Literature DB >> 19805241

In defense of statistical methods for detecting positive selection.

Ziheng Yang, Rasmus Nielsen, Nick Goldman.   

Abstract

Mesh：

Year:  2009        PMID： 19805241      PMCID： PMC2741286          DOI： 10.1073/pnas.0904550106

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


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  5 in total

1.  Bayes empirical bayes inference of amino acid sites under positive selection.

Authors:  Ziheng Yang; Wendy S W Wong; Rasmus Nielsen
Journal:  Mol Biol Evol       Date:  2005-02-02       Impact factor: 16.240

2.  Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites.

Authors:  Wendy S W Wong; Ziheng Yang; Nick Goldman; Rasmus Nielsen
Journal:  Genetics       Date:  2004-10       Impact factor: 4.562

3.  Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.

Authors:  Jianzhi Zhang; Rasmus Nielsen; Ziheng Yang
Journal:  Mol Biol Evol       Date:  2005-08-17       Impact factor: 16.240

4.  PAML 4: phylogenetic analysis by maximum likelihood.

Authors:  Ziheng Yang
Journal:  Mol Biol Evol       Date:  2007-05-04       Impact factor: 16.240

5.  Reliabilities of identifying positive selection by the branch-site and the site-prediction methods.

Authors:  Masafumi Nozawa; Yoshiyuki Suzuki; Masatoshi Nei
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-01       Impact factor: 11.205
  5 in total
  23 in total

1.  Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict.

Authors:  Cheng Deng; C-H Christina Cheng; Hua Ye; Ximiao He; Liangbiao Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-29       Impact factor: 11.205

2.  Evolution of the Cinnamyl/Sinapyl Alcohol Dehydrogenase (CAD/SAD) gene family: the emergence of real lignin is associated with the origin of Bona Fide CAD.

Authors:  Dong-Mei Guo; Jin-Hua Ran; Xiao-Quan Wang
Journal:  J Mol Evol       Date:  2010-08-19       Impact factor: 2.395

3.  Molecular evolutionary analysis of vertebrate transducins: a role for amino acid variation in photoreceptor deactivation.

Authors:  Yi G Lin; Cameron J Weadick; Francesco Santini; Belinda S W Chang
Journal:  J Mol Evol       Date:  2013-10-22       Impact factor: 2.395

4.  Extraordinarily low evolutionary rates of short wavelength-sensitive opsin pseudogenes.

Authors:  Shozo Yokoyama; William T Starmer; Yang Liu; Takashi Tada; Lyle Britt
Journal:  Gene       Date:  2013-10-12       Impact factor: 3.688

5.  Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method.

Authors:  Chengjun Zhang; Jia Wang; Weibo Xie; Gang Zhou; Manyuan Long; Qifa Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2011-04-26       Impact factor: 11.205

Review 6.  Statistics and truth in phylogenomics.

Authors:  Sudhir Kumar; Alan J Filipski; Fabia U Battistuzzi; Sergei L Kosakovsky Pond; Koichiro Tamura
Journal:  Mol Biol Evol       Date:  2011-08-26       Impact factor: 16.240

7.  Synthetic biology of phenotypic adaptation in vertebrates: the next frontier.

Authors:  Shozo Yokoyama
Journal:  Mol Biol Evol       Date:  2013-04-19       Impact factor: 16.240

8.  Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga).

Authors:  Natasha I Bloch; Trevor D Price; Belinda S W Chang
Journal:  Mol Ecol       Date:  2015-04-20       Impact factor: 6.185

9.  Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals.

Authors:  Greg Slodkowicz; Nick Goldman
Journal:  Proc Natl Acad Sci U S A       Date:  2020-03-02       Impact factor: 11.205

10.  Synthesis of Experimental Molecular Biology and Evolutionary Biology: An Example from the World of Vision.

Authors:  Shozo Yokoyama
Journal:  Bioscience       Date:  2012-11       Impact factor: 8.589
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