- 62 LIKELIHOOD CALCULATION IN MOLECULAR PHYLOGENETICS ,1:. 200<;. 1--. \\.B~~ ~ ,~ ~~c..(""." V I
- Syst. Biol. 52(5):705716, 2003 Copyright c Society of Systematic Biologists
- Mol. Biol. Evol. 15(11):14991505. 1998 1998 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
- Gene Conversion and Functional Divergence in the b-Globin Gene Family Gabriela Aguileta, Joseph P. Bielawski, Ziheng Yang
- Genet. Res., Camb. (1997), 69, pp. 111116. With 3 figures. Printed in the United Kingdom # 1997 Cambridge University Press 111 On the estimation of ancestral population sizes of modern
- Molecular Ecology (2004) 13, 757773 doi: 10.1046/j.1365-294X.2004.02106.x 2004 Blackwell Publishing Ltd
- Copyi-ight 0 1995 by the Genetics Society of America A Space-Time Process Modelfor the Evolution of DNA Sequences
- Mol. Biol. Evol. 19(6):908917. 2002 2002 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
- Copyright 0 1996 by the Genetics Society of America Statistical Properties of a DNA Sample Under the Finite-Sites Model
- Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus A
- Phylogenetic Inference Using Whole Genomes
- Syst. Biol. 59(1):7489, 2010 c The Author(s) 2009. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.
- Mol. Biol. Evol. 17(7):10811090. 2000 2000 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
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- RESEARCH ARTICLE Open Access Unusual conservation among genes encoding
- Mol. Biol. Evol. 19(1):4957. 2002 2002 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
- Author's personal copy Short Communication
- Empirical evaluation of a prior for Bayesian phylogenetic inference
- Syst. Biol. 59(2):119131, 2010 c The Author(s) 2009. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.
- The power of phylogenetic comparison in revealing protein function
- 50 (4) :645 -656 , 2004 Acta Zoologica Sinica
- The selective pressure on a protein-coding gene can be measured by comparing silent (synonymous) and replacement
- Copyright 2002 by the Genetics Society of America Likelihood and Bayes Estimation of Ancestral Population Sizes in Hominoids
- 188 I. J. Wilson, M. E. Weale and D. J. Balding Pfeiffer, H., Steighner, R., Fisher, R., Mornstad, H., Yoon, C. L. and Holland, M. M. (1998) Mitochondrial
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- Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1
- PAML (Phylogenetic Analysis by Maximum Likelihood)
- Copyright 1998 by the Genetics Society of America Likelihood Models for Detecting Positively Selected Amino Acid Sites
- Ziheng Yang's 60 most cited papers. Total citations = 13,600, h = 52. ISI (March 2009) Rank Paper Citations
- The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection
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- Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage
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- A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change
- Syst. Biol. 54(5):808818, 2005 Copyright c Society of Systematic Biologists
- Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection Ziheng Yang,* Wendy S.W. Wong, and Rasmus Nielsen
- Copyright 2004 by the Genetics Society of America DOI: 10.1534/genetics.104.031153
- NEWS AND COMMENTARY Comparative genomics...............................................................
- Estimating the Distribution of Selection Coefficients from Phylogenetic Data with Applications to Mitochondrial and Viral DNA
- Mol. Biol. Evol. 18(4):523529. 2001 2001 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
- Copyright 2001 by the Genetics Society of America Substitution Rates in Drosophila Nuclear Genes
- 496 0169-5347/00/$ see front matter 2000 Elsevier Science Ltd. All rights reserved. PII: S0169-5347(00)01994-7 TREE vol. 15, no. 12 December 2000 t has been proved remark-
- Copyright 2000 by the Genetics Society of America Rates of Nucleotide Substitution and Mammalian Nuclear Gene Evolution
- Mol. Biol. Evol. 17(10):14461455. 2000 2000 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
- Copyright 2000 by the Genetics Society of America Codon-Substitution Models for Heterogeneous Selection Pressure
- Mol. Biol. Evol. 17(3):387400. 2000 2000 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
- Complexity of the simplest phylogenetic estimation Ziheng Yang
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- Mol. Biol. Evol. 15(5):568573. 1998 1998 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
- Letter to the Editor How Often Do Wrong Models Produce Better Phylogenies?
- A Codon-based Model of Nucleotide Substitution for Protein-coding DNA Nick Goldman* and Ziheng Yangf-
- Comparison of Models for Nucleotide Substitution Used in Maximum-Likelihood Phylogenetic Estimation
- J Mol Evol (1994) 39:105-111 of Molecular
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- A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution
- Mol. Biol. Evol. 16(10):13571368. 1999 1999 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
- BOOK REVIEW Probability models for DNA sequence
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- On the Varied Pattern of Evolution of 2 Fungal Genomes: A Critique of Hughes and Friedman
- Synonymous and Nonsynonymous Rate Variation in Nuclear Genes Ziheng Yang,1,2,
- PAML 4: Phylogenetic Analysis by Maximum Likelihood Ziheng Yang*
- RELATING PHYSICOCHEMMICAL PROPERTIES OF AMINO ACIDS TO VARIABLE NUCLEOTIDE SUBSTITUTION
- Phylogenetics as applied mathematics Phylogenetics by Charles Semple and Mike Steel. Oxford University Press, 2003. 45.00 hbk (254 pages) ISBN 0 19 850942 1
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- Mol. Biol. Evol. 19(10):17521759. 2002 2002 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
- Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories (Ipomoea)
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- A likelihood look at the supermatrixsupertree controversy Fengrong Ren a
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- have termed "phylophenetics" (examples of which abound in, for instance, the journal Systematic Bi-
- Syst. Biol. 60(1):1631, 2011 c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.
- and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com The Author 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology
- BIOINFORMATICS ORIGINAL PAPER Vol. 27 no. 6 2011, pages 837843
- Statistical Properties of the Branch-Site Test of Positive Ziheng Yang*,1,2
- Author's personal copy Bayesian relaxed clock estimation of divergence times in foraminifera
- c The Author(s) 2011. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com
- Change of Positive Selection Pressure on HIV-1 Envelope Gene Inferred by Early and Recent Samples
- Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times
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- Tail Paradox, Partial Identifiability, and Influential Priors in Bayesian Branch Length Inference
- METHODOLOGY ARTICLE Open Access Rate variation and estimation of divergence times
