131:11-22.
-
(2006)
Reproduction
, vol.131
, pp. 11-22
-
-
Clark, N.1
Aagard, J.2
Swanson, W.3
-
10
-
-
41549122156
-
Pervasive adaptive evolution in primate seminal proteins
-
Clark N, Swanson W. 2005. Pervasive adaptive evolution in primate seminal proteins. PLos Genet. 1:335-342.
-
(2005)
PLos Genet
, vol.1
, pp. 335-342
-
-
Clark, N.1
Swanson, W.2
-
11
-
-
20544464873
-
The evolution of a genetic locus encoding small serine proteinase inhibitors
-
Clauss A, Lilja H, Lundwall A. 2005. The evolution of a genetic locus encoding small serine proteinase inhibitors. Biochem Biophys Res Commun. 333:383-389.
-
(2005)
Biochem Biophys Res Commun
, vol.333
, pp. 383-389
-
-
Clauss, A.1
Lilja, H.2
Lundwall, A.3
-
12
-
-
0026701843
-
Purification, structure, and characterization of caltrin proteins from seminal vesicle of the rat and mouse
-
Coronel C, Winnica D, Novella M, Lardy H. 1992. Purification, structure, and characterization of caltrin proteins from seminal vesicle of the rat and mouse. J Biol Chem. 267: 20909-20915.
-
(1992)
J Biol Chem
, vol.267
, pp. 20909-20915
-
-
Coronel, C.1
Winnica, D.2
Novella, M.3
Lardy, H.4
-
13
-
-
38949166378
-
Adaptive evolution of proteins secreted during sperm maturation: An analysis of the mouse epididymal transcriptome
-
Dean M, Good J, Nachman M. 2007. Adaptive evolution of proteins secreted during sperm maturation: an analysis of the mouse epididymal transcriptome. Mol Biol Evol. 25(2): 383-392.
-
(2007)
Mol Biol Evol
, vol.25
, Issue.2
, pp. 383-392
-
-
Dean, M.1
Good, J.2
Nachman, M.3
-
14
-
-
0037387007
-
Comparison of the genomes of human and mouse lays the foundation of genome zoology
-
Emes R, Goodstadt L, Winter EE, Ponting C. 2003. Comparison of the genomes of human and mouse lays the foundation of genome zoology. Hum Mol Genet. 12:701-709.
-
(2003)
Hum Mol Genet
, vol.12
, pp. 701-709
-
-
Emes, R.1
Goodstadt, L.2
Winter, E.E.3
Ponting, C.4
-
15
-
-
4444358158
-
Comparative evolutionary genomics of androgen-binding protein genes
-
Emes R, Riley M, Laukaitis C, Goodstadt L, Karn R, Ponting C. 2004. Comparative evolutionary genomics of androgen-binding protein genes. Genome Res. 14:1516-1529.
-
(2004)
Genome Res
, vol.14
, pp. 1516-1529
-
-
Emes, R.1
Riley, M.2
Laukaitis, C.3
Goodstadt, L.4
Karn, R.5
Ponting, C.6
-
16
-
-
0027215896
-
Characterization of two novel Ly-6 genes
-
Fleming T, O'hUigin C, Malek T. 1993. Characterization of two novel Ly-6 genes. J Immunol. 150:5379-5390.
-
(1993)
J Immunol
, vol.150
, pp. 5379-5390
-
-
Fleming, T.1
O'hUigin, C.2
Malek, T.3
-
17
-
-
0001528720
-
Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules
-
Franzkiewicz R, Braun W. 1998. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J Comput Chem. 19:319-333.
-
(1998)
J Comput Chem
, vol.19
, pp. 319-333
-
-
Franzkiewicz, R.1
Braun, W.2
-
18
-
-
0042171600
-
Molecular evolution and phylogeny of elapid snake venom three-finger toxins
-
Fry B, Wuster W, Kini R, Brusic V, Khan A, Venkataraman D, Rooney A. 2003. Molecular evolution and phylogeny of elapid snake venom three-finger toxins. J Mol Evol. 57:110-129.
-
(2003)
J Mol Evol
, vol.57
, pp. 110-129
-
-
Fry, B.1
Wuster, W.2
Kini, R.3
Brusic, V.4
Khan, A.5
Venkataraman, D.6
Rooney, A.7
-
19
-
-
1842684068
-
-
Gibbs RA, Weinstock GM, Metzker ML, et al. (230 co-authors). 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428:493-521.
-
Gibbs RA, Weinstock GM, Metzker ML, et al. (230 co-authors). 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428:493-521.
-
-
-
-
20
-
-
0023764283
-
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
-
Hughes A, Nei M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature. 335:167-170.
-
(1988)
Nature
, vol.335
, pp. 167-170
-
-
Hughes, A.1
Nei, M.2
-
21
-
-
0034819515
-
-
Ialenti A, Santagada V, Caliendo G, et al. (10 co-authors). 2001. Synthesis of novel anti-inflammatory peptides derived from the amino acid sequence of the bioactive protein SV-IV. Eur J Biochem. 268:3399-3406.
-
Ialenti A, Santagada V, Caliendo G, et al. (10 co-authors). 2001. Synthesis of novel anti-inflammatory peptides derived from the amino acid sequence of the bioactive protein SV-IV. Eur J Biochem. 268:3399-3406.
-
-
-
-
22
-
-
35748983523
-
Approaches for identifying targets of positive selection
-
Jensen J, Wong A, Aquadro C. 2007. Approaches for identifying targets of positive selection. Trends Genet. 23:568-577.
-
(2007)
Trends Genet
, vol.23
, pp. 568-577
-
-
Jensen, J.1
Wong, A.2
Aquadro, C.3
-
23
-
-
23844541714
-
The mouse epididymal transcriptome: Transcriptional profiling of segmental gene expression in the epididymis
-
Johnston D, Jelinsky S, Bang H, Candeloro P, Wilson E, Kopf G, Turner T. 2005. The mouse epididymal transcriptome: transcriptional profiling of segmental gene expression in the epididymis. Biol Reprod. 73:404-413.
-
(2005)
Biol Reprod
, vol.73
, pp. 404-413
-
-
Johnston, D.1
Jelinsky, S.2
Bang, H.3
Candeloro, P.4
Wilson, E.5
Kopf, G.6
Turner, T.7
-
24
-
-
33847223490
-
Semen-coagulating protein, Svs2, in mouse seminal plasma controls sperm fertility
-
Kawano N, Yoshida M. 2007. Semen-coagulating protein, Svs2, in mouse seminal plasma controls sperm fertility. Biol Reprod. 76:353-361.
-
(2007)
Biol Reprod
, vol.76
, pp. 353-361
-
-
Kawano, N.1
Yoshida, M.2
-
25
-
-
85012712067
-
A half century of biochemistry
-
Semenza G, editor, New York: Elserier. p
-
Lardy H. 1985. A half century of biochemistry. In: Semenza G, editor. A history of biochemistry. New York: Elserier. p. 297-325.
-
(1985)
A history of biochemistry
, pp. 297-325
-
-
Lardy, H.1
-
26
-
-
0037423205
-
Happily at work
-
Lardy H. 2003. Happily at work. J Biol Chem. 278:3499-3509.
-
(2003)
J Biol Chem
, vol.278
, pp. 3499-3509
-
-
Lardy, H.1
-
27
-
-
41849131787
-
-
Laukaitis C, Heger A, Blakley T, Munclinger P, Ponting C, Karn R. Forthcoming. 2008. Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals. BMC Evol Biol. 8:46-55.
-
Laukaitis C, Heger A, Blakley T, Munclinger P, Ponting C, Karn R. Forthcoming. 2008. Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals. BMC Evol Biol. 8:46-55.
-
-
-
-
28
-
-
0036479099
-
Localization of the transglutaminase cross-linking site in Svs III, a novel glycoprotein secreted from mouse seminal vesicle
-
Lin H-J, Luo C-W, Chen Y-H. 2002. Localization of the transglutaminase cross-linking site in Svs III, a novel glycoprotein secreted from mouse seminal vesicle. J Biol Chem. 277:3632-3639.
-
(2002)
J Biol Chem
, vol.277
, pp. 3632-3639
-
-
Lin, H.-J.1
Luo, C.-W.2
Chen, Y.-H.3
-
29
-
-
0344306689
-
Molecular cloning of complementary DNA encoding mouse seminal vesicle-secreted protein SVS I and demonstration of homology with copper amine oxidases
-
Lundwall A, Malm J, Clauss A, Valtonen-Andre C, Olsson AY. 2003. Molecular cloning of complementary DNA encoding mouse seminal vesicle-secreted protein SVS I and demonstration of homology with copper amine oxidases. Biol Reprod. 69:1923-1930.
-
(2003)
Biol Reprod
, vol.69
, pp. 1923-1930
-
-
Lundwall, A.1
Malm, J.2
Clauss, A.3
Valtonen-Andre, C.4
Olsson, A.Y.5
-
30
-
-
0034923103
-
Semenogelin II gene is replaced by a truncated line 1 repeat in the cotton-top tamarin
-
Lundwall A, Olsson A. 2001. Semenogelin II gene is replaced by a truncated line 1 repeat in the cotton-top tamarin. Biol Reprod. 65:420-425.
-
(2001)
Biol Reprod
, vol.65
, pp. 420-425
-
-
Lundwall, A.1
Olsson, A.2
-
31
-
-
0035831547
-
A novel heat-labile phospholipid-binding protein, SVS VII, in mouse seminal vesicle as a sperm motility enhancer
-
Luo C-W, Lin H-J, Chen Y-H. 2001. A novel heat-labile phospholipid-binding protein, SVS VII, in mouse seminal vesicle as a sperm motility enhancer. J Biol Chem. 276:6913-6921.
-
(2001)
J Biol Chem
, vol.276
, pp. 6913-6921
-
-
Luo, C.-W.1
Lin, H.-J.2
Chen, Y.-H.3
-
32
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei M, Gojobori T. 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
-
34
-
-
29444452921
-
Molecular signatures of natural selection
-
Nielsen R. 2005. Molecular signatures of natural selection. Annu Rev Genet. 39:197-218.
-
(2005)
Annu Rev Genet
, vol.39
, pp. 197-218
-
-
Nielsen, R.1
-
35
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 148:929-936.
-
(1998)
Genetics
, vol.148
, pp. 929-936
-
-
Nielsen, R.1
Yang, Z.2
-
36
-
-
9944243134
-
The evolution of the glandular kallikrein locus: Identification of orthologs and pseudogenes in the cotton-top tamarin
-
Olsson A, Valtonen-Andre C, Lilja H, Lundwall A. 2004. The evolution of the glandular kallikrein locus: identification of orthologs and pseudogenes in the cotton-top tamarin. Gene. 343:347-355.
-
(2004)
Gene
, vol.343
, pp. 347-355
-
-
Olsson, A.1
Valtonen-Andre, C.2
Lilja, H.3
Lundwall, A.4
-
37
-
-
33745104040
-
Large-scale and high-confidence proteomic analysis of human seminal plasma
-
Epub
-
Pilch B, Mann M. 2006. Large-scale and high-confidence proteomic analysis of human seminal plasma. Genome Biol. 7:R40 Epub.
-
(2006)
Genome Biol
, vol.7
-
-
Pilch, B.1
Mann, M.2
-
38
-
-
38349134018
-
-
Ramm S, Oliver P, Ponting C, Stockley P, Emes R. Forthcoming. 2008. Sexual selection and the adaptive evolution of mammalian ejaculate proteins. Mol Biol Evol. 25:207-219.
-
Ramm S, Oliver P, Ponting C, Stockley P, Emes R. Forthcoming. 2008. Sexual selection and the adaptive evolution of mammalian ejaculate proteins. Mol Biol Evol. 25:207-219.
-
-
-
-
39
-
-
0035912788
-
Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila
-
Swanson W, Clark A, Waldrip-Dail H, Wolfner M, Aquadro C. 2001. Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc Natl Acad Sci USA. 98:7375-7379.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 7375-7379
-
-
Swanson, W.1
Clark, A.2
Waldrip-Dail, H.3
Wolfner, M.4
Aquadro, C.5
-
40
-
-
0037230001
-
Pervasive adaptive evolution in mammalian fertilization proteins
-
Swanson W, Nielsen R, Yang Q. 2003. Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol. 20:18-20.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 18-20
-
-
Swanson, W.1
Nielsen, R.2
Yang, Q.3
-
41
-
-
85047700164
-
The rapid evolution of reproductive proteins
-
Swanson W, Vacquier V. 2002. The rapid evolution of reproductive proteins. Nat Rev Genet. 3:137-144.
-
(2002)
Nat Rev Genet
, vol.3
, pp. 137-144
-
-
Swanson, W.1
Vacquier, V.2
-
42
-
-
10844274729
-
Evolutionary expressed sequence tag analysis of Drosophila female reproductive tracts identifies genes subjected to positive selection
-
Swanson W, Wong A, Wolfner M, Aquadro C. 2004. Evolutionary expressed sequence tag analysis of Drosophila female reproductive tracts identifies genes subjected to positive selection. Genetics. 168:1457-1465.
-
(2004)
Genetics
, vol.168
, pp. 1457-1465
-
-
Swanson, W.1
Wong, A.2
Wolfner, M.3
Aquadro, C.4
-
43
-
-
33746218184
-
Evolution on the X chromosome: Unusual patterns and processes
-
Vicoso B, Charlesworth B. 2006. Evolution on the X chromosome: unusual patterns and processes. Nat Rev Genet. 7:645-653.
-
(2006)
Nat Rev Genet
, vol.7
, pp. 645-653
-
-
Vicoso, B.1
Charlesworth, B.2
-
44
-
-
1542563409
-
-
Waterston RH, Lindblad-Toh K, Birney E, et al. (221 co-authors). 2002. Initial sequencing and comparative analysis of the mouse genome. Nature. 420:520-562.
-
Waterston RH, Lindblad-Toh K, Birney E, et al. (221 co-authors). 2002. Initial sequencing and comparative analysis of the mouse genome. Nature. 420:520-562.
-
-
-
-
45
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang Z. 1997. PAML: a program 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
-
46
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
47
-
-
0033639150
-
Statistical methods for detecting molecular adaptation
-
Yang Z, Bielawski J. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 15:496-503.
-
(2000)
Trends Ecol Evol
, vol.15
, pp. 496-503
-
-
Yang, Z.1
Bielawski, J.2
-
48
-
-
0031792828
-
Models of amino acid substitution and applications to mitochondrial protein evolution
-
Yang Z, Nielsen R, Hasegawa M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol. 15:1600-1611.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 1600-1611
-
-
Yang, Z.1
Nielsen, R.2
Hasegawa, M.3
-
49
-
-
0033800170
-
Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites
-
Yang Z, Swanson W, Vacquier V. 2000. Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. Mol Biol Evol. 17:1446-1455.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 1446-1455
-
-
Yang, Z.1
Swanson, W.2
Vacquier, V.3
-
50
-
-
16344378246
-
Bayes empirical Bayes inference of amino acid sites under positive selection
-
Yang Z, Wong W, Nielsen R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22:1107-1118.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1107-1118
-
-
Yang, Z.1
Wong, W.2
Nielsen, R.3
-
51
-
-
41149179530
-
Degeneration of the olfactory guanylyl cyclase D gene during primate evolution
-
Young J, Waters H, Dong C, Fülle H-J, Liman E. 2007. Degeneration of the olfactory guanylyl cyclase D gene during primate evolution. PLoS ONE. 2:e884.
-
(2007)
PLoS ONE
, vol.2
-
-
Young, J.1
Waters, H.2
Dong, C.3
Fülle, H.-J.4
Liman, E.5
-
52
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 22:2472-2479.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2472-2479
-
-
Zhang, J.1
Nielsen, R.2
Yang, Z.3
|