Yang, Ziheng

PAML 4: Phylogenetic Analysis by Maximum Likelihood

Yang, Z. (2007) · Molecular Biology and Evolution

Genomics and Phylogenetic StudiesEvolution and Genetic Dynamics

Cited by 13,879

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods.

Yang, Z. (1994) · Journal of Molecular Evolution

Genomics and Phylogenetic StudiesRNA and protein synthesis mechanisms

Cited by 2,960

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

Yang, Z., Nielsen, R., Goldman, N., & Pedersen, A.-M. K. (2000) · Genetics

Evolution and Genetic DynamicsGenomics and Phylogenetic Studies

Cited by 2,286

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

Goldman, N., & Yang, Z. (1994) · Molecular Biology and Evolution

Genomics and Phylogenetic StudiesRNA and protein synthesis mechanisms

Cited by 1,960

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

Nielsen, R., & Yang, Z. (1998) · Genetics

Evolution and Genetic DynamicsGenomics and Phylogenetic Studies

Cited by 1,622

Bayesian species delimitation using multilocus sequence data

Yang, Z., & Rannala, B. (2010) · Proceedings of the National Academy of Sciences

Genetic diversity and population structureGenomics and Phylogenetic Studies

Cited by 1,405

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

Yang, Z., & Nielsen, R. (2002) · Molecular Biology and Evolution

Evolution and Genetic DynamicsGenomics and Phylogenetic Studies

Cited by 1,374

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

Yang, Z., & Rannala, B. (1997) · Molecular Biology and Evolution

Genomics and Phylogenetic StudiesGenetic diversity and population structure

Cited by 1,274

Estimating the pattern of nucleotide substitution

Yang, Z. (1994) · Journal of Molecular Evolution

Genomics and Phylogenetic StudiesRNA and protein synthesis mechanisms

Cited by 1,076

Best Practices for Justifying Fossil Calibrations

Parham, J. F., Donoghue, P. C. J., Bell, C. J., Calway, T. D., Head, J. J., Holroyd, P. A., Inoue, J. G., Irmis, R. B., Joyce, W. G., Ksepka, D. T., et al. (2012) · Systematic Biology

Evolution and Paleontology StudiesGenomics and Phylogenetic Studies

Cited by 780

Phylogenetic tree building in the genomic age

Kapli, P., Yang, Z., & Telford, M. J. (2020) · Nature Reviews Genetics

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 533

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

dos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., & Yang, Z. (2012) · Proceedings of the Royal Society B: Biological Sciences

Evolution and Paleontology StudiesGenomics and Phylogenetic Studies

Cited by 526

Estimation of primate speciation dates using local molecular clocks.

Yoder, A. D., & Yang, Z. (2000) · Molecular Biology and Evolution

Evolution and Paleontology StudiesGenomics and Phylogenetic Studies

Cited by 494

Inferring speciation times under an episodic molecular clock

Rannala, B., & Yang, Z. (2007) · Systematic Biology

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 475

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

dos Reis, M., Thawornwattana, Y., Angelis, K., Telford, M. J., Donoghue, P. C. J., & Yang, Z. (2015) · Current Biology

Evolution and Paleontology StudiesMarine Invertebrate Physiology and Ecology

Cited by 471

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

Yang, Z., & Yoder, A. D. (2003) · Systematic Biology

Evolution and Paleontology StudiesGenomics and Phylogenetic Studies

Cited by 357

Bayesian molecular clock dating of species divergences in the genomics era

dos Reis, M., Donoghue, P. C. J., & Yang, Z. (2016) · Nature Reviews Genetics

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 339

Exploring uncertainty in the calibration of the molecular clock

Warnock, R. C. M., Yang, Z., & Donoghue, P. C. J. (2012) · Biology Letters

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 238

Effects of Models of Rate Evolution on Estimation of Divergence Dates with Special Reference to the Metazoan 18S Ribosomal RNA Phylogeny

Aris-Brosou, S., & Yang, Z. (2002) · Systematic Biology

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 230

Branch-length prior influences Bayesian posterior probability of phylogeny.

Yang, Z., & Rannala, B. (2005) · Systematic Biology

Genomics and Phylogenetic StudiesGenetic diversity and population structure

Cited by 228

Dating primate divergences through an integrated analysis of palaeontological and molecular data

Wilkinson, R. D., Steiper, M. E., Soligo, C., Martin, R. D., Yang, Z., & Tavaré, S. (2011) · Systematic Biology

Evolution and Paleontology StudiesGenetic diversity and population structure

Cited by 218

Multiple Hypothesis Testing to Detect Lineages under Positive Selection that Affects Only a Few Sites

Anisimova, M., & Yang, Z. (2007) · Molecular Biology and Evolution

Genomics and Phylogenetic StudiesEvolution and Genetic Dynamics

Cited by 213

A biologist’s guide to Bayesian phylogenetic analysis

Nascimento, F. F., Reis, M. D., & Yang, Z. (2017) · Nature Ecology & Evolution

Genomics and Phylogenetic StudiesGenetic diversity and population structure

Cited by 212

The unbearable uncertainty of Bayesian divergence time estimation

DOS REIS, M., & YANG, Z. (2013) · Journal of Systematics and Evolution

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 140