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Volumn 23, Issue 5, 2006, Pages 919-926

Control of the false discovery rate applied to the detection of positively selected amino acid sites

Author keywords

False detection rate; Molecular phylogeny; Positive selection

Indexed keywords

AMINO ACID SEQUENCE; CODON; CONFERENCE PAPER; ERROR; EVOLUTION; GENETIC SELECTION; HYPOTHESIS; PROBABILITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SIMULATION; ARTICLE; CHEMISTRY; COMPUTER SIMULATION; GENETIC RECOMBINATION; GENETICS; GENOMICS; LABORATORY DIAGNOSIS; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL MODEL;

EID: 33644978910     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj095     Document Type: Conference Paper
Times cited : (8)

References (26)
  • 1
    • 0001677717 scopus 로고
    • Controlling the false discovery rate - A practical and powerful approach to multiple testing
    • Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57:289-300.
    • (1995) J. R. Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 2
    • 0034370950 scopus 로고    scopus 로고
    • The adaptive control of the false discovery rate in multiple hypothesis testing with independent statistics
    • _. 2000. The adaptive control of the false discovery rate in multiple hypothesis testing with independent statistics. J. Educ. Behav. Stat. 25:60-83.
    • (2000) J. Educ. Behav. Stat. , vol.25 , pp. 60-83
  • 3
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • Benjamini, Y., and D. Yekutieli. 2001. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29:1165-1188.
    • (2001) Ann. Stat. , vol.29 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 4
    • 0003991673 scopus 로고    scopus 로고
    • Sinauer Associates Inc., Sunderland, Mass.
    • Felsenstein, J. 2003. Inferring phylogenies. Sinauer Associates Inc., Sunderland, Mass.
    • (2003) Inferring Phylogenies
    • Felsenstein, J.1
  • 5
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, S., and O. Gascuel. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 6
    • 4444357279 scopus 로고    scopus 로고
    • Modeling the site-specific variation of selection patterns along lineages
    • USA
    • Guindon, S., A. Rodrigo, K. Dyer, and J. Huelsenbeck. 2004. Modeling the site-specific variation of selection patterns along lineages. Proc. Natl. Acad. Sci. USA 101:12957-12962.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 12957-12962
    • Guindon, S.1    Rodrigo, A.2    Dyer, K.3    Huelsenbeck, J.4
  • 7
    • 0002294347 scopus 로고
    • A simple sequentially rejective multiple test procedure
    • Holm, S. 1979. A simple sequentially rejective multiple test procedure. Scand. J. Stat. 6:65-70.
    • (1979) Scand. J. Stat. , vol.6 , pp. 65-70
    • Holm, S.1
  • 8
    • 2942656772 scopus 로고    scopus 로고
    • Bayesian estimation of positively selected sites
    • Huelsenbeck, J., and K. Dyer. 2004. Bayesian estimation of positively selected sites. J. Mol. Evol. 58:661-672.
    • (2004) J. Mol. Evol. , vol.58 , pp. 661-672
    • Huelsenbeck, J.1    Dyer, K.2
  • 9
    • 0030902563 scopus 로고    scopus 로고
    • Phylogenetic methods come of age: Testing hypotheses in an evolutionary context
    • Huelsenbeck, J., and B. Rannala. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:218-219.
    • (1997) Science , vol.276 , pp. 218-219
    • Huelsenbeck, J.1    Rannala, B.2
  • 10
    • 0031436890 scopus 로고    scopus 로고
    • Phylogeny estimation and hypothesis testing using maximum likelihood
    • Huelsenbeck, J. P., and K. A. Crandall. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-466.
    • (1997) Annu. Rev. Ecol. Syst. , vol.28 , pp. 437-466
    • Huelsenbeck, J.P.1    Crandall, K.A.2
  • 11
    • 0023764283 scopus 로고
    • Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
    • Hughes, A., and M. Nei. 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
  • 12
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner, M., and J. Felsenstein. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 459-468
    • Kuhner, M.1    Felsenstein, J.2
  • 13
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93.
    • (1984) J. Mol. Evol. , vol.20 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 14
    • 4444235995 scopus 로고    scopus 로고
    • Detecting differential expression with a semi-parametric hierarchical mixture method
    • Newton, M., A. Noueiry, D. Sarkar, and P. Ahlquist. 2004. Detecting differential expression with a semi-parametric hierarchical mixture method. Biostatistics 5:155-176.
    • (2004) Biostatistics , vol.5 , pp. 155-176
    • Newton, M.1    Noueiry, A.2    Sarkar, D.3    Ahlquist, P.4
  • 15
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and application to the HIV-1 envelope gene
    • Nielsen, R., and Z. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and application to the HIV-1 envelope gene. Genetics 148:929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 17
    • 0036828069 scopus 로고    scopus 로고
    • Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration
    • Ross, H., and A. Rodrigo. 2002. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J. Virol. 76:11715-11720.
    • (2002) J. Virol. , vol.76 , pp. 11715-11720
    • Ross, H.1    Rodrigo, A.2
  • 18
    • 0032849322 scopus 로고    scopus 로고
    • A method for detecting positive selection at single amino acid sites
    • Suzuki, Y., and T. Gojobori. 1999. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16:1315-1328.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1315-1328
    • Suzuki, Y.1    Gojobori, T.2
  • 19
    • 1942533483 scopus 로고    scopus 로고
    • False-positive selection identified by ML-based methods: Examples from the sig1 gene of the diatom Thalassoria weissflogii and the tax gene of a human T-cell lymphotropic virus
    • Suzuki, Y., and M. Nei. 2004. False-positive selection identified by ML-based methods: examples from the sig1 gene of the diatom Thalassoria weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol. Biol. Evol. 21:914-921.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 914-921
    • Suzuki, Y.1    Nei, M.2
  • 20
    • 0035957018 scopus 로고    scopus 로고
    • Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals
    • USA
    • Swanson, W., Z. Yang, M. Wolfner, and C. Aquadro. 2001. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc. Natl. Acad. Sci. USA 98:2509-2514.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 2509-2514
    • Swanson, W.1    Yang, Z.2    Wolfner, M.3    Aquadro, C.4
  • 21
    • 8544225780 scopus 로고    scopus 로고
    • Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
    • Wong, W., Z. Yang, N. Goldman, and R. Nielsen. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051.
    • (2004) Genetics , vol.168 , pp. 1041-1051
    • Wong, W.1    Yang, Z.2    Goldman, N.3    Nielsen, R.4
  • 22
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1
  • 23
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • _. 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
  • 24
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang, Z., and R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 908-917
    • Yang, Z.1    Nielsen, R.2
  • 25
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang, Z., R. Nielsen, N. Goldman, and A.-M. Krabbe Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Krabbe Pedersen, A.-M.4
  • 26
    • 16344378246 scopus 로고    scopus 로고
    • Bayes empirical Bayes inference of amino acid sites under positive selection
    • Yang, Z., W. Wong, and R. Nielsen. 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.