Ziheng Yang

Christoph Pacher, Alexandros Stamatakis, Ziheng Yang, 2012, 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum.

Proposed standard nomenclature for the alpha- and beta-globin gene families.

Joseph P Bielawski, Ziheng Yang, Gabriela Aguileta, 2006, Genes & genetic systems.

Change of Positive Selection Pressure on HIV-1 Envelope Gene Inferred by Early and Recent Samples

Ziheng Yang, W. Sugiura, Hiroshi Tanaka, 2011, PloS one.

Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events.

Joseph P Bielawski, Ziheng Yang, Gabriela Aguileta, 2006, Gene.

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

R. Nielsen, Ziheng Yang, 2005 .

Maximum likelihood methods for detecting adaptive evolution after gene duplication

Joseph P. Bielawski, Ziheng Yang, Ziheng Yang, 2004, Journal of Structural and Functional Genomics.

Widespread Adaptive Evolution in the Human Immunodeficiency Virus Type 1 Genome

Joseph P. Bielawski, Ziheng Yang, Ziheng Yang, 2003, Journal of Molecular Evolution.

Maximum Likelihood Analysis of Adaptive Evolution in HIV-1 Gp120 env Gene

Ziheng Yang, Ziheng Yang, 2000, Pacific Symposium on Biocomputing.

Rate variation and estimation of divergence times using strict and relaxed clocks

Ziheng Yang, Richard P. Brown, 2011, BMC Evolutionary Biology.

Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories (Ipomoea)

Hongya Gu, Ziheng Yang, Ziheng Yang, 2003, Journal of Molecular Evolution.

In defense of statistical methods for detecting positive selection

N. Goldman, R. Nielsen, Ziheng Yang, 2009, Proceedings of the National Academy of Sciences.

Phylogenomic analysis of natural selection pressure in Streptococcus genomes

Maria Anisimova, Ziheng Yang, Joseph Bielawski, 2007, BMC Evolutionary Biology.

The good, the bad, and the ugly: Bayesian model selection produces spurious posterior probabilities for phylogenetic trees.

Ziheng Yang, Tianqi Zhu, 2018, 1810.05398.

Dating phylogenies with sequentially sampled tips.

Tanja Stadler, Ziheng Yang, Ziheng Yang, 2013, Systematic biology.

Species Identification by Bayesian Fingerprinting: A Powerful Alternative to DNA Barcoding

Ziheng Yang, Bruce Rannala, B. Rannala, 2016, bioRxiv.

Species Delimitation

B. Rannala, Ziheng Yang, 2019 .

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

Ziheng Yang, A. Leaché, Jiayi Ji, 2022, Systematic biology.

Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge

Ziheng Yang, J. Stuart, Ming-shun Chen, 2010, BMC Evolutionary Biology.

Chapter 5.5 Species Delimitation

B. Rannala, Ziheng Yang, 2020 .

STATISTICAL TESTS OF HOST‐PARASITE COSPECIATION

Ziheng Yang, Bruce Rannala, B. Rannala, 1997, Evolution; international journal of organic evolution.

Somatosensory Projections to Cochlear Nucleus Are Upregulated after Unilateral Deafness

Ziheng Yang, Ziheng Yang, S. Shore, 2012, The Journal of Neuroscience.

RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results

J. Lüdemann, Ziheng Yang, A. Yoder, 2021, bioRxiv.

Efficient simulation under a population genetics model of carcinogenesis

Tiejun Li, Ziheng Yang, Yucheng Hu, 2011, Bioinform..

Bayesian molecular dating using PAML/multidivtime

H. Kishino, J. Thorne, Ziheng Yang, 2005 .

Bayesian relaxed clock estimation of divergence times in foraminifera.

Ziheng Yang, M. Groussin, J. Pawłowski, 2011, Molecular phylogenetics and evolution.

Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating

Ziheng Yang, M. dos Reis, Jose Barba-Montoya, 2017, Molecular phylogenetics and evolution.

An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times

Ziheng Yang, M. dos Reis, K. Angelis, 2017, Systematic biology.

Prevalence of cryptic species in morphologically uniform taxa - Fast speciation and evolutionary radiation in Asian frogs.

Ziheng Yang, A. Greenberg, S. Shi, 2018, Molecular phylogenetics and evolution.

Estimation of species divergence times in presence of cross-species gene flow

B. Rannala, Ziheng Yang, A. Yoder, 2023, Systematic biology.

Correction: The Trouble with Sliding Windows and the Selective Pressure in BRCA1

Ziheng Yang, Karl Schmid, 2008, PLoS ONE.

Major patterns in the introgression history of Heliconius butterflies

Ziheng Yang, J. Mallet, Y. Thawornwattana, 2023, bioRxiv.

Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

Ziheng Yang, A. Yoder, P. Kappeler, 2014, Genome biology and evolution.

DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies.

N. Goldman, Ziheng Yang, M. Telford, 2023, Systematic biology.

On the general reversible Markov process model of nucleotide substitution: A reply to Saccone et al.

Ziheng Yang, Ziheng Yang, 1995, Journal of Molecular Evolution.

Inferring the Direction of Introgression Using Genomic Sequence Data

Ziheng Yang, J. Mallet, T. Flouri, 2023, bioRxiv.

Robustness of compound Dirichlet priors for Bayesian inference of branch lengths.

Ziheng Yang, Bruce Rannala, B. Rannala, 2012, Systematic biology.

Major patterns in the introgression history of Heliconius butterflies

Ziheng Yang, J. Mallet, Y. Thawornwattana, 2023, bioRxiv.

Codon-substitution models for heterogeneous selection pressure at amino acid sites.

N. Goldman, Z. Yang, R. Nielsen, 2000, Genetics.

A codon-based model of nucleotide substitution for protein-coding DNA sequences.

N. Goldman, Z. Yang, Ziheng Yang, 1994, Molecular biology and evolution.

Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.

Z. Yang, Ziheng Yang, Z Yang, 1998, Molecular biology and evolution.

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.

Z. Yang, Ziheng Yang, 1993, Molecular biology and evolution.

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.

Z. Yang, R. Nielsen, Ziheng Yang, 2000, Molecular biology and evolution.

Beginner's Guide on the Use of PAML to Detect Positive Selection

Ziheng Yang, P. Kapli, Sandra Álvarez-Carretero, 2023, Molecular biology and evolution.

Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.

B. Rannala, Z. Yang, Ziheng Yang, 1997, Molecular biology and evolution.

Estimation of primate speciation dates using local molecular clocks.

Z. Yang, Ziheng Yang, A. Yoder, 2000, Molecular biology and evolution.

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene.

R. Nielsen, Z. Yang, R. Nielsen, 1998, Genetics.

Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions.

Z. Yang, Ziheng Yang, J. Bielawski, 2000, Genetics.

A new method of inference of ancestral nucleotide and amino acid sequences.

M. Nei, Sudhir Kumar, Z. Yang, 1995, Genetics.

Among-site rate variation and its impact on phylogenetic analyses.

Z. Yang, Ziheng Yang, 1996, Trends in ecology & evolution.

CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples

Chris P. Barnes, Ziheng Yang, C. Barnes, 2023, Genome Biology.

CNETML: Maximum likelihood inference of phylogeny from copy number profiles of spatio-temporal samples

Chris P. Barnes, Ziheng Yang, C. Barnes, 2022, bioRxiv.

On the use of nucleic acid sequences to infer early branchings in the tree of life.

Z. Yang, Ziheng Yang, D. Roberts, 1995, Molecular biology and evolution.

Probability models for DNA sequence evolution

Z. Yang, Ziheng Yang, Z Yang, 2004, Heredity.

Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species.

Z. Yang, M. Hasegawa, Ziheng Yang, 1998, Molecular biology and evolution.

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

Angelis, Ziheng Yang, M. dos Reis, 2015, Current Biology.

Edwards and the Origin of Bayesian Phylogenetics

Ziheng Yang, 2015 .

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.

Z. Yang, Ziheng Yang, M. Anisimova, 2001, Molecular biology and evolution.

Models of amino acid substitution and applications to mitochondrial protein evolution.

Z. Yang, R. Nielsen, M. Hasegawa, 1998, Molecular biology and evolution.

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.

N. Goldman, Z. Yang, Ziheng Yang, 1994, Molecular biology and evolution.

How often do wrong models produce better phylogenies?

Z. Yang, Ziheng Yang, Z Yang, 1997, Molecular biology and evolution.

Neutral and adaptive protein evolution

Ziheng Yang, 2006 .

Proposed standard nomenclature for the α – and β-globin gene families

Ziheng Yang, J. Bielawski, G. Aguileta, 2006 .

Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations

Mark N. Puttick, James W. Clark, Ziheng Yang, 2018, Proceedings of the National Academy of Sciences.

Bayesian dating of shallow phylogenies with a relaxed clock.

Ziheng Yang, Richard P. Brown, 2010, Systematic biology.

A space-time process model for the evolution of DNA sequences.

Z. Yang, Ziheng Yang, 1995, Genetics.

The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites

Maria Anisimova, Joseph P. Bielawski, Ziheng Yang, 2001 .

Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.

Ziheng Yang, M. dos Reis, Mario dos Reis, 2011, Molecular biology and evolution.

AWF Edwards and the origin of Bayesian phylogenetics

Ziheng Yang, 2016 .

Bayesian inference in molecular phylogenetics

Ziheng Yang, Ziheng Yang, 2007, Mathematics of Evolution and Phylogeny.

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution

Ziheng Yang, H. Akashi, Tomotaka Matsumoto, 2015, Genetics.

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.

R. Nielsen, Ziheng Yang, 2008, Molecular biology and evolution.

Phylogenetic Analysis by Maximum Likelihood (PAML)

Ziheng Yang, 2002 .

Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees.

L. Excoffier, Z. Yang, Ziheng Yang, 1999, Molecular biology and evolution.

Molecular adaptation of alanine:glyoxylate aminotransferase targeting in primates.

M W Bruford, Z. Yang, Ziheng Yang, 2000, Molecular biology and evolution.

Dating species divergences using rocks and clocks

Ziheng Yang, P. Donoghue, 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results

Ziheng Yang, A. Yoder, Paul A Hohenlohe, 2022 .