Prof Ziheng Yang

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Personal Profile

Name: Ziheng Yang Email: z.yang@ucl.ac.uk
Title: Prof Tel:
Department: Genetics, Evolution & Environment Fax: 020 7679 7096
Position: R A Fisher Chair of Statistical Genetics Address: Department of Biology, Darwin Building, Gower Street, London, WC1E 6BT
Research Domain: Basic Life Sciences, Personalised Medicine Web Page: Personal Web Page

Profile

Research Description

We develop statistical models of DNA or protein evolution to be used in reconstructing species phylogenies and in understanding the mechanisms of molecular sequence evolution. We make extensive use of maximum likelihood and Bayesian methods, as well as computer simulation. Real data analysis is also a major undertaking in the group, with detection of adaptive molecular evolution and comparative genomics to be the current focus. Those serves as the motivation for the theoretical work.

Research Activities

Animal Evolutionary biology

Computational Biology

Computational statistics

molecular evolution & phylogenetics

population genetics

Education Description

UCL Collaborators

Prof Andres Ruiz-Linares; Prof John Hardy; Prof Max Telford; Prof Jim Mallet; Dr Vanessa Diaz; Dr Paola Oliveri; Prof Peter Hammond; Prof David Joseph Balding

External Collaborators

Publications

    2012

    • Parham JF, Donoghue PCJ, Bell CJ, Calway TD, Head JJ, Holroyd PA, Inoue JG, Irmis RB, Joyce WG, Ksepka DT, Patane JSL, Smith ND, Tarver JE, van Tuinen M, Yang Z, Angielczyk KD, Greenwood JM, Hipsley CA, Jacobs L, Makovicky PJ, Mueller J, Smith KT, Theodor JM, Warnock RCM, Benton MJ (2012). Best Practices for Justifying Fossil Calibrations. SYSTEMATIC BIOLOGY, 61(2), 346 - 359. doi:10.1093/sysbio/syr107
    • Rannala B, Zhu T, Yang Z (2012). Tail Paradox, Partial Identifiability, and Influential Priors in Bayesian Branch Length Inference. MOLECULAR BIOLOGY AND EVOLUTION, 29(1), 325 - 335. doi:10.1093/molbev/msr210
    • Zhang C, Rannala B, Yang Z (2012). Robustness of Compound Dirichlet Priors for Bayesian Inference of Branch Lengths. SYSTEMATIC BIOLOGY, 61(5), 779 - 784. doi:10.1093/sysbio/sys030
    • Warnock RCM, Yang Z, Donoghue PCJ (2012). Exploring uncertainty in the calibration of the molecular clock. BIOLOGY LETTERS, 8(1), 156 - 159. doi:10.1098/rsbl.2011.0710

    2011

    • Yoshida I, Sugiura W, Shibata J, Ren F, Yang Z, Tanaka H (2011). Change of Positive Selection Pressure on HIV-1 Envelope Gene Inferred by Early and Recent Samples. PLOS ONE, 6(4), - . doi:10.1371/journal.pone.0018630
    • Zang L-L, Zou X-H, Zhang F-M, Ge S, Yang Z (2011). Phylogeny and species delimitation of the C-genome diploid species in Oryza. Journal of Systematics and Evolution, 49(5), 386 - 395. doi:10.1111/j.1759-6831.2011.00145.x
    • Yang Z, dos Reis M (2011). Statistical properties of the branch-site test of positive selection.. Mol Biol Evol, 28(3), 1217 - 1228. doi:10.1093/molbev/msq303
    • Zhu T, Hu Y, Ma ZM, Zhang DX, Li T, Yang Z (2011). Efficient simulation under a population genetics model of carcinogenesis.. Bioinformatics, 27(6), 837 - 843. doi:10.1093/bioinformatics/btr025
    • dos Reis M, Yang Z (2011). Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.. Mol Biol Evol, 28(7), 2161 - 2172. doi:10.1093/molbev/msr045
    • Brown RP, Yang Z (2011). Rate variation and estimation of divergence times using strict and relaxed clocks. BMC EVOLUTIONARY BIOLOGY, 11, - . doi:10.1186/1471-2148-11-271
    • Zhang C, Zhang DX, Zhu TQ, Yang ZH (2011). Evaluation of a Bayesian Coalescent Method of Species Delimitation. SYST BIOL, 60(6), 747 - 761. doi:10.1093/sysbio/syr071
    • Wilkinson RD, Steiper ME, Soligo C, Martin RD, Yang ZH, Tavare S (2011). Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data. SYST BIOL, 60(1), 16 - 31. doi:10.1093/sysbio/syq054
    • Groussin M, Pawlowski J, Yang Z (2011). Bayesian relaxed clock estimation of divergence times in foraminifera.. Mol Phylogenet Evol, 61(1), 157 - 166. doi:10.1016/j.ympev.2011.06.008

    2010

    • Chen M-S, Liu X, Yang Z, Zhao H, Shukle RH, Stuart JJ, Hulbert S (2010). Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge. BMC EVOLUTIONARY BIOLOGY, 10, - . doi:10.1186/1471-2148-10-296
    • Brown RP, Yang Z (2010). Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. SYSTEMATIC BIOLOGY, 59(2), 119 - 131. doi:10.1093/sysbio/syp082
    • Inoue J, Donoghue PC, Yang Z (2010). The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times.. Syst Biol, 59(1), 74 - 89. doi:10.1093/sysbio/syp078
    • Inoue J, Donoghue PCJ, Yang ZH (2010). The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times. SYST BIOL, 59(1), 74 - 89. doi:10.1093/sysbio/syp096
    • Yang Z (2010). A likelihood ratio test of speciation with gene flow using genomic sequence data.. Genome Biol Evol, 2, 200 - 211. doi:10.1093/gbe/evq011
    • Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson SA, Fagundes N, Chikhi L, Beerli P, Vitalis R, Cornuet JM, Huelsenbeck J, Foll M, Yang ZH, Rousset F, Balding D, Excoffier L (2010). In defence of model-based inference in phylogeography REPLY. MOL ECOL, 19(3), 436 - 446. doi:10.1111/j.1365-294X.2009.04515.x
    • Fletcher W, Yang Z (2010). The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection.. Mol Biol Evol, 27(10), 2257 - 2267. doi:10.1093/molbev/msq115
    • Yang Z, Rannala B (2010). Bayesian species delimitation using multilocus sequence data. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107(20), 9264 - 9269. doi:10.1073/pnas.0913022107

    2009

    • Fletcher W, Yang Z (2009). INDELible: a flexible simulator of biological sequence evolution.. Mol Biol Evol, 26(8), 1879 - 1888. doi:10.1093/molbev/msp098
    • Donoghue P, Benton M, Ziheng Y, Inoue J (2009). CALIBRATING AND CONSTRAINING THE MOLECULAR CLOCK. JOURNAL OF VERTEBRATE PALEONTOLOGY, 29, 89A - 89A.
    • Yang Z, Nielsen R, Goldman N (2009). In defense of statistical methods for detecting positive selection. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(36), E95 - E95. doi:10.1073/pnas.0904550106
    • Rota-Stabelli O, Yang Z, Telford MJ (2009). MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies.. Mol Phylogenet Evol, 52(1), 268 - 272. doi:10.1016/j.ympev.2009.01.011
    • Ren F, Tanaka H, Yang Z (2009). A likelihood look at the supermatrix-supertree controversy. GENE, 441(1-2), 119 - 125. doi:10.1016/j.gene.2008.04.002

    2008

    • Vamathevan JJ, Hasan S, Emes RD, Amrine-Madsen H, Rajagopalan D, Topp SD, Kumar V, Word M, Simmons MD, Foord SM, Sanseau P, Yang Z, Holbrook JD (2008). The role of positive selection in determining the molecular cause of species differences in disease.. BMC Evol Biol, 8, 273 - . doi:10.1186/1471-2148-8-273
    • Burgess R, Yang Z (2008). Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors.. Mol Biol Evol, 25(9), 1979 - 1994. doi:10.1093/molbev/msn148
    • Schmid K, Yang Z (2008). The Trouble with Sliding Windows and the Selective Pressure in BRCA1. PLOS ONE, 3(11), - . doi:10.1371/journal.pone.0003746
    • Emes RD, Yang Z (2008). Duplicated Paralogous Genes Subject to Positive Selection in the Genome of Trypanosoma brucei. PLOS ONE, 3(5), - . doi:10.1371/journal.pone.0002295
    • Furlong RF, Yang Z (2008). Diversifying and purifying selection in the peptide binding region of DRB in mammals.. J Mol Evol, 66(4), 384 - 394. doi:10.1007/s00239-008-9092-6
    • Yang Z, Nielsen R (2008). Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.. Mol Biol Evol, 25(3), 568 - 579. doi:10.1093/molbev/msm284
    • Yang Z (2008). Empirical evaluation of a prior for Bayesian phylogenetic inference.. Philos Trans R Soc Lond B Biol Sci, 363(1512), 4031 - 4039. doi:10.1098/rstb.2008.0164
    • Rannala B, Yang Z (2008). Phylogenetic inference using whole Genomes. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 9, 217 - 231. doi:10.1146/annurev.genom.9.081307.164407
    • Goldman N, Yang Z (2008). Introduction. Statistical and computational challenges in molecular phylogenetics and evolution. PHILOS T R SOC B, 363(1512), 3889 - 3892. doi:10.1098/rstb.2008.0182

    2007

    • Anisimova M, Yang Z (2007). Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites.. Mol Biol Evol, 24(5), 1219 - 1228. doi:10.1093/molbev/msm042
    • Hurley IA, Lockridge Mueller R, Dunn KA, Schmidt EJ, Friedman M, Ho RK, Prince VE, Yang Z, Thomas M, Coates MI (2007). A new time-scale for ray-finned fish evolution. Proceedings of the Royal Society B: Biological Sciences, 274, 489 - 498.
    • Zhou RC, Zeng K, Wu W, Chen XS, Yang ZH, Shi SH, Wu CI (2007). Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. MOL BIOL EVOL, 24(12), 2746 - 2754. doi:10.1093/molbev/msm209
    • Yang Z (2007). Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics.. Mol Biol Evol, 24(8), 1639 - 1655. doi:10.1093/molbev/msm081
    • Yang Z (2007). PAML 4: phylogenetic analysis by maximum likelihood.. Mol Biol Evol, 24(8), 1586 - 1591. doi:10.1093/molbev/msm088
    • Rannala B, Yang Z (2007). Inferring speciation times under an episodic molecular clock. SYSTEMATIC BIOLOGY, 56(3), 453 - 466. doi:10.1080/10635150701420643
    • Anisimova M, Bielawski J, Dunn K, Yang Z (2007). Phylogenomic analysis of natural selection pressure in Streptococcus genomes.. BMC Evol Biol, 7, 154 - . doi:10.1186/1471-2148-7-154

    2006

    • Yang Z, Rannala B (2006). Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution, 23, 212 - 226. doi:10.1093/molbev/msj024
    • Yang Z (2006). On the varied pattern of evolution of two fungal genomes: a critique of Hughes and Friedman. Molecular Biology and Evolution, 23, 2279 - 2282.
    • Aguileta G, Bielawski JP, Yang Z (2006). Proposed standard nomenclature for the alpha- and beta-globin gene families.. Genes Genet Syst, 81(5), 367 - 371.
    • Aguileta G, Bielawski JP, Yang Z (2006). Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events.. Gene, 380(1), 21 - 29. doi:10.1016/j.gene.2006.04.019
    • Yang Z (2006). Computational Molecular Evolution.
    • Ren F, Tsubota A, Hirokawa T, Kumada H, Yang Z, Tanaka H (2006). 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, 383, 43 - 51. doi:10.1016/j.gene.2006.07.018

    2005

    • Yang Z, Rannala B (2005). Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology, 54, 455 - 470. doi:10.1080/10635150590945313
    • Yang Z, Wong WSW, Nielsen R (2005). Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution, 22, 1107 - 1118. doi:10.1093/molbev/msi097
    • Ren F, Tanaka H, Yang Z (2005). An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Systematic Biology, 54, 808 - 818.
    • Yang Z (2005). Bayesian inference in molecular phylogenetics. In Gascuel O (Ed.), Mathematics of Evolution and Phylogeny (pp. 63 - 90). : Oxford University Press.
    • Zhang J, Nielsen N, Yang Z (2005). Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution, 22, 2472 - 2479.
    • Bielawski JP, Yang Z (2005). Maximum likelihood methods for detecting adaptive protein evolution. In Nielsen R (Ed.), Statistical Methods in Molecular Evolution (pp. 103 - 124). : Springer-Verlag.
    • Yang Z (2005). The power of phylogenetic comparison in revealing protein function. Proceedings of the National Academy of Sciences of the United States of America, 102, 3179 - 3180.
    • Sainudiin R, Wong WSW, Yogeeswaran K, Nasrallah J, Yang Z, Nielsen R (2005). 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. Journal of Molecular Evolution, 60, 315 - 326.

    2004

    • Yang Z (2004). A probabilist’s account of modern molecular population genetics, Review of Probability Models for DNA Sequence Evolution (by Rick Durrett. Heredity, 92, 474 - 474.
    • Yang Z (2004). A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times. Acta Zoologica Sinica, 50(645), 656 - .
    • Schein M, Yang Z, Mitchell-Olds T, Schmid KJ (2004). Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thalianaand closely related species. Molecular Biology and Evolution, 21, 659 - 669.
    • Anisimova A, Yang Z (2004). Molecular evolution of hepatitis delta virus antigen gene: recombination or positive selection?. Journal of Molecular Evolution, 59, 815 - 826.
    • Yang J, Gu H, Yang Z (2004). Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in the morning glories (Ipomoea). Journal of Molecular Evolution, 58, 54 - 63.
    • Aguileta G, Bielawski JP, Yang Z (2004). Gene conversion and functional divergence in the ß-globin gene family. Journal of Molecular Evolution, 2004, 177 - 189.
    • Yoder AD, Yang Z (2004). Divergence dates for Malagasy lemurs estimated from multiple gene loci: fit with climatological events and speciation models. Molecular Ecology, 13(757), 773 - .
    • Wong WSW, Yang Z, Goldman N, Nielsen R (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.
    • Bielawski JP, Yang Z (2004). A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of Molecular Evolution, 50, 121 - 132.

    2003

    • Bielawski JP, Yang Z (2003). Maximum likelihood methods for detecting adaptive evolution after gene duplication. Gene and Genome Duplications and the Origin of Novel Gene Functions. In Meyer AYVDP (Ed.), Genome Evolution (pp. 201 - 212). : Kluwer Academic Publishers.
    • Bielawski JP, Yang Z (2003). Maximum likelihood methods for detecting adaptive evolution after gene duplication. Journal of Structural and Functional Genomics, 3, 201 - 212.
    • Yang W, Bielawski JP, Yang Z (2003). Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. Journal of Molecular Evolution, 57, 212 - 221.
    • Yang Z (2003). Phylogenetics as applied mathematics. Review of Phylogenetics. In Charles SAMS (Ed.), Trends in Ecology and Evolution (pp. 558 - 559). : Oxford University Press.
    • Nielsen R, Yang Z (2003). Estimating the distribution of selection coefficients from phylogenetic data with applications to mtDNA. Molecular Biology and Evolution, 20, 1231 - 1239.
    • Anisimova M, Nielsen R, Yang Z (2003). Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics, 164, 1229 - 1236.
    • Yang Z, Yoder AD (2003). 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. Systematic Biology, 52, 705 - 716.
    • Furlong RF, Yang Z (2003). Comparative genomics coming of age. Heredity, 91, 533 - 534.
    • Aris-Brosou S, Yang Z (2003). Bayesian models of episodic evolution support a late pre-cambrian explosive diversification of the Metazoa. Molecular Biology and Evolution, 20, 1947 - 1954.
    • Rannala B, Yang Z (2003). Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164, 1645 - 1656.
    • Yang Z (2003). Adaptive molecular evolution. In Balding D, Bishop M, Cannings C (Ed.), Handbook of statistical genetics (pp. 229 - 254). : Wiley.
    • Yang Z, Ro S, Rannala B (2003). Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics, 165, 695 - 705.

    2002

    • Yang Z, Swanson WJ (2002). Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Molecular Biology and Evolution, 19, 49 - 57.
    • Yang J, Huang H, Gu Y, Zhong Y, Yang Z (2002). Duplication and adaptive evolution of chalcone synthase genes in the genus Dendranthema (Asteraceae). Molecular Biology and Evolution, 19, 1752 - 1759.
    • Yang Z (2002). Likelihood and Bayes estimation of ancestral population sizes in Hominoids using data from multiple loci. Genetics, 162, 1811 - 1823.
    • Yang Z (2002). Molecular clock. In Pagel M (Ed.), Oxford Encyclopaedia of Evolution (pp. 747 - 750). : Oxford University Press.
    • Yang Z (2002). Inference of selection from multiple species alignments. Current Opinion in Genetics and Development, 12, 688 - 694.
    • Aris-Brosou S, Yang Z (2002). The effects of models of rate evolution on estimation of divergence dates with a special reference to the metazoan 18S rRNA phylogeny. Systematic Biology, 51, 703 - 714.
    • Jiggins CD, Hurst GDD, Yang Z (2002). Host-symbiont conflicts: Positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Molecular Biology and Evolution, 19, 1341 - 1349.
    • Anisimova M, Bielawski JP, Yang Z (2002). Accuracy and power of Bayes prediction of amino acid sites under positive selection. Molecular Biology and Evolution, 19, 950 - 958.
    • Yang Z, Nielsen R (2002). Codon-substitution models for detecting molecular adaptation at individual sites among specific lineages. Molecular Biology and Evolution, 19, 908 - 917.

    2001

    • Anisimova M, Bielawski JP, Yang Z (2001). The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites. Molecular Biology and Evolution, 18, 1585 - 1592.
    • Anisimova M, Bielawski JP, Yang Z (2001). Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.. Mol Biol Evol, 18(8), 1585 - 1592.
    • Yang Z (2001). Adaptive molecular evolution. In Balding D, Bishop M, Cannings C (Ed.), Handbook of statistical genetics (pp. 327 - 350). : Wiley.
    • Jiggins CD, Linares M, Naisbit RE, Salazar C, Yang Z, Mallet J (2001). Sex-linked hybrid sterility in a butterfly. Evolution, 55, 1631 - 1638.
    • Dunn KA, Bielawski JP, Yang Z (2001). Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics, 157, 317 - 330.
    • Dunn KA, Bielawski JP, Yang Z (2001). Substitution rates in Drosophila nuclear genes: implications for translational selection.. Genetics, 157(1), 295 - 305.
    • Bielawski JP, Yang Z (2001). Positive and negative selection in the DAZ gene family. Molecular Biology and Evolution, 18, 523 - 529.
    • Swanson WJ, Yang Z, Wolfner MF, Aquadro CF (2001). Positive Darwinian selection in the evolution of mammalian female reproductive proteins. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF U S A, 98, 2509 - 2514.
    • Yang Z (2001). Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. Pacific Symposium on BioComputing 2001, , 226 - 237.

    2000

    • Yang Z (2000). Relating physicochemical properties of amino acids to variable nucleotide substitution patterns among sites. Pacific Symposium on Computational Biology 2000, , 81 - 92.
    • Yang Z, Bielawski JP (2000). Statistical methods for detecting molecular adaptation. Trends in Ecology and Evolution, 15, 496 - 503.
    • Yang Z, Nielsen R, Goldman N, Pederson AMK (2000). Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 155, 431 - 449.
    • Yang Z (2000). Complexity of the simplest phylogenetic estimation problem. Proceedings of the Royal Society B: Biological Sciences, 267, 109 - 116.
    • Yang Z, Nielsen R (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution, 17, 32 - 43.
    • Yang Z (2000). Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. Journal of Molecular Evolution, 51, 423 - 432.
    • Thomas MG, Hagelberg E, Jones H, Yang Z, Lister AM (2000). Molecular and Morphological Evidence on the Phylogeny of the Elephantidae. Proceedings of the Royal Society B: Biological Sciences, 267, 2493 - 2500.
    • Bielawski JP, Dunn K, Yang Z (2000). Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics, 156, 1299 - 1308.
    • Holbrook JD, Birdsey GM, Yang Z, Bruford MF, Danpure CJ (2000). Molecular adaptation of alanine: glyoxylate aminotransferase targeting in primates. Molecular Biology and Evolution, 17, 387 - 400.
    • Yoder AD, Yang Z (2000). Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution, 17, 1081 - 1090.
    • Yang Z, Swanson WJ, Vacquier VD (2000). Maximum likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. Molecular Biology and Evolution, 17, 1446 - 1455.

    1999

    • Yang Z, Yoder AD (1999). Estimation of the transition/transversion rate bias and species sampling. Journal of Molecular Evolution, 48, 274 - 283.
    • Excoffier L, Yang Z (1999). Substitution rate variation among sites in the mitochondrial hypervariable region I of humans and chimpanzees. Molecular Biology and Evolution, 16, 1357 - 1368.

    1998

    • Yang Z (1998). On the best evolutionary rate for phylogenetic analysis. Systematic Biology, 47, 125 - 133.
    • Hasegawa M, Cao Y, Yang Z (1998). Preponderance of slightly deleterious polymorphism in mitochondrial DNA: replacement/synonymous rate ratio is much higher within species than between species. Molecular Biology and Evolution, 15, 1499 - 1505.
    • Yang Z, Nielsen R (1998). Synonymous and nonsynonymous rate variation in nuclear genes of mammals. Journal of Molecular Evolution, 46, 409 - 418.
    • Rannala B, Huelsenbeck JP, Yang Z, Nielsen R (1998). Taxon sampling and the accuracy of large phylogenies. Systematic Biology, 47, 702 - 709.
    • Yang Z, Nielsen R, Hasegawa M (1998). Models of amino acid substitution and applications to mitochondrial protein evolution. Molecular Biology and Evolution, 15, 1600 - 1611.
    • Yang Z (1998). Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution, 15, 568 - 573.
    • Nielsen R, Yang Z (1998). Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148, 929 - 936.

    1997

    • Yang Z (1997). How often do wrong models produce better phylogenies?. Molecular Biology and Evolution, 14, 105 - 108.
    • Yang Z (1997). On the estimation of ancestral population sizes of modern humans. Genetical Research, 69, 111 - 116.
    • Yang Z (1997). PAML: a program for package for phylogenetic analysis by maximum likelihood. CABIOS, 15, 555 - 556.
    • Huelsenbeck JP, Rannala B, Yang Z (1997). Satistical tests of host-parasite coevolution. Evolution, 51, 410 - 419.
    • Yang Z, Goldman N (1997). Are big trees indeed easy?. Trends in Ecology and Evolution, 12, 357 - .
    • (1997). Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Molecular Biology and Evolution, 14, 717 - 724.

    • Dunn K, Yang Z, Coates MI, Thomas MG (). Molecular Evolution: Evolution, genomics, bioinformatics meeting.