Ziheng Yang

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 36

Top Topics

Dna Methylation

Genetic Diversity

Top Venues

Molecular biology and evolution

Systematic biology

Proceedings of the National Academy of Sciences of the United States of America

Nature ecology & evolution

This page only lists publications with an associated author ORCID identifier.

Publications

Anna A Nagel, Tomáš Flouri, Ziheng Yang, Bruce Rannala
Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences. Systematic biology (2024)
Carlos J Pavón-Vázquez, Qaantah Rana, Keaka Farleigh, Erika Crispo, Mimi Zeng, Jeevanie Liliah, Daniel Mulcahy, Alfredo Ascanio, Tereza Jezkova, Adam D Leaché, Tomas Flouri, Ziheng Yang, Christopher Blair
Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards. Systematic biology 73 (2) (2024)
Carlos J Pavón-Vázquez, Qaantah Rana, Keaka Farleigh, Erika Crispo, Mimi Zeng, Jeevanie Liliah, Daniel Mulcahy, Alfredo Ascanio, Tereza Jezkova, Adam D Leaché, Tomas Flouri, Ziheng Yang, Christopher Blair
Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards. Systematic biology 73 (2) (2024)
Edmund R R Moody, Sandra Álvarez-Carretero, Tara A Mahendrarajah, James W Clark, Holly C Betts, Nina Dombrowski, Lénárd L Szánthó, Richard A Boyle, Stuart Daines, Xi Chen, Nick Lane, Ziheng Yang, Graham A Shields, Gergely J Szöllősi, Anja Spang, Davide Pisani, Tom A Williams, Timothy M Lenton, Phillip C J Donoghue
The nature of the last universal common ancestor and its impact on the early Earth system. Nature ecology & evolution (2024)
Daniel Kornai, Xiyun Jiao, Jiayi Ji, Tomáš Flouri, Ziheng Yang
Hierarchical Heuristic Species Delimitation under the Multispecies Coalescent Model with Migration. Systematic biology (2024)
Carlos J Pavón-Vázquez, Qaantah Rana, Keaka Farleigh, Erika Crispo, Mimi Zeng, Jeevanie Liliah, Daniel Mulcahy, Alfredo Ascanio, Tereza Jezkova, Adam D Leaché, Tomas Flouri, Ziheng Yang, Christopher Blair
Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards. Systematic biology (2024)
Yuttapong Thawornwattana, Jun Huang, Tomá Š Flouri, James Mallet, Ziheng Yang
Inferring the direction of introgression using genomic sequence data. Molecular biology and evolution (2023)
Paschalia Kapli, Ioanna Kotari, Maximilian J Telford, Nick Goldman, Ziheng Yang
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies. Systematic biology (2023)
George P Tiley, Tomás Flouri, Xiyun Jiao, Jelmer W Poelstra, Bo Xu, Tianqi Zhu, Bruce Rannala, Anne D Yoder, Ziheng Yang
Estimation of species divergence times in presence of cross-species gene flow. Systematic biology (2023)
Tomáš Flouri, Xiyun Jiao, Jun Huang, Bruce Rannala, Ziheng Yang
Efficient Bayesian inference under the multispecies coalescent with migration. Proceedings of the National Academy of Sciences of the United States of America 120 (44) (2023)
Sandra Álvarez-Carretero, Paschalia Kapli, Ziheng Yang
Beginner's Guide on the Use of PAML to Detect Positive Selection. Molecular biology and evolution 40 (4) (2023)
Sandra Álvarez-Carretero, Paschalia Kapli, Ziheng Yang
Beginner's Guide on the Use of PAML to Detect Positive Selection. Molecular biology and evolution 40 (4) (2023)
Sandra Álvarez-Carretero, Paschalia Kapli, Ziheng Yang
Beginner's Guide on the Use of PAML to Detect Positive Selection. Molecular biology and evolution 40 (4) (2023)
Sandra Álvarez-Carretero, Paschalia Kapli, Ziheng Yang
Beginner's Guide on the Use of PAML to Detect Positive Selection. Molecular biology and evolution 40 (4) (2023)
Jun Huang, Yuttapong Thawornwattana, Tomá Š Flouri, James Mallet, Ziheng Yang
Inference of Gene Flow between Species under Misspecified Models. Molecular biology and evolution 39 (12) (2022)
Tianqi Zhu, Ziheng Yang
Complexity of the simplest species tree problem. Molecular biology and evolution 38 (9) (2022)
Ziheng Yang, Tomá Š Flouri
Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability. Molecular biology and evolution 39 (5) (2022)
Tianqi Zhu, Tomáš Flouri, Ziheng Yang
A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model. Molecular ecology 31 (10) (2022)
Jun Huang, Yuttapong Thawornwattana, Tomá Š Flouri, James Mallet, Ziheng Yang
Inference of Gene Flow between Species under Misspecified Models. Molecular biology and evolution 39 (12) (2022)
Jun Huang, Yuttapong Thawornwattana, Tomá Š Flouri, James Mallet, Ziheng Yang
Inference of Gene Flow between Species under Misspecified Models. Molecular biology and evolution 39 (12) (2022)
Jelmer W Poelstra, B Karina Montero, Jan Lüdemann, Ziheng Yang, S Jacques Rakotondranary, Paul A Hohenlohe, Nadine Stetter, Jörg U Ganzhorn, Anne D Yoder
RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results. Proceedings. Biological sciences 289 (1980) (2022)
Tomá Š Flouri, Jun Huang, Xiyun Jiao, Paschalia Kapli, Bruce Rannala, Ziheng Yang
Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent. Molecular biology and evolution 39 (8) (2022)
Jun Huang, Jeremy Bennett, Tomáš Flouri, Adam D Leaché, Ziheng Yang
Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model. Systematic biology (2021)
Yuanqing Feng, Hongzhan Xu, Jinghao Liu, Ning Xie, Lei Gao, Yanyun He, Yuan Yao, Fengxiang Lv, Yan Zhang, Jian Lu, Wei Zhang, Chuan-Yun Li, Xinli Hu, Ziheng Yang, Rui-Ping Xiao
Functional and Adaptive Significance of Promoter Mutations That Affect Divergent Myocardial Expressions of TRIM72 in Primates. Molecular biology and evolution 38 (7) (2021)
Xiyun Jiao, Tomá Š Flouri, Ziheng Yang
Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow. National science review 8 (12) (2021)
Sandra Álvarez-Carretero, Asif U Tamuri, Matteo Battini, Fabrícia F Nascimento, Emily Carlisle, Robert J Asher, Ziheng Yang, Phillip C J Donoghue, Mario Dos Reis
A species-level timeline of mammal evolution integrating phylogenomic data. Nature 602 (7896) (2021)
Paschalia Kapli, Ziheng Yang, Maximilian J Telford
Phylogenetic tree building in the genomic age. Nature reviews. Genetics 21 (7) (2020)
Jennifer L Morris, Mark N Puttick, James W Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H Wellman, Ziheng Yang, Harald Schneider, Philip C J Donoghue
The timescale of early land plant evolution. Proceedings of the National Academy of Sciences of the United States of America 115 (10) (2018)
Jennifer L Morris, Mark N Puttick, James W Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H Wellman, Ziheng Yang, Harald Schneider, Philip C J Donoghue
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 115 (41) (2018)
Ziheng Yang, Tianqi Zhu
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 115 (8) (2018)
Rachel C M Warnock, Ziheng Yang, Phillip C J Donoghue
Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution. Proceedings. Biological sciences 284 (1857) (2018)
Bo Xu, Ziheng Yang
Challenges in Species Tree Estimation Under the Multispecies Coalescent Model. Genetics 204 (4) (2017)
Fabrícia F Nascimento, Mario Dos Reis, Ziheng Yang
A biologist's guide to Bayesian phylogenetic analysis. Nature ecology & evolution 1 (10) (2017)
Phillip C J Donoghue, Ziheng Yang
The evolution of methods for establishing evolutionary timescales. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 371 (1699) (2017)
Ziheng Yang, Bruce Rannala
Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses. Molecular ecology 26 (11) (2017)
Ziheng Yang, Phillip C J Donoghue
Dating species divergences using rocks and clocks. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 371 (1699) (2017)
Tomotaka Matsumoto, Hiroshi Akashi, Ziheng Yang
Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution. Genetics 200 (3) (2015)