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

173 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
2022 Poelstra JW, Montero BK, Lüdemann J, Yang Z, Rakotondranary SJ, Hohenlohe P, Stetter N, Ganzhorn JU, Yoder AD. RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results. Proceedings. Biological Sciences. 289: 20220596. PMID 35946151 DOI: 10.1098/rspb.2022.0596  0.371
2022 Flouri T, Huang J, Jiao X, Kapli P, Rannala B, Yang Z. Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent. Molecular Biology and Evolution. 39. PMID 35907248 DOI: 10.1093/molbev/msac161  0.46
2022 Yang Z, Flouri T. Estimation of Cross-Species Introgression Rates using Genomic Data Despite Model Unidentifiability. Molecular Biology and Evolution. PMID 35417543 DOI: 10.1093/molbev/msac083  0.385
2022 Zhu T, Flouri T, Yang Z. A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model. Molecular Ecology. PMID 35313033 DOI: 10.1111/mec.16433  0.457
2022 Thawornwattana Y, Seixas FA, Yang Z, Mallet J. Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies. Systematic Biology. PMID 35169847 DOI: 10.1093/sysbio/syac009  0.391
2021 Jiao X, Flouri T, Yang Z. Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow. National Science Review. 8: nwab127. PMID 34987842 DOI: 10.1093/nsr/nwab127  0.378
2021 Álvarez-Carretero S, Tamuri AU, Battini M, Nascimento FF, Carlisle E, Asher RJ, Yang Z, Donoghue PCJ, Dos Reis M. A Species-Level Timeline of Mammal Evolution Integrating Phylogenomic Data. Nature. PMID 34937052 DOI: 10.1038/s41586-021-04341-1  0.809
2021 Finger N, Farleigh K, Bracken JT, Leaché AD, François O, Yang Z, Flouri T, Charran T, Jezkova T, Williams DA, Blair C. Genome-scale data reveal deep lineage divergence and a complex demographic history in the Texas horned lizard (Phrynosoma cornutum) throughout the southwestern and central US. Genome Biology and Evolution. PMID 34849831 DOI: 10.1093/gbe/evab260  0.32
2021 Huang J, Bennett J, Flouri T, Leaché AD, Yang Z. Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model. Systematic Biology. PMID 34143216 DOI: 10.1093/sysbio/syab047  0.308
2021 Zhu T, Yang Z. Complexity of the simplest species tree problem. Molecular Biology and Evolution. PMID 33492385 DOI: 10.1093/molbev/msab009  0.419
2020 Huang J, Liu Y, Zhu T, Yang Z. The asymptotic behavior of bootstrap support values in molecular phylogenetics. Systematic Biology. PMID 33377913 DOI: 10.1093/sysbio/syaa100  0.387
2020 Tiley GP, Poelstra JW, Dos Reis M, Yang Z, Yoder AD. Molecular Clocks without Rocks: New Solutions for Old Problems. Trends in Genetics : Tig. PMID 32709458 DOI: 10.1016/J.Tig.2020.06.002  0.689
2020 Huang J, Flouri T, Yang Z. A simulation study to examine the information content in phylogenomic datasets under the multispecies coalescent model. Molecular Biology and Evolution. PMID 32642765 DOI: 10.1093/Molbev/Msaa166  0.535
2020 Jiao X, Yang Z. Defining Species When There is Gene Flow. Systematic Biology. PMID 32617579 DOI: 10.1093/Sysbio/Syaa052  0.438
2020 Kapli P, Yang Z, Telford MJ. Phylogenetic tree building in the genomic age. Nature Reviews. Genetics. PMID 32424311 DOI: 10.1038/S41576-020-0233-0  0.498
2020 Weber CC, Perron U, Casey D, Yang Z, Goldman N. Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space. Systematic Biology. PMID 32353118 DOI: 10.1093/Sysbio/Syaa036  0.61
2020 Jiao X, Flouris T, Rannala B, Yang Z. The Impact of Cross-Species Gene Flow on Species Tree Estimation. Systematic Biology. PMID 31977022 DOI: 10.1093/Sysbio/Syaa001  0.486
2020 Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends in Ecology & Evolution. 15: 496-503. PMID 11114436 DOI: 10.1016/S0169-5347(00)01994-7  0.398
2019 Flouris T, Jiao X, Rannala B, Yang Z. A Bayesian implementation of the multispecies coalescent model with introgression for phylogenomic analysis. Molecular Biology and Evolution. PMID 31825513 DOI: 10.1093/Molbev/Msz296  0.55
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  0.691
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  0.668
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  0.818
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  0.6
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  0.481
2018 Flouri T, Jiao X, Rannala B, Yang Z. Species Tree Inference with bpp Using Genomic Sequences and the Multispecies Coalescent. Molecular Biology and Evolution. PMID 30053098 DOI: 10.1093/Molbev/Msy147  0.489
2018 Leaché AD, Zhu T, Rannala B, Yang Z. The Spectre of Too Many Species. Systematic Biology. PMID 29982825 DOI: 10.1093/Sysbio/Syy051  0.516
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  0.446
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  0.614
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  0.402
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  0.759
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  0.57
2017 Shi CM, Yang Z. Coalescent-based analyses of genomic sequence data provide a robust resolution of phylogenetic relationships among major groups of gibbons. Molecular Biology and Evolution. PMID 29087487 DOI: 10.1093/Molbev/Msx277  0.532
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  0.831
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  0.437
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  0.658
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  0.835
2017 Yang Z, Rannala B. Bayesian Species Identification under the Multispecies Coalescent Provides Significant Improvements to DNA Barcoding Analyses. Molecular Ecology. PMID 28281309 DOI: 10.1111/Mec.14093  0.446
2017 Rannala B, Yang Z. Efficient Bayesian species tree inference under the multispecies coalescent. Systematic Biology. PMID 28053140 DOI: 10.1093/Sysbio/Syw119  0.48
2016 Xu B, Yang Z. Challenges in Species Tree Estimation Under the Multispecies Coalescent Model. Genetics. 204: 1353-1368. PMID 27927902 DOI: 10.1534/Genetics.116.190173  0.541
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  0.528
2016 Donoghue PC, Yang Z. The evolution of methods for establishing evolutionary timescales. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 371. PMID 27325838 DOI: 10.1098/Rstb.2016.0020  0.674
2016 Yang Z, Donoghue PC. Dating species divergences using rocks and clocks. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 371. PMID 27325825 DOI: 10.1098/Rstb.2015.0126  0.682
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  0.77
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  0.759
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  0.51
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  0.747
2015 Liu J, Zhang DX, Yang Z. A discrete-beta model for testing gene flow after speciation Methods in Ecology and Evolution. 6: 715-724. DOI: 10.1111/2041-210X.12356  0.464
2015 Yang Z. The BPP program for species tree estimation and species delimitation Current Zoology. 61: 854-865. DOI: 10.1093/Czoolo/61.5.854  0.445
2014 Yang Z, Rannala B. Unguided species delimitation using DNA sequence data from multiple Loci. Molecular Biology and Evolution. 31: 3125-35. PMID 25274273 DOI: 10.1093/Molbev/Msu279  0.469
2014 Zhang C, Rannala B, Yang Z. Bayesian species delimitation can be robust to guide-tree inference errors. Systematic Biology. 63: 993-1004. PMID 25096853 DOI: 10.1093/Sysbio/Syu052  0.483
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  0.69
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  0.717
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  0.684
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  0.633
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  0.478
2013 Yang Z, Rodríguez CE. Searching for efficient Markov chain Monte Carlo proposal kernels. Proceedings of the National Academy of Sciences of the United States of America. 110: 19307-12. PMID 24218600 DOI: 10.1073/Pnas.1311790110  0.309
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  0.679
2013 Stadler T, Yang Z. Dating phylogenies with sequentially sampled tips. Systematic Biology. 62: 674-88. PMID 23628961 DOI: 10.1093/Sysbio/Syt030  0.541
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  0.505
2013 Rannala B, Yang Z. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 194: 245-53. PMID 23502678 DOI: 10.1534/Genetics.112.149039  0.421
2013 Dos Reis M, Yang Z. The unbearable uncertainty of Bayesian divergence time estimation Journal of Systematics and Evolution. 51: 30-43. DOI: 10.1111/J.1759-6831.2012.00236.X  0.711
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  0.766
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  0.49
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  0.603
2012 Yang Z, Rannala B. Molecular phylogenetics: principles and practice. Nature Reviews. Genetics. 13: 303-14. PMID 22456349 DOI: 10.1038/Nrg3186  0.459
2012 Zhang C, Rannala B, Yang Z. Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Systematic Biology. 61: 779-84. PMID 22328570 DOI: 10.1093/Sysbio/Sys030  0.406
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  0.804
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  0.432
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  0.802
2012 Yang Z, Goldman N. Are big trees indeed easy? Trends in Ecology & Evolution. 12: 357. PMID 21238103 DOI: 10.1016/S0169-5347(97)83196-5  0.518
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  0.513
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  0.487
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  0.813
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  0.304
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  0.712
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  0.604
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  0.525
2011 ZANG L, ZOU X, ZHANG F, YANG Z, GE S. Phylogeny and species delimitation of the C-genome diploid species in Oryza Journal of Systematics and Evolution. 49: 386-395. DOI: 10.1111/J.1759-6831.2011.00145.X  0.403
2010 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, ... ... Yang Z, et al. In defence of model-based inference in phylogeography. Molecular Ecology. 19: 436-446. PMID 29284924 DOI: 10.1111/J.1365-294X.2009.04515.X  0.413
2010 Yang Z. A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biology and Evolution. 2: 200-11. PMID 20624726 DOI: 10.1093/Gbe/Evq011  0.46
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  0.512
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  0.706
2010 Fletcher W, Yang Z. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Molecular Biology and Evolution. 27: 2257-67. PMID 20447933 DOI: 10.1093/Molbev/Msq115  0.351
2010 Yang Z, Rannala B. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences of the United States of America. 107: 9264-9. PMID 20439743 DOI: 10.1073/Pnas.0913022107  0.492
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  0.569
2009 Fletcher W, Yang Z. INDELible: a flexible simulator of biological sequence evolution. Molecular Biology and Evolution. 26: 1879-88. PMID 19423664 DOI: 10.1093/Molbev/Msp098  0.443
2009 Ren F, Tanaka H, Yang Z. A likelihood look at the supermatrix-supertree controversy. Gene. 441: 119-25. PMID 18502054 DOI: 10.1016/J.Gene.2008.04.002  0.486
2008 Schmid K, Yang Z. The trouble with sliding windows and the selective pressure in BRCA1. Plos One. 3: e3746. PMID 19015730 DOI: 10.1371/Journal.Pone.0003746  0.364
2008 Yang Z. Empirical evaluation of a prior for Bayesian phylogenetic inference. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 4031-9. PMID 18852106 DOI: 10.1098/Rstb.2008.0164  0.465
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  0.567
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  0.384
2008 Rannala B, Yang Z. Phylogenetic inference using whole genomes. Annual Review of Genomics and Human Genetics. 9: 217-31. PMID 18767964 DOI: 10.1146/Annurev.Genom.9.081307.164407  0.482
2008 Burgess R, Yang Z. Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution. 25: 1979-94. PMID 18603620 DOI: 10.1093/Molbev/Msn148  0.467
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  0.338
2008 Furlong RF, Yang Z. Diversifying and purifying selection in the peptide binding region of DRB in mammals. Journal of Molecular Evolution. 66: 384-94. PMID 18347751 DOI: 10.1007/S00239-008-9092-6  0.39
2008 Yang Z, Nielsen R. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Molecular Biology and Evolution. 25: 568-79. PMID 18178545 DOI: 10.1093/Molbev/Msm284  0.415
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  0.401
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  0.329
2007 Rannala B, Yang Z. Inferring speciation times under an episodic molecular clock. Systematic Biology. 56: 453-66. PMID 17558967 DOI: 10.1080/10635150701420643  0.581
2007 Yang Z. Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics. Molecular Biology and Evolution. 24: 1639-55. PMID 17488737 DOI: 10.1093/Molbev/Msm081  0.428
2007 Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution. 24: 1586-91. PMID 17483113 DOI: 10.1093/Molbev/Msm088  0.507
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  0.499
2007 Anisimova M, Yang Z. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Molecular Biology and Evolution. 24: 1219-28. PMID 17339634 DOI: 10.1093/Molbev/Msm042  0.396
2006 Yang Z. On the varied pattern of evolution of 2 fungal genomes: a critique of Hughes and Friedman. Molecular Biology and Evolution. 23: 2279-82. PMID 16982818 DOI: 10.1093/Molbev/Msl122  0.392
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  0.433
2006 Yang Z, Rannala B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution. 23: 212-26. PMID 16177230 DOI: 10.1093/Molbev/Msj024  0.556
2005 Ren F, Tanaka H, Yang Z. An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Systematic Biology. 54: 808-18. PMID 16243764 DOI: 10.1080/10635150500354688  0.486
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  0.368
2005 Yang Z, Rannala B. Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology. 54: 455-70. PMID 16012111 DOI: 10.1080/10635150590945313  0.54
2005 Sainudiin R, Wong WS, Yogeeswaran K, Nasrallah JB, Yang Z, Nielsen R. 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: 315-26. PMID 15871042 DOI: 10.1007/S00239-004-0153-1  0.331
2005 Yang Z. The power of phylogenetic comparison in revealing protein function. Proceedings of the National Academy of Sciences of the United States of America. 102: 3179-80. PMID 15728394 DOI: 10.1073/Pnas.0500371102  0.428
2005 Yang Z, Wong WS, Nielsen R. Bayes empirical bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution. 22: 1107-18. PMID 15689528 DOI: 10.1093/Molbev/Msi097  0.455
2004 Anisimova M, Yang Z. Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection? Journal of Molecular Evolution. 59: 815-26. PMID 15599513 DOI: 10.1007/S00239-004-0112-X  0.371
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  0.583
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  0.363
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  0.387
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 DOI: 10.1046/J.1365-294X.2004.02106.X  0.493
2004 Yang J, Gu H, Yang Z. Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea). Journal of Molecular Evolution. 58: 54-63. PMID 14743314 DOI: 10.1007/S00239-003-2525-3  0.324
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  0.436
2004 Yang Z. Probability models for DNA sequence evolution Heredity. 92: 474-474. DOI: 10.1038/Sj.Hdy.6800419  0.32
2003 Furlong RF, Yang Z. Comparative genomics coming of age. Heredity. 91: 533-4. PMID 14571261 DOI: 10.1038/Sj.Hdy.6800372  0.449
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  0.35
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 DOI: 10.1080/10635150390235557  0.582
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  0.778
2003 Rannala B, Yang Z. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 164: 1645-56. PMID 12930768  0.447
2003 Anisimova M, Nielsen R, Yang Z. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics. 164: 1229-36. PMID 12871927  0.31
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: 10.1007/978-94-010-0263-9_20  0.393
2003 Nielsen R, Yang Z. Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Molecular Biology and Evolution. 20: 1231-9. PMID 12777508 DOI: 10.1093/Molbev/Msg147  0.429
2003 Hasegawa M, Cao Y, Yang Z. Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species. Molecular Biology and Evolution. 15: 1499-505. PMID 12572613 DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A025877  0.371
2003 Yang Z. Phylogenetics as applied mathematics Trends in Ecology & Evolution. 18: 558-559. DOI: 10.1016/S0169-5347(03)00194-0  0.529
2002 Yang Z. Inference of selection from multiple species alignments. Current Opinion in Genetics & Development. 12: 688-94. PMID 12433583 DOI: 10.1016/S0959-437X(02)00348-9  0.432
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  0.761
2002 Yang J, Huang J, Gu H, Zhong Y, Yang Z. Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). Molecular Biology and Evolution. 19: 1752-9. PMID 12270901 DOI: 10.1093/Oxfordjournals.Molbev.A003997  0.308
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 DOI: 10.1093/Oxfordjournals.Molbev.A004195  0.322
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 DOI: 10.1093/Oxfordjournals.Molbev.A004152  0.389
2002 Yang Z, Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution. 19: 908-17. PMID 12032247 DOI: 10.1093/Oxfordjournals.Molbev.A004148  0.427
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 DOI: 10.1093/Oxfordjournals.Molbev.A003981  0.364
2001 Anisimova M, Bielawski JP, Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution Molecular Biology and Evolution. 18: 1585-1592. PMID 11470850 DOI: 10.1093/Oxfordjournals.Molbev.A003945  0.383
2001 Bielawski JP, Yang Z. Positive and negative selection in the DAZ gene family Molecular Biology and Evolution. 18: 523-529. PMID 11264403 DOI: 10.1093/Oxfordjournals.Molbev.A003831  0.364
2000 Thomas MG, Hagelberg E, Jone HB, Yang Z, Lister AM. Molecular and morphological evidence on the phylogeny of the Elephantidae. Proceedings. Biological Sciences / the Royal Society. 267: 2493-500. PMID 11197124 DOI: 10.1098/Rspb.2000.1310  0.468
2000 Yang Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A Journal of Molecular Evolution. 51: 423-432. PMID 11080365 DOI: 10.1007/S002390010105  0.506
2000 Yang Z, Swanson WJ, Vacquier VD. Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. Molecular Biology and Evolution. 17: 1446-55. PMID 11018152 DOI: 10.1093/Oxfordjournals.Molbev.A026245  0.426
2000 Yoder AD, Yang Z. Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution. 17: 1081-90. PMID 10889221 DOI: 10.1093/Oxfordjournals.Molbev.A026389  0.564
2000 Holbrook JD, Birdsey GM, Yang Z, Bruford MW, Danpure CJ. Molecular adaptation of alanine:glyoxylate aminotransferase targeting in primates. Molecular Biology and Evolution. 17: 387-400. PMID 10723739 DOI: 10.1093/Oxfordjournals.Molbev.A026318  0.351
2000 Yang Z. Complexity of the simplest phylogenetic estimation problem. Proceedings. Biological Sciences. 267: 109-16. PMID 10687814 DOI: 10.1098/Rspb.2000.0974  0.475
2000 Yang Z, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution. 17: 32-43. PMID 10666704 DOI: 10.1093/Oxfordjournals.Molbev.A026236  0.493
1999 Excoffier L, Yang Z. Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees. Molecular Biology and Evolution. 16: 1357-68. PMID 10563016 DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A026046  0.417
1999 Yang Z, Yoder AD. Estimation of the transition/transversion rate bias and species sampling. Journal of Molecular Evolution. 48: 274-83. PMID 10093216 DOI: 10.1007/Pl00006470  0.545
1999 Yang Z, Nielsen R, Hasegawa M. Models of amino acid substitution and applications to mitochondrial protein evolution. Molecular Biology and Evolution. 15: 1600-11. PMID 9866196 DOI: 10.1093/Oxfordjournals.Molbev.A025888  0.373
1998 Yang Z. On the Best Evolutionary Rate for Phylogenetic Analysis Systematic Biology. 47: 125-133. PMID 12064232 DOI: 10.1080/106351598261067  0.51
1998 Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution. 15: 568-73. PMID 9580986 DOI: 10.1093/Oxfordjournals.Molbev.A025957  0.476
1998 Yang Z, Nielsen R. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. Journal of Molecular Evolution. 46: 409-18. PMID 9541535 DOI: 10.1007/Pl00006320  0.517
1997 Huelsenbeck JP, Rannala B, Yang Z. STATISTICAL TESTS OF HOST-PARASITE COSPECIATION. Evolution; International Journal of Organic Evolution. 51: 410-419. PMID 28565354 DOI: 10.1111/J.1558-5646.1997.Tb02428.X  0.468
1997 Yang Z. On the estimation of ancestral population sizes of modern humans Genetical Research. 69: 111-116. PMID 10191720 DOI: 10.1017/S001667239700270X  0.478
1997 Yang Z. PAML: A program package for phylogenetic analysis by maximum likelihood Computer Applications in the Biosciences. 13: 555-556. PMID 9367129 DOI: 10.1093/Bioinformatics/13.5.555  0.494
1997 Yang Z, Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. Molecular Biology and Evolution. 14: 717-24. PMID 9214744 DOI: 10.1093/Oxfordjournals.Molbev.A025811  0.488
1997 Yang Z. How often do wrong models produce better phylogenies? Molecular Biology and Evolution. 14: 105-108. PMID 9000758 DOI: 10.1093/Oxfordjournals.Molbev.A025695  0.49
1997 Rannala B, Yang Z. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution. 43: 304-11. PMID 8703097 DOI: 10.1007/Bf02338839  0.563
1996 Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution. 11: 367-372. PMID 21237881 DOI: 10.1016/0169-5347(96)10041-0  0.414
1996 Yang Z. Phylogenetic analysis using parsimony and likelihood methods Journal of Molecular Evolution. 42: 294-307. PMID 8919881 DOI: 10.1007/Bf02198856  0.559
1996 Yang Z, Kumar S. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Molecular Biology and Evolution. 13: 650-9. PMID 8676739 DOI: 10.1093/Oxfordjournals.Molbev.A025625  0.497
1996 Yang Z. Maximum-likelihood models for combined analyses of multiple sequence data Journal of Molecular Evolution. 42: 587-596. DOI: 10.1007/Bf02352289  0.553
1995 Yang Z, Roberts D. On the use of nucleic acid sequences to infer early branchings in the tree of life. Molecular Biology and Evolution. 12: 451-8. PMID 7739387 DOI: 10.1093/Oxfordjournals.Molbev.A040220  0.513
1995 Yang Z, Lauder IJ, Lin HJ. Molecular evolution of the hepatitis B virus genome Journal of Molecular Evolution. 41: 587-596. PMID 7490773 DOI: 10.1007/Bf00175817  0.426
1995 Yang Z, Wang T. Mixed Model Analysis of DNA Sequence Evolution Biometrics. 51: 552. DOI: 10.2307/2532943  0.429
1995 Yang Z, Goldman N, Friday A. Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem Systematic Biology. 44: 384-399. DOI: 10.1093/Sysbio/44.3.384  0.791
1995 Yang Z. Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites Journal of Molecular Evolution. 40: 689-697. DOI: 10.1007/Bf00160518  0.51
1994 Yang Z, Goldman N, Friday A. Comparison of models for nucleotide substitution used in maximum- likelihood phylogenetic estimation Molecular Biology and Evolution. 11: 316-324. PMID 8170371 DOI: 10.1093/Oxfordjournals.Molbev.A040112  0.823
1994 Yang Z. Estimating the pattern of nucleotide substitution Journal of Molecular Evolution. 39: 105-111. PMID 8064867 DOI: 10.1007/Bf00178256  0.528
1994 Goldman N, Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences Molecular Biology and Evolution. 11: 725-736. PMID 7968486 DOI: 10.1093/Oxfordjournals.Molbev.A040153  0.628
1994 Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods Journal of Molecular Evolution. 39: 306-314. PMID 7932792 DOI: 10.1007/Bf00160154  0.466
1994 Yang Z. Statistical Properties of the Maximum Likelihood Method of Phylogenetic Estimation and Comparison With Distance Matrix Methods Systematic Biology. 43: 329-342. DOI: 10.1093/Sysbio/43.3.329  0.501
1993 Yang Z. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites Molecular Biology and Evolution. 10: 1396-1401. PMID 8277861 DOI: 10.1093/Oxfordjournals.Molbev.A040082  0.458
Show low-probability matches.