Ziheng Yang

Q: What Schools Are Affiliated With Ziheng Yang

Ziheng Yang is affiliated with the following schools: Sun Yat-sen University, University College London, University of Tokyo, Gansu Agricultural University, Tsinghua University, Beijing Normal University, Fudan University, Peking University, Harvard University, China Agricultural University

Ziheng Yang's AcademicInfluence.com Rankings

Ziheng Yang

Biology

#1639

World Rank

#2691

Historical Rank

Biotechnology

#18

World Rank

#18

Historical Rank

biology Degrees

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Biology

Ziheng Yang's Degrees

PhD Biology Peking University
Masters Biotechnology Tsinghua University
Bachelors Biological Sciences Peking University

Why Is Ziheng Yang Influential?

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According to Wikipedia, Ziheng Yang FRS is a Chinese biologist. He holds the R.A. Fisher Chair of Statistical Genetics at University College London, and is the Director of R.A. Fisher Centre for Computational Biology at UCL. He was elected a Fellow of the Royal Society in 2006.

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Ziheng Yang's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

PAML 4: phylogenetic analysis by maximum likelihood. (2007) (10178)
PAML: a program package for phylogenetic analysis by maximum likelihood (1997) (5536)
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods (1994) (2404)
Bayes empirical bayes inference of amino acid sites under positive selection. (2005) (2049)
Statistical methods for detecting molecular adaptation (2000) (1658)
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. (2005) (1633)
Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference (1996) (1407)
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. (2002) (1235)
Bayesian species delimitation using multilocus sequence data (2010) (1192)
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. (2003) (1001)
Estimating the pattern of nucleotide substitution (1994) (885)
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. (2006) (707)
Molecular phylogenetics: principles and practice (2012) (594)
Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites (2004) (575)
Best Practices for Justifying Fossil Calibrations (2011) (557)
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. (2003) (536)
The timescale of early land plant evolution (2018) (516)
The BPP program for species tree estimation and species delimitation (2015) (511)
Computational Molecular Evolution (2006) (500)
Synonymous and nonsynonymous rate variation in nuclear genes of mammals (1998) (466)
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny (2012) (442)
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci (2014) (429)
Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals (2001) (416)
Phylogenetic Analysis by Maximum Likelihood (PAML) (2002) (391)
Accuracy and power of bayes prediction of amino acid sites under positive selection. (2002) (381)
INDELible: A Flexible Simulator of Biological Sequence Evolution (2009) (380)
Inferring speciation times under an episodic molecular clock. (2007) (374)
Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. (2002) (361)
Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene Loci and calibration points, with application to a radiation of cute-looking mouse lemur species. (2003) (342)
A new time-scale for ray-finned fish evolution (2007) (332)
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales (2015) (323)
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. (2008) (309)
The Timetree of Life (2010) (306)
Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context (2004) (298)
Statistical properties of the branch-site test of positive selection. (2011) (296)
Maximum-likelihood models for combined analyses of multiple sequence data (1996) (292)
The influence of gene flow on species tree estimation: a simulation study. (2014) (282)
PAMLX: a graphical user interface for PAML. (2013) (267)
MAXIMUM LIKELIHOOD TREES FROM DNA SEQUENCES: A PECULIAR STATISTICAL ESTIMATION PROBLEM (1995) (257)
The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. (2010) (251)
A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution (2004) (245)
Evaluation of a bayesian coalescent method of species delimitation. (2011) (242)
The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. (2010) (241)
Improved Reversible Jump Algorithms for Bayesian Species Delimitation (2013) (237)
Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus A (2000) (233)
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. (2011) (213)
Estimation of the Transition/Transversion Rate Bias and Species Sampling (1999) (213)
Branch-length prior influences Bayesian posterior probability of phylogeny. (2005) (209)
Exploring uncertainty in the calibration of the molecular clock (2012) (209)
Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. (2002) (207)
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent (2018) (205)
Bayesian molecular clock dating of species divergences in the genomics era (2015) (205)
Dating primate divergences through an integrated analysis of palaeontological and molecular data. (2011) (202)
Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. (2002) (193)
Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. (2007) (189)
Inference of selection from multiple species alignments. (2002) (182)
Phylogenetic analysis using parsimony and likelihood methods (1996) (181)
Phylogenetic inference using whole genomes. (2008) (178)
In defence of model‐based inference in phylogeography (2010) (170)
Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. (2008) (167)
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. (2003) (159)
The Spectre of Too Many Species (2018) (153)
Maximum likelihood methods for detecting adaptive evolution after gene duplication (2004) (143)
Phylogenetic tree building in the genomic age (2020) (142)
Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. (2003) (140)
A biologist’s guide to Bayesian phylogenetic analysis (2017) (132)
Statistical Properties of the Maximum Likelihood Method of Phylogenetic Estimation and Comparison With Distance Matrix Methods (1994) (130)
Efficient Bayesian Species Tree Inference under the Multispecies Coalescent (2015) (128)
STATISTICAL TESTS OF HOST‐PARASITE COSPECIATION (1997) (123)
An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. (2005) (119)
Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case (2017) (118)
Molecular Evolution: A Statistical Approach (2014) (114)
Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution (2018) (114)
Challenges in Species Tree Estimation Under the Multispecies Coalescent Model (2016) (111)
SEX‐LINKED HYBRID STERILITY IN A BUTTERFLY (2001) (109)
Rate variation and estimation of divergence times using strict and relaxed clocks (2011) (106)
The unbearable uncertainty of Bayesian divergence time estimation (2012) (102)
Widespread Adaptive Evolution in the Human Immunodeficiency Virus Type 1 Genome (2003) (99)
The power of phylogenetic comparison in revealing protein function. (2005) (99)
Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. (2002) (96)
Species Delimitation (2019) (92)
Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals (2014) (89)
Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. (2012) (85)
MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. (2009) (83)
Somatosensory Projections to Cochlear Nucleus Are Upregulated after Unilateral Deafness (2012) (82)
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 (2005) (81)
Bayesian molecular dating using PAML/multidivtime (2005) (81)
The role of positive selection in determining the molecular cause of species differences in disease (2008) (80)
Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates (2014) (79)
The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple Loci (2014) (79)
A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis (2019) (73)
The evolution of methods for establishing evolutionary timescales (2016) (73)
Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics. (2007) (72)
Molecular and morphological evidence on the phylogeny of the Elephantidae (2000) (69)
Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci (2014) (69)
Maximum Likelihood Methods for Detecting Adaptive Protein Evolution (2005) (64)
Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees (2018) (64)
Dating phylogenies with sequentially sampled tips. (2013) (63)
Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses (2017) (61)
Complexity of the simplest phylogenetic estimation problem (2000) (60)
Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex (2018) (59)
Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. (2012) (59)
Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. (2012) (59)
Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). (2002) (58)
Bayesian dating of shallow phylogenies with a relaxed clock. (2010) (58)
Bayesian Species Delimitation Can Be Robust to Guide-Tree Inference Errors (2014) (58)
Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. (2004) (58)
Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge (2010) (57)
Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. (2007) (56)
A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times (2004) (55)
Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons (2017) (54)
A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data (2010) (54)
Phylogenomic analysis of natural selection pressure in Streptococcus genomes (2007) (53)
Maximum likelihood methods for detecting adaptive evolution after gene duplication. Gene and Genome Duplications and the Origin of Novel Gene Functions (2003) (52)
Diversifying and Purifying Selection in the Peptide Binding Region of DRB in Mammals (2008) (49)
Searching for efficient Markov chain Monte Carlo proposal kernels (2013) (46)
The Trouble with Sliding Windows and the Selective Pressure in BRCA1 (2008) (45)
Maximum Likelihood Implementation of an Isolation‐with‐Migration Model for Three Species (2016) (44)
In defense of statistical methods for detecting positive selection (2009) (41)
The Multi-species Coalescent Model and Species Tree Inference (2020) (40)
A likelihood look at the supermatrix-supertree controversy. (2009) (40)
Adaptive Molecular Evolution (2004) (39)
Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating (2017) (39)
Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites (1995) (38)
Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution (2017) (38)
Bayesian relaxed clock estimation of divergence times in foraminifera. (2011) (38)
The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites (2001) (38)
Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events. (2006) (37)
Duplicated Paralogous Genes Subject to Positive Selection in the Genome of Trypanosoma brucei (2008) (37)
Likelihood models of somatic mutation and codon substitution in cancer genes. (2003) (37)
Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution (2015) (35)
Looking for Darwin in genomic sequences--validity and success of statistical methods. (2012) (33)
Maximum Likelihood Analysis of Adaptive Evolution in HIV-1 Gp120 env Gene (2000) (31)
Molecular evolution of the hepatitis B virus genome (1995) (31)
Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters. (2019) (31)
Prevalence of cryptic species in morphologically uniform taxa - Fast speciation and evolutionary radiation in Asian frogs. (2018) (30)
Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus. (2013) (30)
Empirical evaluation of a prior for Bayesian phylogenetic inference (2008) (29)
Positive Darwinian selection in the evolution of mammalian female reproductive proteins (2001) (28)
Bayesian Molecular Clock Dating Using Genome-Scale Datasets. (2019) (28)
An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times (2017) (28)
A species-level timeline of mammal evolution integrating phylogenomic data (2021) (28)
Change of Positive Selection Pressure on HIV-1 Envelope Gene Inferred by Early and Recent Samples (2011) (27)
Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons? (2013) (27)
Molecular Evolution of the Hepatitis Delta Virus Antigen Gene: Recombination or Positive Selection? (2004) (26)
SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model (2012) (26)
Gene conversion and functional divergence in the beta-globin gene family. (2004) (26)
A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change. (2006) (25)
Proposed standard nomenclature for the alpha- and beta-globin gene families. (2006) (25)
Rapid morphological evolution in placental mammals post-dates the origin of the crown group (2019) (24)
Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories (Ipomoea) (2003) (23)
The Impact of Cross-Species Gene Flow on Species Tree Estimation (2019) (21)
Molecular Clocks without Rocks: New Solutions for Old Problems. (2020) (21)
Bayesian inference in molecular phylogenetics (2007) (21)
Defining Species When There is Gene Flow. (2020) (21)
Introduction. Statistical and computational challenges in molecular phylogenetics and evolution (2008) (19)
Gene Conversion and Functional Divergence in the β-Globin Gene Family (2004) (17)
Designing Simple and Efficient Markov Chain Monte Carlo Proposal Kernels (2017) (17)
A tutorial of BPP for species tree estimation and species delimitation (2015) (17)
A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis (2019) (16)
Complexity of the simplest species tree problem (2021) (15)
Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow (2021) (12)
Bayesian Estimation of Nonsynonymous/Synonymous Rate Ratios for Pairwise Sequence Comparisons (2014) (12)
Efficient simulation under a population genetics model of carcinogenesis (2011) (11)
Species Identification by Bayesian Fingerprinting: A Powerful Alternative to DNA Barcoding (2016) (10)
On the varied pattern of evolution of 2 fungal genomes: a critique of Hughes and Friedman. (2006) (10)
Phylogeny and species delimitation of the C‐genome diploid species in Oryza (2011) (10)
A simulation study to examine the information content in phylogenomic datasets under the multispecies coalescent model. (2020) (9)
Dating species divergences using rocks and clocks (2016) (9)
On the general reversible Markov process model of nucleotide substitution: A reply to Saccone et al. (1995) (8)
A Tutorial on the Use of BPP for Species Tree Estimation and Species Delimitation (2020) (8)
Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations (2018) (8)
Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model (2021) (8)
SEX-LINKED HYBRID STERILITY IN A BUTTERFLY (2001) (7)
Neutral and adaptive protein evolution (2006) (6)
RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results (2021) (5)
The good, the bad, and the ugly: Bayesian model selection produces spurious posterior probabilities for phylogenetic trees. (2018) (5)
Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States (2021) (5)
Phylogenetics as applied mathematics (2003) (4)
Complex introgression history of the erato-sara clade of Heliconius butterflies (2021) (4)
A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model (2022) (4)
Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability (2021) (4)
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies (2021) (4)
Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters (2018) (4)
Significant cross-species gene flow detected in the Tamias quadrivittatus group of North American chipmunks (2021) (4)
Molecular clock dating (2013) (3)
Rates of Evolution in Ancient DNA from Ade «lie Penguins (2002) (3)
Proposed standard nomenclature for the α – and β-globin gene families (2006) (3)
Functional and Adaptive Significance of Promoter Mutations That Affect Divergent Myocardial Expressions of TRIM72 in Primates (2021) (3)
Estimation of species divergence times in presence of cross-species gene flow. (2023) (2)
Proteins: Structure, Function and Evolution (2001) (2)
Correction: The Trouble with Sliding Windows and the Selective Pressure in BRCA1 (2008) (2)
Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks. (2022) (2)
The asymptotic behavior of bootstrap support values in molecular phylogenetics. (2020) (2)
Molecular clock and estimation of species divergence times (2006) (2)
Bayesian Phylogenetic Methods (2016) (2)
A probabilist’s account of modern molecular population genetics, Review of Probability Models for DNA Sequence Evolution (by Rick Durrett (2004) (2)
Comparative genomics coming of age. (2003) (2)
Divergence dates for Malagasy lemurs estimated from multiple gene loci: fit with climatological events and speciation models (2004) (2)
Estimating the distribution of selection coefficients from phylogenetic data with applications to mtDNA (2003) (2)
Maximum likelihood methods (2006) (2)
Models of nucleotide substitution (2006) (2)
Phylogeny reconstruction: overview (2006) (2)
Models of amino acid and codon substitution (2006) (1)
Title: Best Practices for Justifying Fossil Calibrations (2011) (1)
Inference of Gene Flow between Species under Misspecified Models (2022) (1)
A discrete‐beta model for testing gene flow after speciation (2015) (1)
Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data (2010) (1)
Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space (2019) (1)
Simulating molecular evolution (2006) (1)
Duplication and adaptive evolution of chalcone synthase genes in the genus Dendranthema (Asteraceae) (2002) (1)
Data from: The spectre of too many species (2018) (0)
Bayesian inference from genomic sequence data under the multispecies coalescent (2017) (0)
Satistical tests of host-parasite coevolution (1997) (0)
Proteins: Structure, Function and Evolution - Session Introduction (2002) (0)
Bayesian computation (MCMC) (2014) (0)
Phylogenetics as applied mathematics. Review of Phylogenetics (2003) (0)
A biologist’s guide to Bayesian phylogenetic analysis (2017) (0)
Evolution (2010) (0)
Enclose it or Lose it ! Computer-aided Proofs in Statistics (2010) (0)
Phylogenetic tree building in the genomic age (2020) (0)
Faculty Opinions recommendation of The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection. (2003) (0)
Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites 1 (1998) (0)
Faculty Opinions recommendation of Recreating a functional ancestral archosaur visual pigment. (2002) (0)
Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent (2022) (0)
Beginner's Guide on the Use of PAML to Detect Positive Selection (2023) (0)
Chapter 5.5 Species Delimitation (2020) (0)
II.3. Molecular Clock Dating (2013) (0)
Bay es Empir i cal Bay es Infer ence of Amino A c i d S i t es under P os i t i ve S ele c t i on (2005) (0)
Coalescent theory and species trees (2014) (0)
CNETML: Maximum likelihood inference of phylogeny from copy number profiles of spatio-temporal samples (2022) (0)
Did the butterfly species Heliconius heuripa originate throughinter specific hybridization (2001) (0)
Comparison of methods and tests on trees (2006) (0)
Supplementary material from "Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution" (2017) (0)
Comparative genomics: Comparative genomics coming of age (2003) (0)
Comparison of phylogenetic methods and tests on trees (2014) (0)
Integrative Analysis Methods for Biological Problems Using Data Reduction Approaches (2017) (0)
Faculty Opinions recommendation of Bayesian inference of recent migration rates using multilocus genotypes. (2003) (0)
AWF Edwards and the origin of Bayesian phylogenetics (2016) (0)
Edwards and the Origin of Bayesian Phylogenetics (2015) (0)
EvolutionThe Timetree of Life.Edited byS.BlairHedgesand, SudhirKumar; foreword by, JamesD.Watson. Oxford and New York: Oxford University Press. $200.00. xxi + 551 p.; ill.; index. 9780199535033. 2009. (2010) (0)

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Ziheng Yang's Academic­Influence.com Rankings