PubRank

Ziheng Yang

Author PubWeight™ 115.45‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 2005 8.74
2 Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 2003 7.05
3 Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 2004 4.22
4 Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. Mol Biol Evol 2003 4.10
5 Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 2003 3.89
6 Inferring speciation times under an episodic molecular clock. Syst Biol 2007 3.85
7 INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol 2009 3.29
8 Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol 2002 3.26
9 The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst Biol 2009 3.04
10 Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet 2008 2.98
11 A new time-scale for ray-finned fish evolution. Proc Biol Sci 2007 2.92
12 Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol 2008 2.90
13 Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci 2012 2.68
14 Best practices for justifying fossil calibrations. Syst Biol 2011 2.51
15 Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol 2003 2.29
16 Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst Biol 2002 2.15
17 Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol Ecol 2004 2.01
18 The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol 2010 2.01
19 Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol 2010 1.85
20 Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol 2007 1.77
21 Exploring uncertainty in the calibration of the molecular clock. Biol Lett 2011 1.74
22 A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol 2004 1.70
23 An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst Biol 2005 1.69
24 Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Curr Biol 2015 1.66
25 Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics 2003 1.61
26 Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol Biol Evol 2011 1.58
27 Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol 2003 1.49
28 Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Mol Biol Evol 2002 1.46
29 Evaluation of a bayesian coalescent method of species delimitation. Syst Biol 2011 1.34
30 PAMLX: a graphical user interface for PAML. Mol Biol Evol 2013 1.30
31 Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. J Mol Evol 2005 1.19
32 Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol 2007 1.14
33 The role of positive selection in determining the molecular cause of species differences in disease. BMC Evol Biol 2008 1.11
34 MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Mol Phylogenet Evol 2009 1.10
35 Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol Lett 2014 1.08
36 Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Mol Biol Evol 2011 1.06
37 Improved reversible jump algorithms for Bayesian species delimitation. Genetics 2013 1.05
38 The influence of gene flow on species tree estimation: a simulation study. Syst Biol 2013 1.04
39 Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. Mol Biol Evol 2004 1.04
40 Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Syst Biol 2012 1.04
41 Somatosensory projections to cochlear nucleus are upregulated after unilateral deafness. J Neurosci 2012 1.02
42 Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Mol Biol Evol 2007 0.99
43 Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evol Biol 2011 0.97
44 In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci U S A 2009 0.96
45 The trouble with sliding windows and the selective pressure in BRCA1. PLoS One 2008 0.96
46 Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. PLoS One 2008 0.95
47 A likelihood look at the supermatrix-supertree controversy. Gene 2008 0.94
48 Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Mol Biol Evol 2012 0.93
49 Looking for Darwin in genomic sequences--validity and success of statistical methods. Mol Biol Evol 2012 0.92
50 Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events. Gene 2006 0.92
51 Proposed standard nomenclature for the alpha- and beta-globin gene families. Genes Genet Syst 2006 0.90
52 Gene conversion and functional divergence in the beta-globin gene family. J Mol Evol 2004 0.90
53 Introduction. Statistical and computational challenges in molecular phylogenetics and evolution. Philos Trans R Soc Lond B Biol Sci 2008 0.90
54 Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge. BMC Evol Biol 2010 0.89
55 Dating phylogenies with sequentially sampled tips. Syst Biol 2013 0.88
56 Bayesian dating of shallow phylogenies with a relaxed clock. Syst Biol 2009 0.88
57 Efficient simulation under a population genetics model of carcinogenesis. Bioinformatics 2011 0.88
58 Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus. New Phytol 2013 0.87
59 Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). Mol Biol Evol 2002 0.87
60 A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change. Gene 2006 0.87
61 Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection? J Mol Evol 2004 0.86
62 Bayesian relaxed clock estimation of divergence times in foraminifera. Mol Phylogenet Evol 2011 0.86
63 Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples. PLoS One 2011 0.85
64 Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea). J Mol Evol 2004 0.84
65 Diversifying and purifying selection in the peptide binding region of DRB in mammals. J Mol Evol 2008 0.84
66 Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics 2013 0.81
67 Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biol Evol 2014 0.80
68 Comparative genomics coming of age. Heredity (Edinb) 2003 0.76