Ziheng Yang, Professor - Publications

Affiliations: 
Dpt of Biology University College of London (UCL), London, England, United Kingdom 
Area:
Phylogenetics, Population genomics
Website:
http://abacus.gene.ucl.ac.uk/ziheng/ziheng.html

70 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Dos Reis M, Yang Z. Bayesian Molecular Clock Dating Using Genome-Scale Datasets. Methods in Molecular Biology (Clifton, N.J.). 1910: 309-330. PMID 31278669 DOI: 10.1007/978-1-4939-9074-0_10  1
2019 Halliday TJD, Dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z, Goswami A. Rapid morphological evolution in placental mammals post-dates the origin of the crown group. Proceedings. Biological Sciences. 286: 20182418. PMID 30836875 DOI: 10.1098/rspb.2018.2418  1
2019 Álvarez-Carretero S, Goswami A, Yang Z, Dos Reis M. Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters. Systematic Biology. PMID 30816937 DOI: 10.1093/sysbio/syz015  1
2018 Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ. Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations. Proceedings of the National Academy of Sciences of the United States of America. PMID 30266794 DOI: 10.1073/pnas.1812816115  0.64
2018 Thawornwattana Y, Dalquen D, Yang Z. Coalescent analysis of phylogenomic data confidently resolves the species relationships in the Anopheles gambiae species complex. Molecular Biology and Evolution. PMID 30102363 DOI: 10.1093/molbev/msy158  0.6
2018 Leaché AD, Zhu T, Rannala B, Yang Z. The Spectre of Too Many Species. Systematic Biology. PMID 29982825 DOI: 10.1093/sysbio/syy051  0.56
2018 Liu Z, Chen G, Zhu T, Zeng Z, Lyu Z, Wang J, Messenger K, Greenberg AJ, Guo Z, Yang Z, Shi S, Wang Y. Prevalence of cryptic species in morphologically uniform taxa - fast speciation and evolutionary radiation in Asian toads. Molecular Phylogenetics and Evolution. PMID 29920336 DOI: 10.1016/j.ympev.2018.06.020  0.56
2018 Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ. The timescale of early land plant evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 29463716 DOI: 10.1073/pnas.1719588115  0.64
2018 Yang Z, Zhu T. Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees. Proceedings of the National Academy of Sciences of the United States of America. PMID 29432193 DOI: 10.1073/pnas.1712673115  0.56
2018 Barba-Montoya J, Dos Reis M, Schneider H, Donoghue PCJ, Yang Z. Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. The New Phytologist. PMID 29399804 DOI: 10.1111/nph.15011  1
2018 Dos Reis M, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z, Yoder AD. Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. Systematic Biology. PMID 29342307 DOI: 10.1093/sysbio/syy001  1
2017 Angelis K, Álvarez-Carretero S, Dos Reis M, Yang Z. An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times. Systematic Biology. PMID 29029343 DOI: 10.1093/sysbio/syx061  1
2017 Nascimento FF, Dos Reis M, Yang Z. A biologist's guide to Bayesian phylogenetic analysis. Nature Ecology & Evolution. 1: 1446-1454. PMID 28983516 DOI: 10.1038/s41559-017-0280-x  1
2017 Barba-Montoya J, Dos Reis M, Yang Z. Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Molecular Phylogenetics and Evolution. PMID 28709986 DOI: 10.1016/j.ympev.2017.07.005  1
2017 Warnock RCM, Yang Z, Donoghue PCJ. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution. Proceedings. Biological Sciences. 284. PMID 28637852 DOI: 10.1098/rspb.2017.0227  0.64
2016 Dalquen D, Zhu T, Yang Z. Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species. Systematic Biology. PMID 27486180 DOI: 10.1093/sysbio/syw063  0.56
2015 Dos Reis M, Donoghue PC, Yang Z. Bayesian molecular clock dating of species divergences in the genomics era. Nature Reviews. Genetics. PMID 26688196 DOI: 10.1038/nrg.2015.8  0.44
2015 Dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PC, Yang Z. Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Current Biology : Cb. PMID 26603774 DOI: 10.1016/j.cub.2015.09.066  1
2015 Matsumoto T, Akashi H, Yang Z. Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution. Genetics. 200: 873-90. PMID 25948563 DOI: 10.1534/genetics.115.177386  1
2015 Zhu T, Dos Reis M, Yang Z. Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci. Systematic Biology. 64: 267-80. PMID 25503979 DOI: 10.1093/sysbio/syu109  1
2014 Angelis K, Dos Reis M, Yang Z. Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons Molecular Biology and Evolution. 31: 1902-1913. PMID 24748652 DOI: 10.1093/molbev/msu142  1
2014 Dos Reis M, Zhu T, Yang Z. The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci. Systematic Biology. 63: 555-65. PMID 24658316 DOI: 10.1093/sysbio/syu020  1
2014 dos Reis M, Donoghue PC, Yang Z. Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biology Letters. 10: 20131003. PMID 24429684 DOI: 10.1098/rsbl.2013.1003  1
2014 Yoder AD, Chan LM, dos Reis M, Larsen PA, Campbell CR, Rasoloarison R, Barrett M, Roos C, Kappeler P, Bielawski J, Yang Z. Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biology and Evolution. 6: 213-27. PMID 24398377 DOI: 10.1093/gbe/evu006  1
2014 Leaché AD, Harris RB, Rannala B, Yang Z. The influence of gene flow on species tree estimation: a simulation study. Systematic Biology. 63: 17-30. PMID 23945075 DOI: 10.1093/sysbio/syt049  1
2013 Xu B, Yang Z. PAMLX: a graphical user interface for PAML. Molecular Biology and Evolution. 30: 2723-4. PMID 24105918 DOI: 10.1093/molbev/mst179  1
2013 Dos Reis M, Yang Z. Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics. 195: 195-204. PMID 23792953 DOI: 10.1534/genetics.113.152025  1
2013 Stadler T, Yang Z. Dating phylogenies with sequentially sampled tips. Systematic Biology. 62: 674-88. PMID 23628961 DOI: 10.1093/sysbio/syt030  1
2013 Zou XH, Yang Z, Doyle JJ, Ge S. Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus. The New Phytologist. 198: 1155-64. PMID 23574344 DOI: 10.1111/nph.12230  1
2012 dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PC, Yang Z. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proceedings. Biological Sciences / the Royal Society. 279: 3491-500. PMID 22628470 DOI: 10.1098/rspb.2012.0683  1
2012 Zhu T, Yang Z. Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Molecular Biology and Evolution. 29: 3131-42. PMID 22504520 DOI: 10.1093/molbev/mss118  0.56
2012 Zhai W, Nielsen R, Goldman N, Yang Z. Looking for Darwin in genomic sequences--validity and success of statistical methods. Molecular Biology and Evolution. 29: 2889-93. PMID 22490825 DOI: 10.1093/molbev/mss104  1
2012 Parham JF, Donoghue PC, Bell CJ, Calway TD, Head JJ, Holroyd PA, Inoue JG, Irmis RB, Joyce WG, Ksepka DT, Patané JS, Smith ND, Tarver JE, van Tuinen M, Yang Z, et al. Best practices for justifying fossil calibrations. Systematic Biology. 61: 346-59. PMID 22105867 DOI: 10.1093/sysbio/syr107  1
2012 Rannala B, Zhu T, Yang Z. Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Molecular Biology and Evolution. 29: 325-35. PMID 21890479 DOI: 10.1093/molbev/msr210  0.56
2012 Warnock RC, Yang Z, Donoghue PC. Exploring uncertainty in the calibration of the molecular clock. Biology Letters. 8: 156-9. PMID 21865245 DOI: 10.1098/rsbl.2011.0710  1
2011 Brown RP, Yang Z. Rate variation and estimation of divergence times using strict and relaxed clocks. Bmc Evolutionary Biology. 11: 271. PMID 21943087 DOI: 10.1186/1471-2148-11-271  1
2011 Zhang C, Zhang DX, Zhu T, Yang Z. Evaluation of a bayesian coalescent method of species delimitation. Systematic Biology. 60: 747-61. PMID 21876212 DOI: 10.1093/sysbio/syr071  1
2011 Groussin M, Pawlowski J, Yang Z. Bayesian relaxed clock estimation of divergence times in foraminifera. Molecular Phylogenetics and Evolution. 61: 157-66. PMID 21723398 DOI: 10.1016/j.ympev.2011.06.008  1
2011 Yoshida I, Sugiura W, Shibata J, Ren F, Yang Z, Tanaka H. Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples. Plos One. 6: e18630. PMID 21526184 DOI: 10.1371/journal.pone.0018630  1
2011 dos Reis M, Yang Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Molecular Biology and Evolution. 28: 2161-72. PMID 21310946 DOI: 10.1093/molbev/msr045  1
2011 Zhu T, Hu Y, Ma ZM, Zhang DX, Li T, Yang Z. Efficient simulation under a population genetics model of carcinogenesis. Bioinformatics (Oxford, England). 27: 837-43. PMID 21247938 DOI: 10.1093/bioinformatics/btr025  1
2011 Yang Z, dos Reis M. Statistical properties of the branch-site test of positive selection. Molecular Biology and Evolution. 28: 1217-28. PMID 21087944 DOI: 10.1093/molbev/msq303  1
2011 Wilkinson RD, Steiper ME, Soligo C, Martin RD, Yang Z, Tavaré S. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Systematic Biology. 60: 16-31. PMID 21051775 DOI: 10.1093/sysbio/syq054  1
2010 Brown RP, Yang Z. Bayesian dating of shallow phylogenies with a relaxed clock. Systematic Biology. 59: 119-31. PMID 20525625 DOI: 10.1093/sysbio/syp082  1
2010 Inoue J, Donoghue PC, Yang Z. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Systematic Biology. 59: 74-89. PMID 20525621 DOI: 10.1093/sysbio/syp078  1
2009 Yang Z, Nielsen R, Goldman N. In defense of statistical methods for detecting positive selection. Proceedings of the National Academy of Sciences of the United States of America. 106: E95; author reply E9. PMID 19805241 DOI: 10.1073/pnas.0904550106  1
2009 Rota-Stabelli O, Yang Z, Telford MJ. MtZoa: A general mitochondrial amino acid substitutions model for animal evolutionary studies Molecular Phylogenetics and Evolution. 52: 268-272. PMID 19475713 DOI: 10.1016/j.ympev.2009.01.011  1
2008 Goldman N, Yang Z. Introduction. Statistical and computational challenges in molecular phylogenetics and evolution. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3889-92. PMID 18852095 DOI: 10.1098/rstb.2008.0182  1
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. The role of positive selection in determining the molecular cause of species differences in disease. Bmc Evolutionary Biology. 8: 273. PMID 18837980 DOI: 10.1186/1471-2148-8-273  1
2008 Emes RD, Yang Z. Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. Plos One. 3: e2295. PMID 18509460 DOI: 10.1371/journal.pone.0002295  1
2007 Zhou R, Zeng K, Wu W, Chen X, Yang Z, Shi S, Wu CI. Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Molecular Biology and Evolution. 24: 2746-54. PMID 17906000 DOI: 10.1093/molbev/msm209  1
2007 Anisimova M, Bielawski J, Dunn K, Yang Z. Phylogenomic analysis of natural selection pressure in Streptococcus genomes. Bmc Evolutionary Biology. 7: 154. PMID 17760998 DOI: 10.1186/1471-2148-7-154  1
2007 Hurley IA, Mueller RL, Dunn KA, Schmidt EJ, Friedman M, Ho RK, Prince VE, Yang Z, Thomas MG, Coates MI. A new time-scale for ray-finned fish evolution. Proceedings. Biological Sciences / the Royal Society. 274: 489-98. PMID 17476768 DOI: 10.1098/rspb.2006.3749  1
2006 Aguileta G, Bielawski JP, Yang Z. Proposed standard nomenclature for the alpha- and beta-globin gene families. Genes & Genetic Systems. 81: 367-71. PMID 17159299 DOI: JST.JSTAGE/ggs/81.367  1
2006 Aguileta G, Bielawski JP, Yang Z. Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events. Gene. 380: 21-9. PMID 16843621 DOI: 10.1016/j.gene.2006.04.019  1
2005 Zhang J, Nielsen R, Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution. 22: 2472-9. PMID 16107592 DOI: 10.1093/molbev/msi237  1
2004 Wong WS, Yang Z, Goldman N, Nielsen R. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics. 168: 1041-51. PMID 15514074 DOI: 10.1534/genetics.104.031153  1
2004 Aguileta G, Bielawski JP, Yang Z. Gene conversion and functional divergence in the beta-globin gene family. Journal of Molecular Evolution. 59: 177-89. PMID 15486692 DOI: 10.1007/s00239-004-2612-0  1
2004 Bielawski JP, Yang Z. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of Molecular Evolution. 59: 121-32. PMID 15383915 DOI: 10.1007/s00239-004-2597-8  1
2004 Yoder AD, Yang Z. Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Molecular Ecology. 13: 757-73. PMID 15012754  0.44
2004 Schein M, Yang Z, Mitchell-Olds T, Schmid KJ. Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. Molecular Biology and Evolution. 21: 659-69. PMID 14739246 DOI: 10.1093/molbev/msh059  1
2003 Yang Z, Ro S, Rannala B. Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics. 165: 695-705. PMID 14573481  1
2003 Yang W, Bielawski JP, Yang Z. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. Journal of Molecular Evolution. 57: 212-21. PMID 14562964 DOI: 10.1007/s00239-003-2467-9  1
2003 Yang Z, Yoder AD. 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: 705-16. PMID 14530137  0.44
2003 Aris-Brosou S, Yang Z. Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. Molecular Biology and Evolution. 20: 1947-54. PMID 12949122 DOI: 10.1093/molbev/msg226  1
2003 Bielawski JP, Yang Z. Maximum likelihood methods for detecting adaptive evolution after gene duplication. Journal of Structural and Functional Genomics. 3: 201-12. PMID 12836699 DOI: 10.1023/A:1022642807731  1
2002 Aris-Brosou S, Yang Z. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Systematic Biology. 51: 703-14. PMID 12396585 DOI: 10.1080/10635150290102375  1
2002 Jiggins FM, Hurst GD, Yang Z. Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Molecular Biology and Evolution. 19: 1341-9. PMID 12140246  1
2002 Anisimova M, Bielawski JP, Yang Z. Accuracy and power of bayes prediction of amino acid sites under positive selection. Molecular Biology and Evolution. 19: 950-8. PMID 12032251  1
2002 Yang Z, Swanson WJ. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Molecular Biology and Evolution. 19: 49-57. PMID 11752189  1
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