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Ziheng Yang

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Concepts & Ideas

Phenomena

Chemicals & Drugs

Activities & Behaviors

Computer Simulation

Physiology

Genes & Molecular Sequences

Living Beings

Primates

Procedures

Sequence Alignment

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Co-Publications
Name
12
Bielawski, Joseph
6
Rannala, Bruce
6
Anisimova, Maria
5
Nielsen, Rasmus
4
Nielsen, Rasmus
3
Aguileta, Gabriela
2
Aris-Brosou, Stéphane
2
Dunn, Katherine
2
Gu, Hongya
2
Yang, Ji
2
Yoder, Anne
2
Emes, Richard
2
Wong, Wendy
2
Thomas, Mark
1
Wu, Chung-I

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Publications

TOP 3
Yang Ziheng; Nielsen Rasmus; Goldman Nick
In defense of statistical methods for detecting positive selection.
Fletcher William; Yang Ziheng
INDELible: a flexible simulator of biological sequence evolution.
Rota-Stabelli Omar; Yang Ziheng; Telford Maximilian J
MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies.

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All Publications

2009: Yang Ziheng; Nielsen Rasmus; Goldman Nick
In defense of statistical methods for detecting positive selection.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(36):E95; author reply E96.
2009: Fletcher William; Yang Ziheng
INDELible: a flexible simulator of biological sequence evolution.
Molecular biology and evolution 2009;26(8):1879-88.
2009: Rota-Stabelli Omar; Yang Ziheng; Telford Maximilian J
MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies.
Molecular phylogenetics and evolution 2009;52(1):268-72.
2009: Ren Fengrong; Tanaka Hiroshi; Yang Ziheng
A likelihood look at the supermatrix-supertree controversy.
Gene 2009;441(1-2):119-25.
2009: Yang Zhi; Sinha Sumedha P; Booi Rebecca C; Roubidoux Marilyn A; Ma Bing; Fowlkes J Brian; LeCarpentier Gerald L; Carson Paul L
Breast ultrasound image improvement by pixel compounding of compression sequence.
IEEE transactions on ultrasonics, ferroelectrics, and frequency control 2009;56(3):465-73.
2008: Yang Ziheng
Empirical evaluation of a prior for Bayesian phylogenetic inference.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2008;363(1512):4031-9.
2008: Goldman Nick; Yang Ziheng
Introduction. Statistical and computational challenges in molecular phylogenetics and evolution.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2008;363(1512):3889-92.
2008: Burgess Ralph; Yang Ziheng
Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors.
Molecular biology and evolution 2008;25(9):1979-94.
2008: Furlong Rebecca F; Yang Ziheng
Diversifying and purifying selection in the peptide binding region of DRB in mammals.
Journal of molecular evolution 2008;66(4):384-94.
2008: Yang Ziheng; Nielsen Rasmus
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.
Molecular biology and evolution 2008;25(3):568-79.
2008: Schmid Karl; Yang Ziheng
The trouble with sliding windows and the selective pressure in BRCA1.
PloS one 2008;3(11):e3746.
2008: Vamathevan Jessica J; Hasan Samiul; Emes Richard D; Amrine-Madsen Heather; Rajagopalan Dilip; Topp Simon D; Kumar Vinod; Word Michael; Simmons Mark D; Foord Steven M; Sanseau Philippe; Yang Ziheng; Holbrook Joanna D
The role of positive selection in determining the molecular cause of species differences in disease.
BMC evolutionary biology 2008;8():273.
2008: Rannala Bruce; Yang Ziheng
Phylogenetic inference using whole genomes.
Annual review of genomics and human genetics 2008;9():217-31.
2008: Emes Richard D; Yang Ziheng
Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei.
PloS one 2008;3(5):e2295.
2007: Zhou Renchao; Zeng Kai; Wu Wei; Chen Xiaoshu; Yang Ziheng; Shi Suhua; Wu Chung-I
Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves.
Molecular biology and evolution 2007;24(12):2746-54.
2007: Yang Ziheng
Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics.
Molecular biology and evolution 2007;24(8):1639-55.
2007: Yang Ziheng
PAML 4: phylogenetic analysis by maximum likelihood.
Molecular biology and evolution 2007;24(8):1586-91.
2007: Rannala Bruce; Yang Ziheng
Inferring speciation times under an episodic molecular clock.
Systematic biology 2007;56(3):453-66.
2007: Anisimova Maria; Yang Ziheng
Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites.
Molecular biology and evolution 2007;24(5):1219-28.
2007: Hurley Imogen A; Mueller Rachel Lockridge; Dunn Katherine A; Schmidt Eric J; Friedman Matt; Ho Robert K; Prince Victoria E; Yang Ziheng; Thomas Mark G; Coates Michael I
A new time-scale for ray-finned fish evolution.
Proceedings. Biological sciences / The Royal Society 2007;274(1609):489-98.
2007: Anisimova Maria; Bielawski Joseph; Dunn Katherine; Yang Ziheng
Phylogenomic analysis of natural selection pressure in Streptococcus genomes.
BMC evolutionary biology 2007;7():154.
2006: Yang Ziheng
On the varied pattern of evolution of 2 fungal genomes: a critique of Hughes and Friedman.
Molecular biology and evolution 2006;23(12):2279-82.
2006: Ren Fengrong; Tsubota Asahito; Hirokawa Takatsugu; Kumada Hiromitsu; Yang Ziheng; Tanaka Hiroshi
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;383():43-51.
2006: Aguileta Gabriela; Bielawski Joseph P; Yang Ziheng
Proposed standard nomenclature for the alpha- and beta-globin gene families.
Genes & genetic systems 2006;81(5):367-71.
2006: Aguileta Gabriela; Bielawski Joseph P; Yang Ziheng
Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events.
Gene 2006;380(1):21-9.
2006: Yang Ziheng; Rannala Bruce
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.
Molecular biology and evolution 2006;23(1):212-26.
2005: Zhang Jianzhi; Nielsen Rasmus; Yang Ziheng
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.
Molecular biology and evolution 2005;22(12):2472-9.
2005: Ren Fengrong; Tanaka Hiroshi; Yang Ziheng
An empirical examination of the utility of codon-substitution models in phylogeny reconstruction.
Systematic biology 2005;54(5):808-18.
2005: Yang Ziheng; Rannala Bruce
Branch-length prior influences Bayesian posterior probability of phylogeny.
Systematic biology 2005;54(3):455-70.
2005: Yang Ziheng; Wong Wendy S W; Nielsen Rasmus
Bayes empirical bayes inference of amino acid sites under positive selection.
Molecular biology and evolution 2005;22(4):1107-18.
2005: Sainudiin Raazesh; Wong Wendy Shuk Wan; Yogeeswaran Krithika; Nasrallah June B; Yang Ziheng; Nielsen Rasmus
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 2005;60(3):315-26.
2005: Yang Ziheng
The power of phylogenetic comparison in revealing protein function.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(9):3179-80.
2004: Anisimova Maria; Yang Ziheng
Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection?
Journal of molecular evolution 2004;59(6):815-26.
2004: Wong Wendy S W; Yang Ziheng; Goldman Nick; Nielsen Rasmus
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites.
Genetics 2004;168(2):1041-51.
2004: Aguileta Gabriela; Bielawski Joseph P; Yang Ziheng
Gene conversion and functional divergence in the beta-globin gene family.
Journal of molecular evolution 2004;59(2):177-89.
2004: Berry V; Yang Z; Addison P K F; Francis P J; Ionides A; Karan G; Jiang L; Lin W; Hu J; Yang R; Moore A; Zhang K; Bhattacharya S S
Recurrent 17 bp duplication in PITX3 is primarily associated with posterior polar cataract (CPP4).
Journal of medical genetics 2004;41(8):e109.
2004: Bielawski Joseph P; Yang Ziheng
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution.
Journal of molecular evolution 2004;59(1):121-32.
2004: Yoder Anne D; Yang Ziheng
Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context.
Molecular ecology 2004;13(4):757-73.
2004: Schein Manja; Yang Ziheng; Mitchell-Olds Thomas; Schmid Karl J
Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species.
Molecular biology and evolution 2004;21(4):659-69.
2004: Yang Ji; Gu Hongya; Yang Ziheng
Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea).
Journal of molecular evolution 2004;58(1):54-63.
2003: Furlong Rebecca F; Yang Ziheng
Comparative genomics coming of age.
Heredity 2003;91(6):533-4.
2003: Aris-Brosou Stephane; Yang Ziheng
Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa.
Molecular biology and evolution 2003;20(12):1947-54.
2003: Yang Ziheng; Ro Simon; Rannala Bruce
Likelihood models of somatic mutation and codon substitution in cancer genes.
Genetics 2003;165(2):695-705.
2003: Yang Ziheng; Yoder Anne D
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 2003;52(5):705-16.
2003: Yang Wa; Bielawski Joseph P; Yang Ziheng
Widespread adaptive evolution in the human immunodeficiency virus type 1 genome.
Journal of molecular evolution 2003;57(2):212-21.
2003: Rannala Bruce; Yang Ziheng
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.
Genetics 2003;164(4):1645-56.
2003: Nielsen Rasmus; Yang Ziheng
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.
Molecular biology and evolution 2003;20(8):1231-9.
2003: Anisimova Maria; Nielsen Rasmus; Yang Ziheng
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.
Genetics 2003;164(3):1229-36.
2003: Bielawski Joseph P; Yang Ziheng
Maximum likelihood methods for detecting adaptive evolution after gene duplication.
Journal of structural and functional genomics 2003;3(1-4):201-12.
2002: Yang Ziheng
Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci.
Genetics 2002;162(4):1811-23.
2002: Yang Ziheng
Inference of selection from multiple species alignments.
Current opinion in genetics & development 2002;12(6):688-94.
2002: Aris-Brosou Stéphane; Yang Ziheng
Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny.
Systematic biology 2002;51(5):703-14.
2002: Yang Ji; Huang Jinxia; Gu Hongya; Zhong Yang; Yang Ziheng
Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae).
Molecular biology and evolution 2002;19(10):1752-9.
2002: Jiggins Francis M; Hurst Gregory D D; Yang Ziheng
Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae.
Molecular biology and evolution 2002;19(8):1341-9.
2002: Anisimova Maria; Bielawski Joseph P; Yang Ziheng
Accuracy and power of bayes prediction of amino acid sites under positive selection.
Molecular biology and evolution 2002;19(6):950-8.
2002: Yang Ziheng; Nielsen Rasmus
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.
Molecular biology and evolution 2002;19(6):908-17.
2002: Yang Ziheng; Swanson Willie J
Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes.
Molecular biology and evolution 2002;19(1):49-57.
2001: Anisimova M; Bielawski J P; Yang Z
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.
Molecular biology and evolution 2001;18(8):1585-92.
2001: Bielawski J P; Yang Z
Positive and negative selection in the DAZ gene family.
Molecular biology and evolution 2001;18(4):523-9.
2001: Swanson W J; Yang Z; Wolfner M F; Aquadro C F
Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(5):2509-14.
2001: Dunn K A; Bielawski J P; Yang Z
Substitution rates in Drosophila nuclear genes: implications for translational selection.
Genetics 2001;157(1):295-305.
2001: Yang Z
Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():226-37.
2000: Thomas M G; Hagelberg E; Jone H B; Yang Z; Lister A M
Molecular and morphological evidence on the phylogeny of the Elephantidae.
Proceedings. Biological sciences / The Royal Society 2000;267(1461):2493-500.
2000: Yang Z
Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A.
Journal of molecular evolution 2000;51(5):423-32.
2000: Bielawski J P; Dunn K A; Yang Z
Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions.
Genetics 2000;156(3):1299-308.
2000: Yang Z; Swanson W J; Vacquier V D
Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites.
Molecular biology and evolution 2000;17(10):1446-55.
2000: Yoder A D; Yang Z
Estimation of primate speciation dates using local molecular clocks.
Molecular biology and evolution 2000;17(7):1081-90.
2000: Yang Z; Nielsen R; Goldman N; Pedersen A M
Codon-substitution models for heterogeneous selection pressure at amino acid sites.
Genetics 2000;155(1):431-49.
2000: Holbrook J D; Birdsey G M; Yang Z; Bruford M W; Danpure C J
Molecular adaptation of alanine:glyoxylate aminotransferase targeting in primates.
Molecular biology and evolution 2000;17(3):387-400.
2000: Yang Z
Complexity of the simplest phylogenetic estimation problem.
Proceedings. Biological sciences / The Royal Society 2000;267(1439):109-16.
2000: Yang Z; Nielsen R
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.
Molecular biology and evolution 2000;17(1):32-43.
2000: Yang Z
Relating physicochemical properties of amino acids to variable nucleotide substitution patterns among sites.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000;():81-92.
1999: Yang Z; Whyte A; Attygalle A B; Weldon P J; Eisner T; Meinwald J
Reptilian chemistry: characterization of a family of dianeackerone-related steroidal esters from a crocodile secretion.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(22):12251-6.
1999: Yang Z; Yoder A D
Estimation of the transition/transversion rate bias and species sampling.
Journal of molecular evolution 1999;48(3):274-83.
1998: Yang Z; Nielsen R; Hasegawa M
Models of amino acid substitution and applications to mitochondrial protein evolution.
Molecular biology and evolution 1998;15(12):1600-11.
1998: Charlesworth D; Yang Z
Allozyme diversity in Leavenworthia populations with different inbreeding levels.
Heredity 1998;81 ( Pt 4)():453-61.
1998: Yang Z
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.
Molecular biology and evolution 1998;15(5):568-73.

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