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Ziheng Yang

January 01, 1970

The native form of this personal name is Yang Ziheng. This article uses Western name order when mentioning individuals.

Ziheng Yang FRS (Chinese: 杨子恒; born 1 November 1964) is a Chinese biologist. He holds the R.A. Fisher Chair of Statistical Genetics[1] at University College London,[2] and is the Director of R.A. Fisher Centre for Computational Biology at UCL. He was elected a Fellow of the Royal Society in 2006.[2]

Ziheng Yang
Born1 November 1964 (1964-11) (age 59)
Gansu, China
CitizenshipUnited Kingdom
Alma materBeijing Agricultural University
Known forModels of DNA sequence evolution and methods of statistical inference in molecular evolution and phylogenetics
AwardsDarwin–Wallace Medal (2023)
Frink Medal (2010)
Royal Society Wolfson Research Merit Award (2009)

SSB Presidents' Award for Lifetime Achievement (2008)

Fellow of the Royal Society (2006)
Young Investigator’s Prize, American Society of Naturalists (1995)
Scientific career
Fieldsmolecular evolution
molecular phylogenetics
population genetics
computational biology
computational statistics
Markov chain Monte Carlo
InstitutionsUniversity College London
Beijing Agricultural University
Websiteabacus.gene.ucl.ac.uk

Academic career edit

Yang graduated from Gansu Agricultural University with a BSc in 1984, and from Beijing Agricultural University with a MSc in 1987, and PhD in 1992.[3]

After the PhD, he worked as a postdoctoral researcher in Department of Zoology, University of Cambridge (1992–3), The Natural History Museum (London) (1993–4), Pennsylvania State University (1994–5), and University of California at Berkeley (1995–7), before taking up a faculty position in Department of Biology, University College London. He was a Lecturer (1997), Reader (2000), and then Professor (2001) in the same department. He was appointed to the R.A. Fisher Chair in Statistical Genetics in UCL in 2010.

Yang held a number of visiting appointments. He was a Visiting Associate Professor at Institute of Statistical Mathematics (Tokyo, 1997–8), a Visiting Professor at University of Tokyo (2007–8), Institute of Zoology in Beijing (2010–1), Peking University (2010), National Institute of Genetics, Mishima, Japan (2011), and Swiss Institute of Technology (ETH), Zurich (2011). In 2008–2011, he was the Changjiang Chair Professor at Sun Yat-sen University, with an award from the Ministry of Education of China. From 2016 to 2019, he was a Visiting Professor at National Institute of Genetics, Japan. In 2017–8, he was a Radcliffe Fellow at Harvard University's Radcliffe Institute for Advanced Study.[4]

Work in molecular evolution and phylogenetics edit

Yang developed a number of statistical models and methods in the 1990s, which have been implemented in maximum likelihood and Bayesian software programs for phylogenetic analysis of DNA and protein sequence data. Two decades ago, Felsenstein had described the pruning algorithm for calculating the likelihood on a phylogeny.[5][6] However, the assumed model of character change was simple and, for example, does not account for variable rates among sites in the sequence. By illustrating the power of statistical models to accommodate major features of the evolutionary process and to address important evolutionary questions using molecular sequence data, the models and methods Yang developed had a major impact on the cladistic-statistical controversy at the time and played a major role in the transformation of molecular phylogenetics.

Yang developed a maximum likelihood model of gamma-distributed evolutionary rate variation among sites in the sequence in 1993–4.[7][8] The models he developed for combined analysis of heterogeneous data [9][10] are later known as partition models and mixture models.

Together with Nick Goldman, Yang developed the codon model of nucleotide substitution in 1994.[11] This formed the basis for phylogenetic analysis of protein-coding genes to detect molecular adaptation or Darwinian evolution at the molecular level. A stream of papers followed this to extend the original model to accommodate variable selection pressures (measured by the dN/dS ratio) among evolutionary lineages or among sites in the protein sequence. The branch models allow different branches to have different dN/dS ratios among branches on the tree and can be used to test for positive selection affecting particular lineages.[12] The site models allow different selective pressures on different amino acids in the protein and can be used to test for positive selection affecting only a few amino acid sites.[13][14][15] And the branch-site models attempt to detect positive selection that affects only a few amino acid sites along pre-specific lineages.[16][15] A recent book reviews the recent developments in this area.[17]

Yang developed the statistical (empirical Bayes) method for reconstructing ancestral sequences in 1995.[18] Compared with the parsimony method of ancestral sequence reconstruction (that is, the Fitch–Hartigan algorithm),[19][20] this has the advantages of using branch-length information and of providing a probabilistic assessment of the reconstruction uncertainties.

Together with Bruce Rannala, Yang introduced Bayesian statistics into molecular phylogenetics in 1996.[21][22] The Bayesian is now one of the most popular statistical methodologies used in modeling and inference in molecular phylogenetics. Recent exciting developments in Bayesian phylogenetics are summarized in an edited book[23] and in chapter 8 of Yang's book.[24]

Yang and Rannala also developed the multispecies coalescent model,[25] which has emerged as the natural framework for comparative analysis of genomic sequence data from multiple species, incorporating the coalescent process in both modern species and extinct ancestors. The model has been used to estimate the species tree despite gene tree heterogeneity among genomic regions,[26][27][28] and to delimit/identify species.[29] Yang champions the Bayesian full-likelihood method of inference, using Markov chain Monte Carlo to average over gene trees (gene genealogies), accommodating phylogenetic uncertainties.[28]

Yang maintains the program package PAML (for Phylogenetic Analysis by Maximum Likelihood)[30] and the Bayesian Markov chain Monte Carlo program BPP (for Bayesian Phylogenetics and Phylogeography).[31]

Work in principles of statistical inference and computational statistics edit

Yang studied the star tree paradox, which is that Bayesian model selection produces spuriously high posterior probabilities for the binary trees if the data are simulated under the star tree.[32][33] A simpler case showing similar behaviours is the fair-coin paradox.[33] The work suggests that Bayesian model selection may produce unpleasant polarized behavior supporting one model with full force while rejecting the others, when the competing models are all misspecified and equally wrong.[34]

Yang has worked extensively on Markov chain Monte Carlo algorithms, deriving many Metropolis-Hastings algorithms in Bayesian phylogenetics.[35] A study examining the efficiency of simple MCMC proposals revealed that the well-studied Gaussian random-walk move is less efficient than the simple uniform random-walk move, which is in turn less efficient than the Bactrian moves, bimodal moves that suppress values very close to the current state.[36]

Professional activities edit

Yang taught in Woods Hole Workshop on Molecular Evolution.

He was a co-organizer of the Royal Society Discussion Meeting on "Statistical and computational challenges in molecular phylogenetics and evolution" on 28–29 April 2008,[37] and the Royal Society Discussion Meeting on "Dating species divergence using rocks and clocks", on 9–10 November 2015.[38]

Since 2009, he has been a co-organizer of an annual workshop on Computational Molecular Evolution (CoME), which has been running in Sanger/Hinxton in odd years and in Hiraklion, Crete in even years.[1]

He also organized and taught in a number of workshops in Beijing, China.

Awards and honours edit

2023, Darwin–Wallace Medal, Linnean Society of London[39]

2010, Frink Medal for British Zoologists, Zoological Society of London[40]

2009, Royal Society Wolfson Research Merit Award

2008, President's Award for Lifetime Achievement, Society for Systematic Biology [41]

2006, Fellow of the Royal Society, The Royal Society of London [2]

1995, Young Investigator’s Prize, American Society of Naturalists [3]

Books edit

  • Computational molecular evolution. Oxford University Press. 2006. ISBN 978-0-19-856702-8.
  • Molecular Evolution: A Statistical Approach. Oxford University Press. 2014. ISBN 978-0-19-960261-2.

References edit

  1. ^ "Genetics, Evolution and Environment". Ucl.ac.uk. Retrieved 2017-06-23.
  2. ^ a b ‘YANG, Prof. Ziheng’, Who's Who 2011, A & C Black, 2011; online edn, Oxford University Press, Dec 2010; online edn, Oct 2010 accessed 11 May 2011(subscription required)
  3. ^ "Iris View Profile". Iris.ucl.ac.uk. Retrieved 2017-06-23.
  4. ^ "Ziheng Yang | Radcliffe Institute for Advanced Study at Harvard University". www.radcliffe.harvard.edu. Retrieved 2017-12-01.
  5. ^ Felsenstein, Joe (1973). "Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters". Syst. Zool. 22 (3): 240–249. doi:10.2307/2412304. JSTOR 2412304.
  6. ^ Felsenstein, Joe (1981). "Evolutionary trees from DNA sequences: a maximum likelihood approach". J. Mol. Evol. 17 (6): 368–376. Bibcode:1981JMolE..17..368F. doi:10.1007/bf01734359. PMID 7288891. S2CID 8024924.
  7. ^ Yang, Ziheng (1993). "Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites". Mol. Biol. Evol. 10 (6): 1396–1401. doi:10.1093/oxfordjournals.molbev.a040082. PMID 8277861.
  8. ^ Yang, Z (1994). "Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods". J Mol Evol. 39 (3): 306–314. Bibcode:1994JMolE..39..306Y. CiteSeerX 10.1.1.305.951. doi:10.1007/bf00160154. PMID 7932792. S2CID 17911050.
  9. ^ Yang Z, Lauder IJ, Lin HJ (1995). "Molecular evolution of the hepatitis B virus genome". J. Mol. Evol. 41 (5): 587–596. Bibcode:1995JMolE..41..587Y. doi:10.1007/bf00175817. PMID 7490773. S2CID 9176917.
  10. ^ Yang Z. (1996). "Maximum-likelihood models for combined analyses of multiple sequence data". J. Mol. Evol. 42 (5): 587–596. Bibcode:1996JMolE..42..587Y. CiteSeerX 10.1.1.19.6773. doi:10.1007/bf02352289. PMID 8662011. S2CID 12660243.
  11. ^ Goldman N, Yang Z (1994). "A codon-based model of nucleotide substitution for protein-coding DNA sequences". Mol Biol Evol. 11 (5): 725–736. doi:10.1093/oxfordjournals.molbev.a040153. PMID 7968486.
  12. ^ Yang, Ziheng (1998). "Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution". Mol. Biol. Evol. 15 (5): 568–573. doi:10.1093/oxfordjournals.molbev.a025957. PMID 9580986.
  13. ^ Nielsen, R.; Yang, Z. (1998). "Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene". Genetics. 148 (3): 929–936. doi:10.1093/genetics/148.3.929. PMC 1460041. PMID 9539414.
  14. ^ Yang, Z.; Nielsen, R.; Goldman, N.; Pedersen, A.-M.K. (2000). "Codon-substitution models for heterogeneous selection pressure at amino acid sites". Genetics. 155 (1): 431–449. doi:10.1093/genetics/155.1.431. PMC 1461088. PMID 10790415.
  15. ^ a b Yang, Ziheng; Wong, Wendy S. W.; Nielsen, Rasmus (2005-04-01). "Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection". Molecular Biology and Evolution. 22 (4): 1107–1118. doi:10.1093/molbev/msi097. ISSN 0737-4038. PMID 15689528.
  16. ^ Yang, Z.; Nielsen, R. (2002). "Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages". Mol. Biol. Evol. 19 (6): 908–917. doi:10.1093/oxfordjournals.molbev.a004148. hdl:1813/32161. PMID 12032247.
  17. ^ Cannarozzi, Gina M.; Schneider, Adrian, eds. (2012). Codon evolution : mechanisms and models. Oxford: Oxford University Press. ISBN 9780199601165. OCLC 784949340.
  18. ^ Yang Z, Kumar S, Nei M (1995). "A new method of inference of ancestral nucleotide and amino acid sequences". Genetics. 141 (4): 1641–1650. doi:10.1093/genetics/141.4.1641. PMC 1206894. PMID 8601501.
  19. ^ Fitch, Walter M. (1971). "Toward defining the course of evolution: minimum change for a specific tree topology". Syst. Zool. 20 (4): 406–416. doi:10.2307/2412116. JSTOR 2412116.
  20. ^ Hartigan, J.A. (1973). "Minimum evolution fits to a given tree". Biometrics. 29 (1): 53–65. doi:10.2307/2529676. JSTOR 2529676.
  21. ^ Rannala B, Yang Z (1996). "Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference". J. Mol. Evol. 43 (3): 304–311. Bibcode:1996JMolE..43..304R. doi:10.1007/bf02338839. PMID 8703097. S2CID 8269826.
  22. ^ Yang Z, Rannala B (1997). "Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo Method". Mol. Biol. Evol. 14 (7): 717–724. doi:10.1093/oxfordjournals.molbev.a025811. PMID 9214744.
  23. ^ Chen, Ming-Hui; Kuo, Lynn; Lewis, Paul O., eds. (2014-05-27). Bayesian phylogenetics : methods, algorithms, and applications. Boca Raton: Chapman & Hall/CRC. ISBN 9781466500792. OCLC 881387408.
  24. ^ Ziheng, Yang (2014). Molecular evolution : a statistical approach (First ed.). Oxford: Oxford University Press. ISBN 9780199602605. OCLC 869346345.
  25. ^ Rannala B, Yang Z (2003). "Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci". Genetics. 164 (4): 1645–1656. doi:10.1093/genetics/164.4.1645. PMC 1462670. PMID 12930768.
  26. ^ Yang, Ziheng; Rannala, Bruce (2014-12-01). "Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci". Molecular Biology and Evolution. 31 (12): 3125–3135. doi:10.1093/molbev/msu279. ISSN 0737-4038. PMC 4245825. PMID 25274273.
  27. ^ Rannala, Bruce; Yang, Ziheng (2017-09-01). "Efficient Bayesian Species Tree Inference under the Multispecies Coalescent". Systematic Biology. 66 (5): 823–842. arXiv:1512.03843. doi:10.1093/sysbio/syw119. ISSN 1063-5157. PMC 8562347. PMID 28053140. S2CID 3554064.
  28. ^ a b Xu, Bo; Yang, Ziheng (2016-12-01). "Challenges in Species Tree Estimation Under the Multispecies Coalescent Model". Genetics. 204 (4): 1353–1368. doi:10.1534/genetics.116.190173. ISSN 0016-6731. PMC 5161269. PMID 27927902.
  29. ^ Yang, Ziheng; Rannala, Bruce (2010-05-18). "Bayesian species delimitation using multilocus sequence data". Proceedings of the National Academy of Sciences. 107 (20): 9264–9269. Bibcode:2010PNAS..107.9264Y. doi:10.1073/pnas.0913022107. ISSN 0027-8424. PMC 2889046. PMID 20439743.
  30. ^ Yang, Ziheng (2007). "PAML 4: Phylogenetic analysis by maximum likelihood". Mol. Biol. Evol. 24 (8): 1586–1591. doi:10.1093/molbev/msm088. PMID 17483113.
  31. ^ Yang, Ziheng (2015-10-01). "The BPP program for species tree estimation and species delimitation". Current Zoology. 61 (5): 854–865. doi:10.1093/czoolo/61.5.854. ISSN 1674-5507.
  32. ^ Yang, Ziheng; Rannala, Bruce; Lewis, Paul (2005-06-01). "Branch-Length Prior Influences Bayesian Posterior Probability of Phylogeny". Systematic Biology. 54 (3): 455–470. doi:10.1080/10635150590945313. ISSN 1063-5157. PMID 16012111.
  33. ^ a b Yang, Ziheng (2007-08-01). "Fair-Balance Paradox, Star-tree Paradox, and Bayesian Phylogenetics". Molecular Biology and Evolution. 24 (8): 1639–1655. doi:10.1093/molbev/msm081. ISSN 0737-4038. PMID 17488737.
  34. ^ Yang, Ziheng; Zhu, Tianqi (5 February 2018). "Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees". Proceedings of the National Academy of Sciences. 115 (8): 1854–1859. Bibcode:2018PNAS..115.1854Y. doi:10.1073/pnas.1712673115. PMC 5828583. PMID 29432193.
  35. ^ Ziheng, Yang (2014). Molecular evolution : a statistical approach (First ed.). Oxford: Oxford University Press. ISBN 9780199602612. OCLC 869346345.
  36. ^ Yang, Ziheng; Rodríguez, Carlos E. (2013-11-26). "Searching for efficient Markov chain Monte Carlo proposal kernels". Proceedings of the National Academy of Sciences. 110 (48): 19307–19312. Bibcode:2013PNAS..11019307Y. doi:10.1073/pnas.1311790110. ISSN 0027-8424. PMC 3845170. PMID 24218600.
  37. ^ "Statistical and computational challenges in molecular phylogenetics and evolution". Royal Society.
  38. ^ "Dating species divergences using rocks and clocks". Royal Society.
  39. ^ "The Darwin-Wallace Medal". Retrieved 2023-06-09.
  40. ^ "Winners of the ZSL Frink Medal for British Zoologists" (PDF). Static.zsl.org. Retrieved 2017-06-23.
  41. ^ "Society of Systematic Biologists (SSB)". Society of Systematic Biologists.

External links edit

  • Professor Ziheng Yang's group page at UCL
  • Computational Molecular Evolution, Oxford University Press
  • Molecular Evolution: A Statistical Approach, Oxford University Press
  • "Calibrating the molecular clock to date species divergences", Darwin China 200 Conference

January 01, 1970
ziheng, yang, native, form, this, personal, name, yang, ziheng, this, article, uses, western, name, order, when, mentioning, individuals, chinese, 杨子恒, born, november, 1964, chinese, biologist, holds, fisher, chair, statistical, genetics, university, college, . The native form of this personal name is Yang Ziheng This article uses Western name order when mentioning individuals Ziheng Yang FRS Chinese 杨子恒 born 1 November 1964 is a Chinese biologist He holds the R A Fisher Chair of Statistical Genetics 1 at University College London 2 and is the Director of R A Fisher Centre for Computational Biology at UCL He was elected a Fellow of the Royal Society in 2006 2 Ziheng YangBorn1 November 1964 1964 11 age 59 Gansu ChinaCitizenshipUnited KingdomAlma materBeijing Agricultural UniversityKnown forModels of DNA sequence evolution and methods of statistical inference in molecular evolution and phylogeneticsAwardsDarwin Wallace Medal 2023 Frink Medal 2010 Royal Society Wolfson Research Merit Award 2009 SSB Presidents Award for Lifetime Achievement 2008 Fellow of the Royal Society 2006 Young Investigator s Prize American Society of Naturalists 1995 Scientific careerFieldsmolecular evolution molecular phylogenetics population genetics computational biology computational statistics Markov chain Monte CarloInstitutionsUniversity College LondonBeijing Agricultural UniversityWebsiteabacus wbr gene wbr ucl wbr ac wbr uk Contents 1 Academic career 2 Work in molecular evolution and phylogenetics 3 Work in principles of statistical inference and computational statistics 4 Professional activities 5 Awards and honours 6 Books 7 References 8 External linksAcademic career editYang graduated from Gansu Agricultural University with a BSc in 1984 and from Beijing Agricultural University with a MSc in 1987 and PhD in 1992 3 After the PhD he worked as a postdoctoral researcher in Department of Zoology University of Cambridge 1992 3 The Natural History Museum London 1993 4 Pennsylvania State University 1994 5 and University of California at Berkeley 1995 7 before taking up a faculty position in Department of Biology University College London He was a Lecturer 1997 Reader 2000 and then Professor 2001 in the same department He was appointed to the R A Fisher Chair in Statistical Genetics in UCL in 2010 Yang held a number of visiting appointments He was a Visiting Associate Professor at Institute of Statistical Mathematics Tokyo 1997 8 a Visiting Professor at University of Tokyo 2007 8 Institute of Zoology in Beijing 2010 1 Peking University 2010 National Institute of Genetics Mishima Japan 2011 and Swiss Institute of Technology ETH Zurich 2011 In 2008 2011 he was the Changjiang Chair Professor at Sun Yat sen University with an award from the Ministry of Education of China From 2016 to 2019 he was a Visiting Professor at National Institute of Genetics Japan In 2017 8 he was a Radcliffe Fellow at Harvard University s Radcliffe Institute for Advanced Study 4 Work in molecular evolution and phylogenetics editYang developed a number of statistical models and methods in the 1990s which have been implemented in maximum likelihood and Bayesian software programs for phylogenetic analysis of DNA and protein sequence data Two decades ago Felsenstein had described the pruning algorithm for calculating the likelihood on a phylogeny 5 6 However the assumed model of character change was simple and for example does not account for variable rates among sites in the sequence By illustrating the power of statistical models to accommodate major features of the evolutionary process and to address important evolutionary questions using molecular sequence data the models and methods Yang developed had a major impact on the cladistic statistical controversy at the time and played a major role in the transformation of molecular phylogenetics Yang developed a maximum likelihood model of gamma distributed evolutionary rate variation among sites in the sequence in 1993 4 7 8 The models he developed for combined analysis of heterogeneous data 9 10 are later known as partition models and mixture models Together with Nick Goldman Yang developed the codon model of nucleotide substitution in 1994 11 This formed the basis for phylogenetic analysis of protein coding genes to detect molecular adaptation or Darwinian evolution at the molecular level A stream of papers followed this to extend the original model to accommodate variable selection pressures measured by the dN dS ratio among evolutionary lineages or among sites in the protein sequence The branch models allow different branches to have different dN dS ratios among branches on the tree and can be used to test for positive selection affecting particular lineages 12 The site models allow different selective pressures on different amino acids in the protein and can be used to test for positive selection affecting only a few amino acid sites 13 14 15 And the branch site models attempt to detect positive selection that affects only a few amino acid sites along pre specific lineages 16 15 A recent book reviews the recent developments in this area 17 Yang developed the statistical empirical Bayes method for reconstructing ancestral sequences in 1995 18 Compared with the parsimony method of ancestral sequence reconstruction that is the Fitch Hartigan algorithm 19 20 this has the advantages of using branch length information and of providing a probabilistic assessment of the reconstruction uncertainties Together with Bruce Rannala Yang introduced Bayesian statistics into molecular phylogenetics in 1996 21 22 The Bayesian is now one of the most popular statistical methodologies used in modeling and inference in molecular phylogenetics Recent exciting developments in Bayesian phylogenetics are summarized in an edited book 23 and in chapter 8 of Yang s book 24 Yang and Rannala also developed the multispecies coalescent model 25 which has emerged as the natural framework for comparative analysis of genomic sequence data from multiple species incorporating the coalescent process in both modern species and extinct ancestors The model has been used to estimate the species tree despite gene tree heterogeneity among genomic regions 26 27 28 and to delimit identify species 29 Yang champions the Bayesian full likelihood method of inference using Markov chain Monte Carlo to average over gene trees gene genealogies accommodating phylogenetic uncertainties 28 Yang maintains the program package PAML for Phylogenetic Analysis by Maximum Likelihood 30 and the Bayesian Markov chain Monte Carlo program BPP for Bayesian Phylogenetics and Phylogeography 31 Work in principles of statistical inference and computational statistics editYang studied the star tree paradox which is that Bayesian model selection produces spuriously high posterior probabilities for the binary trees if the data are simulated under the star tree 32 33 A simpler case showing similar behaviours is the fair coin paradox 33 The work suggests that Bayesian model selection may produce unpleasant polarized behavior supporting one model with full force while rejecting the others when the competing models are all misspecified and equally wrong 34 Yang has worked extensively on Markov chain Monte Carlo algorithms deriving many Metropolis Hastings algorithms in Bayesian phylogenetics 35 A study examining the efficiency of simple MCMC proposals revealed that the well studied Gaussian random walk move is less efficient than the simple uniform random walk move which is in turn less efficient than the Bactrian moves bimodal moves that suppress values very close to the current state 36 Professional activities editYang taught in Woods Hole Workshop on Molecular Evolution He was a co organizer of the Royal Society Discussion Meeting on Statistical and computational challenges in molecular phylogenetics and evolution on 28 29 April 2008 37 and the Royal Society Discussion Meeting on Dating species divergence using rocks and clocks on 9 10 November 2015 38 Since 2009 he has been a co organizer of an annual workshop on Computational Molecular Evolution CoME which has been running in Sanger Hinxton in odd years and in Hiraklion Crete in even years 1 He also organized and taught in a number of workshops in Beijing China Awards and honours edit2023 Darwin Wallace Medal Linnean Society of London 39 2010 Frink Medal for British Zoologists Zoological Society of London 40 2009 Royal Society Wolfson Research Merit Award2008 President s Award for Lifetime Achievement Society for Systematic Biology 41 2006 Fellow of the Royal Society The Royal Society of London 2 1995 Young Investigator s Prize American Society of Naturalists 3 Books editComputational molecular evolution Oxford University Press 2006 ISBN 978 0 19 856702 8 Molecular Evolution A Statistical Approach Oxford University Press 2014 ISBN 978 0 19 960261 2 References edit Genetics Evolution and Environment Ucl ac uk Retrieved 2017 06 23 a b YANG Prof Ziheng Who s Who 2011 A amp C Black 2011 online edn Oxford University Press Dec 2010 online edn Oct 2010 accessed 11 May 2011 subscription required Iris View Profile Iris ucl ac uk Retrieved 2017 06 23 Ziheng Yang Radcliffe Institute for Advanced Study at Harvard University www radcliffe harvard edu Retrieved 2017 12 01 Felsenstein Joe 1973 Maximum likelihood and minimum steps methods for estimating evolutionary trees from data on discrete characters Syst Zool 22 3 240 249 doi 10 2307 2412304 JSTOR 2412304 Felsenstein Joe 1981 Evolutionary trees from DNA sequences a maximum likelihood approach J Mol Evol 17 6 368 376 Bibcode 1981JMolE 17 368F doi 10 1007 bf01734359 PMID 7288891 S2CID 8024924 Yang Ziheng 1993 Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites Mol Biol Evol 10 6 1396 1401 doi 10 1093 oxfordjournals molbev a040082 PMID 8277861 Yang Z 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites approximate methods J Mol Evol 39 3 306 314 Bibcode 1994JMolE 39 306Y CiteSeerX 10 1 1 305 951 doi 10 1007 bf00160154 PMID 7932792 S2CID 17911050 Yang Z Lauder IJ Lin HJ 1995 Molecular evolution of the hepatitis B virus genome J Mol Evol 41 5 587 596 Bibcode 1995JMolE 41 587Y doi 10 1007 bf00175817 PMID 7490773 S2CID 9176917 Yang Z 1996 Maximum likelihood models for combined analyses of multiple sequence data J Mol Evol 42 5 587 596 Bibcode 1996JMolE 42 587Y CiteSeerX 10 1 1 19 6773 doi 10 1007 bf02352289 PMID 8662011 S2CID 12660243 Goldman N Yang Z 1994 A codon based model of nucleotide substitution for protein coding DNA sequences Mol Biol Evol 11 5 725 736 doi 10 1093 oxfordjournals molbev a040153 PMID 7968486 Yang Ziheng 1998 Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution Mol Biol Evol 15 5 568 573 doi 10 1093 oxfordjournals molbev a025957 PMID 9580986 Nielsen R Yang Z 1998 Likelihood models for detecting positively selected amino acid sites and applications to the HIV 1 envelope gene Genetics 148 3 929 936 doi 10 1093 genetics 148 3 929 PMC 1460041 PMID 9539414 Yang Z Nielsen R Goldman N Pedersen A M K 2000 Codon substitution models for heterogeneous selection pressure at amino acid sites Genetics 155 1 431 449 doi 10 1093 genetics 155 1 431 PMC 1461088 PMID 10790415 a b Yang Ziheng Wong Wendy S W Nielsen Rasmus 2005 04 01 Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection Molecular Biology and Evolution 22 4 1107 1118 doi 10 1093 molbev msi097 ISSN 0737 4038 PMID 15689528 Yang Z Nielsen R 2002 Codon substitution models for detecting molecular adaptation at individual sites along specific lineages Mol Biol Evol 19 6 908 917 doi 10 1093 oxfordjournals molbev a004148 hdl 1813 32161 PMID 12032247 Cannarozzi Gina M Schneider Adrian eds 2012 Codon evolution mechanisms and models Oxford Oxford University Press ISBN 9780199601165 OCLC 784949340 Yang Z Kumar S Nei M 1995 A new method of inference of ancestral nucleotide and amino acid sequences Genetics 141 4 1641 1650 doi 10 1093 genetics 141 4 1641 PMC 1206894 PMID 8601501 Fitch Walter M 1971 Toward defining the course of evolution minimum change for a specific tree topology Syst Zool 20 4 406 416 doi 10 2307 2412116 JSTOR 2412116 Hartigan J A 1973 Minimum evolution fits to a given tree Biometrics 29 1 53 65 doi 10 2307 2529676 JSTOR 2529676 Rannala B Yang Z 1996 Probability distribution of molecular evolutionary trees a new method of phylogenetic inference J Mol Evol 43 3 304 311 Bibcode 1996JMolE 43 304R doi 10 1007 bf02338839 PMID 8703097 S2CID 8269826 Yang Z Rannala B 1997 Bayesian phylogenetic inference using DNA sequences a Markov chain Monte Carlo Method Mol Biol Evol 14 7 717 724 doi 10 1093 oxfordjournals molbev a025811 PMID 9214744 Chen Ming Hui Kuo Lynn Lewis Paul O eds 2014 05 27 Bayesian phylogenetics methods algorithms and applications Boca Raton Chapman amp Hall CRC ISBN 9781466500792 OCLC 881387408 Ziheng Yang 2014 Molecular evolution a statistical approach First ed Oxford Oxford University Press ISBN 9780199602605 OCLC 869346345 Rannala B Yang Z 2003 Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci Genetics 164 4 1645 1656 doi 10 1093 genetics 164 4 1645 PMC 1462670 PMID 12930768 Yang Ziheng Rannala Bruce 2014 12 01 Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci Molecular Biology and Evolution 31 12 3125 3135 doi 10 1093 molbev msu279 ISSN 0737 4038 PMC 4245825 PMID 25274273 Rannala Bruce Yang Ziheng 2017 09 01 Efficient Bayesian Species Tree Inference under the Multispecies Coalescent Systematic Biology 66 5 823 842 arXiv 1512 03843 doi 10 1093 sysbio syw119 ISSN 1063 5157 PMC 8562347 PMID 28053140 S2CID 3554064 a b Xu Bo Yang Ziheng 2016 12 01 Challenges in Species Tree Estimation Under the Multispecies Coalescent Model Genetics 204 4 1353 1368 doi 10 1534 genetics 116 190173 ISSN 0016 6731 PMC 5161269 PMID 27927902 Yang Ziheng Rannala Bruce 2010 05 18 Bayesian species delimitation using multilocus sequence data Proceedings of the National Academy of Sciences 107 20 9264 9269 Bibcode 2010PNAS 107 9264Y doi 10 1073 pnas 0913022107 ISSN 0027 8424 PMC 2889046 PMID 20439743 Yang Ziheng 2007 PAML 4 Phylogenetic analysis by maximum likelihood Mol Biol Evol 24 8 1586 1591 doi 10 1093 molbev msm088 PMID 17483113 Yang Ziheng 2015 10 01 The BPP program for species tree estimation and species delimitation Current Zoology 61 5 854 865 doi 10 1093 czoolo 61 5 854 ISSN 1674 5507 Yang Ziheng Rannala Bruce Lewis Paul 2005 06 01 Branch Length Prior Influences Bayesian Posterior Probability of Phylogeny Systematic Biology 54 3 455 470 doi 10 1080 10635150590945313 ISSN 1063 5157 PMID 16012111 a b Yang Ziheng 2007 08 01 Fair Balance Paradox Star tree Paradox and Bayesian Phylogenetics Molecular Biology and Evolution 24 8 1639 1655 doi 10 1093 molbev msm081 ISSN 0737 4038 PMID 17488737 Yang Ziheng Zhu Tianqi 5 February 2018 Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees Proceedings of the National Academy of Sciences 115 8 1854 1859 Bibcode 2018PNAS 115 1854Y doi 10 1073 pnas 1712673115 PMC 5828583 PMID 29432193 Ziheng Yang 2014 Molecular evolution a statistical approach First ed Oxford Oxford University Press ISBN 9780199602612 OCLC 869346345 Yang Ziheng Rodriguez Carlos E 2013 11 26 Searching for efficient Markov chain Monte Carlo proposal kernels Proceedings of the National Academy of Sciences 110 48 19307 19312 Bibcode 2013PNAS 11019307Y doi 10 1073 pnas 1311790110 ISSN 0027 8424 PMC 3845170 PMID 24218600 Statistical and computational challenges in molecular phylogenetics and evolution Royal Society Dating species divergences using rocks and clocks Royal Society The Darwin Wallace Medal Retrieved 2023 06 09 Winners of the ZSL Frink Medal for British Zoologists PDF Static zsl org Retrieved 2017 06 23 Society of Systematic Biologists SSB Society of Systematic Biologists External links editProfessor Ziheng Yang s group page at UCL Computational Molecular Evolution Oxford University Press Molecular Evolution A Statistical Approach Oxford University Press Calibrating the molecular clock to date species divergences Darwin China 200 Conference Retrieved from https en wikipedia org w index php title Ziheng Yang amp oldid 1220088629, wikipedia, wiki, book, books, library,

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