Ziheng Yang

56.0k citations

228 papers · 38.9k indexed · 27 hit papers · h-index 84

Molecular Biology top 0.05%
Genetics top 0.01%
Ecology, Evolution, Behavior and Systematics top 0.02%
Plant Science top 0.1%
Paleontology top 0.02%

Co-authors: Bruce Rannala Rasmus Nielsen Joseph P. Bielawski Nick Goldman Anne D. Yoder Philip C. J. Donoghue Maria Anisimova Mario dos Reis
Topics: Genomics and Phylogenetic Studies (133 papers)Genetic diversity and population structure (108 papers)Evolution and Paleontology Studies (53 papers)
Cited by: Paleontology Genetics Ecology, Evolution, Behavior and Systematics
Journals: Nature Proceedings of the National Academy of Sciences Journal of Neuroscience
Partner nations: United Kingdom United States China

In The Last Decade

Ziheng Yang

222 papers receiving 38.1k citations

Hit Papers

5 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

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

1994 2.3k citations Ziheng Yang profile →
Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites

2000 1.9k citations Ziheng Yang, Nick Goldman et al. profile →
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection

2005 1.9k citations Ziheng Yang Molecular Biology and Evolution profile →
Statistical methods for detecting molecular adaptation

2000 1.4k citations Ziheng Yang et al. profile →
Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models

2000 1.4k citations Ziheng Yang et al. Molecular Biology and Evolution profile →
Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference

1996 1.3k citations Bruce Rannala, Ziheng Yang profile →
Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene

1998 1.3k citations Ziheng Yang et al. profile →
Bayesian species delimitation using multilocus sequence data

2010 1.1k citations Ziheng Yang, Bruce Rannala Proceedings of the National Academy of Sciences profile →
Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages

2002 1.1k citations Ziheng Yang et al. Molecular Biology and Evolution profile →
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method

1997 1.0k citations Ziheng Yang, Bruce Rannala Molecular Biology and Evolution profile →
Among-site rate variation and its impact on phylogenetic analyses

1996 978 citations Ziheng Yang profile →
Estimating the pattern of nucleotide substitution

1994 894 citations Ziheng Yang profile →
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

2003 879 citations Bruce Rannala, Ziheng Yang profile →
Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.

1993 830 citations Ziheng Yang Molecular Biology and Evolution profile →
Computational Molecular Evolution

2006 613 citations Ziheng Yang UCL Discovery (University College London) profile →
Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds

2005 609 citations Ziheng Yang, Bruce Rannala Molecular Biology and Evolution profile →
The timescale of early land plant evolution

2018 606 citations Jennifer L. Morris, Mark N. Puttick et al. Proceedings of the National Academy of Sciences profile →
Accuracy and Power of the Likelihood Ratio Test in Detecting Adaptive Molecular Evolution

2001 583 citations Ziheng Yang et al. Molecular Biology and Evolution profile →
The BPP program for species tree estimation and species delimitation

2015 547 citations Ziheng Yang profile →
Synonymous and nonsynonymous rate variation in nuclear genes of mammals

1998 501 citations Ziheng Yang et al. profile →
Molecular phylogenetics: principles and practice

2012 450 citations Ziheng Yang, Bruce Rannala profile →
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

2014 429 citations Ziheng Yang, Bruce Rannala Molecular Biology and Evolution profile →
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

2015 325 citations Mario dos Reis, Yuttapong Thawornwattana et al. profile →
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

2018 285 citations Tomáš Flouri, Xiyun Jiao et al. Molecular Biology and Evolution profile →
Phylogenetic tree building in the genomic age

2020 274 citations Ziheng Yang et al. profile →
Beginner's Guide on the Use of PAML to Detect Positive Selection

2023 85 citations Sandra Álvarez-Carretero, Ziheng Yang et al. Molecular Biology and Evolution profile →
The nature of the last universal common ancestor and its impact on the early Earth system

2024 74 citations Edmund R. R. Moody, Sandra Álvarez-Carretero et al. Nature Ecology & Evolution profile →

Peers

Countries citing papers authored by Ziheng Yang

Since Specialization

Citations

This map shows the geographic impact of Ziheng Yang's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Ziheng Yang with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Ziheng Yang more than expected).

Fields of papers citing papers by Ziheng Yang

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Ziheng Yang. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Ziheng Yang. The network helps show where Ziheng Yang may publish in the future.

Co-authorship network of co-authors of Ziheng Yang

This figure shows the co-authorship network connecting the top 25 collaborators of Ziheng Yang. A scholar is included among the top collaborators of Ziheng Yang based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Ziheng Yang. Ziheng Yang is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

#	Work	Indexed citations
1	Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila 2025 ·Systematic Biology ·Jiayi Ji,(unknown),Tomáš Flouri,Ziheng Yang	1
2	Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration 2024 ·Systematic Biology ·(unknown),Xiyun Jiao,Jiayi Ji,Tomáš Flouri,Ziheng Yang	12
3	The nature of the last universal common ancestor and its impact on the early Earth systembreakdown → 2024 ·Nature Ecology & Evolution ·Edmund R. R. Moody,Sandra Álvarez-Carretero,Tara Mahendrarajah,James Clark,(unknown),Nina Dombrowski,Lénárd L. Szánthó,Richard A. Boyle,Stuart J. Daines,Xi Chen,Nick Lane,Ziheng Yang,Graham Shields,Gergely J. Szöllősi,Anja Spang,Davide Pisani,Tom A. Williams,Timothy M. Lenton,Philip C. J. Donoghue	74
4	Inferring the Direction of Introgression Using Genomic Sequence Data 2023 ·Molecular Biology and Evolution ·Yuttapong Thawornwattana,Jun Huang,Tomáš Flouri,James Mallet,Ziheng Yang	14
5	Major patterns in the introgression history of Heliconius butterflies 2023 ·eLife ·Yuttapong Thawornwattana,Fernando Seixas,Ziheng Yang,James Mallet	4
6	Major patterns in the introgression history of Heliconius butterflies 2023 ·eLife ·Yuttapong Thawornwattana,Fernando Seixas,Ziheng Yang,James Mallet	4
7	Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies 2022 ·Systematic Biology ·Yuttapong Thawornwattana,Fernando Seixas,Ziheng Yang,James Mallet	27
8	Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability 2022 ·Molecular Biology and Evolution ·Ziheng Yang,Tomáš Flouri	10
9	RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results 2022 ·Proceedings of the Royal Society B Biological Sciences ·Jelmer W. Poelstra,(unknown),Jan Lüdemann,Ziheng Yang,S. Jacques Rakotondranary,Paul A. Hohenlohe,(unknown),Jörg U. Ganzhorn,Anne D. Yoder	8
10	Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model 2021 ·Systematic Biology ·Jun Huang,(unknown),Tomáš Flouri,Adam D. Leaché,Ziheng Yang	16
11	Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space 2020 ·Systematic Biology ·Claudia Weber,(unknown),(unknown),Ziheng Yang,Nick Goldman	2
12	The Impact of Cross-Species Gene Flow on Species Tree Estimation 2020 ·Systematic Biology ·Xiyun Jiao,Tomáš Flouri,Bruce Rannala,Ziheng Yang	33
13	Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters 2019 ·Systematic Biology ·Sandra Álvarez-Carretero,Anjali Goswami,Ziheng Yang,Mario dos Reis	25
14	A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis 2019 ·Molecular Biology and Evolution ·Tomáš Flouri,Xiyun Jiao,Bruce Rannala,Ziheng Yang	117
15	The Spectre of Too Many Species 2018 ·Systematic Biology ·Adam D. Leaché,Tianqi Zhu,Bruce Rannala,Ziheng Yang	207
16	The timescale of early land plant evolutionbreakdown → 2018 ·Proceedings of the National Academy of Sciences ·Jennifer L. Morris,Mark N. Puttick,James Clark,Dianne Edwards,Paul Kenrick,Silvia Pressel,Charles H. Wellman,Ziheng Yang,Harald Schneider,Philip C. J. Donoghue	606
17	Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals 2014 ·Biology Letters ·Mario dos Reis,Philip C. J. Donoghue,Ziheng Yang	67
18	A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data 2010 ·Genome Biology and Evolution ·Ziheng Yang	47
19	A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times 2004 ·UCL Discovery (University College London) ·Ziheng Yang	27
20	STATISTICAL TESTS OF HOST-PARASITE COSPECIATION 1997 ·Evolution ·John P. Huelsenbeck,Bruce Rannala,Ziheng Yang	93

About Ziheng Yang

Ziheng Yang is a scholar working on Paleontology, Genetics and Ecological Modeling, having authored 228 papers that have together received 38.9k indexed citations. Recurring topics across this work include Genomics and Phylogenetic Studies (133 papers), Genetic diversity and population structure (108 papers) and Evolution and Paleontology Studies (53 papers). The work is most often cited by research in Paleontology (6.1k citations), Genetics (15.8k citations) and Ecology, Evolution, Behavior and Systematics (7.9k citations). Ziheng Yang has collaborated with scholars based in United Kingdom, United States and China. Frequent co-authors include Bruce Rannala, Rasmus Nielsen, Joseph P. Bielawski, Nick Goldman, Anne D. Yoder, Philip C. J. Donoghue, Maria Anisimova, Mario dos Reis, Willie J. Swanson and William A. Fletcher. Their work appears in journals such as Nature, Proceedings of the National Academy of Sciences and Journal of Neuroscience.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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