Publications
Preprints (BioRxiv)
A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA
Lianting Fu, Jieyi Chen, Da Lian, Siyuan Du, Dongya Wu, Chentao Yang, Ziyi Wang, Hongyi Ma, Zhengtong Li, Nicole J. Lake, APG Consortium, Xiangyu Yang, Yongyong Shi, Guojie Zhang, Kaiyue Ma, Yafei Mao.
bioRxiv 2026
Joint segmental duplication co-option drives human-specific transcriptional readthrough and expression fine-tuning of NPEPPS-TBC1D3
Kaiyue Ma, Zikun Yang, Zhengtong Li, Jingyi Guo, Da Lian, Ziyi Wang, Hongyi Ma, Shilong Zhang, Lianting Fu, Hezheng Lyu, Xinrui Jiang, Qiujin Xie, Guanting Li, Chenhao Yang, Jieyi Chen, Juan Zhang, Peng Liu, Xiangyu Yang, Zhen-Ge Luo, Guojie Zhang, Yafei Mao.
bioRxiv 2026
A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias
Shilong Zhang, Ning Xu, Yong Lu, Yanhong Nie, Zhengtong Li, Luciana de Gennaro, Lianting Fu, Zhendong Zhang, Jieyi Chen, Kaiyue Ma, Xiangyu Yang, Juan Zhang, Matthew T. Schmitz, Francesca Antonacci, Trygve E. Bakken, Mario Ventura, Adam M. Phillippy, Qiang Sun, Yafei Mao.
bioRxiv 2025
Tibetan near-complete pangenome reveals complex variants underlying high-altitude adaptation
Yaoxi He, Kai Liu, Leyan Mao, Feifei Zhou, Jiaxu Song, Xuebin Qi, Dongya Wu, Junmin Han, Lianting Fu, Jiangguo Li, Yu Zhang, Chaoying Cui, Ouzhuluobu, Guojie Zhang, Yafei Mao, Bing Su
bioRxiv 2025
2025
A refined analysis of neanderthal-introgressed sequences in modern humans with a complete reference genome
Liang, S. A., Ren, T., Zhang, J., He, J., Wang, X., Jiang, X., ... Mao, Y.*. & Chen, L.*
Genome Biology
Integrated analysis of the complete sequence of a macaque genome
Zhang, S., Xu, N., Fu, L., Yang, X., Li, Y., Yang, Z., Li, Z., Feng. Y., Jiang, X., Han, J., Hu, R., Zhang, L., Lian, D., … Sun, Q.*, & Mao, Y.*
Nature
Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation
Yang, Z., Zhang, L., Jiang, X., Yang, X., Ma, K., Yoo, D., ... Sun, Q.*, Eichler, E. E.* & Mao, Y.*
Cell Genomics
Complete sequencing of ape genomes
Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G. A., Solar, S. J., … Mao, Y., ... Makova, K. D.*, Phillippy, A. M.* & Eichler, E. E.*
Nature
2024
The variation and evolution of complete human centromeres
Logsdon, G.A., Rozanski, A.N., Ryabov, F., … Mao, Y., ... & Eichler, E. E.*
Nature
Comparative transcriptome in rhesus macaques and crab-eating macaques
Mao, Y., Li, Y., Yang, Z., Xu, N., Zhang, S., Wang, X., Yang, X., Sun, Q.* & Mao, Y.*
Zoological Research
Structurally divergent and recurrently mutated regions of primate genomes
Mao, Y.*, Harvey, W. T., Porubsky, D., Munson, K. M., Hoekzema, K., Lewis, A. P., Audano, P. A., Rozanski, A., Yang, X., Zhang, S., ... & Eichler, E. E.*
Cell
Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies
Ma, K., Yang, X., Mao, Y.*
Trends in Genetics
2023
The complete and fully-phased diploid genome of a male Han Chinese
Yang, C., Zhou, Y., Song, Y., ... Zhang, S., ... Mao, Y., ... & Zhang, G.*
Cell Research
The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
Li, Z.*, Liu, X., Wang, C., ... Mao, Y., ... & Chen, Y.*
Genome Research
Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing.
Yang, X., Mao, Y., Wang, X., … Li, Z.*, Takahashi, E.* & Li, W.*
Zoological Research
TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function
Okhovat, M.*, VanCampen, J., Nevonen, K. A., ... Mao, Y., ... & Carbone, L.*
Nature Communications
Exploring the primate genome: Unraveling the mysteries of evolution and human disease
He, Y.*, & Mao, Y.*
The Innovation
Characterization of large-scale genomic differences in the first complete human genome
Yang, X., Wang, X., Zou, Y., Zhang, S., Xia, M., Fu, L., ... Meng, D., ... & Mao, Y.*
Genome Biology
2022
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics
Mao, Y.*, & Zhang, G.
Nature Methods
2021
The structure, function and evolution of a complete human chromosome 8
Logsdon, G.A., Vollger, M.R., Hsieh, P., Mao, Y., ... & Eichler, E.E.
Nature
Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans
Hsieh, P., Dang, V., Vollger, M.R., Mao, Y., ... & Eichler, E.E.
Nature Communications
A high-quality bonobo genome refines the analysis of hominid evolution.
Yafei Mao., Catacchio, C.R., Hillier, L.W., Porubsky, D., Li, R., Sulovari, A., ... & Eichler, E.E.*
Nature
2020
TREEasy: an automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data
Mao, Y.*, Hou, S., Shi, J., & Economo, E.P.
Molecular Ecology Resources
2019
A likely ancient genome duplication in the speciose reef-building coral genus, Acropora
Mao, Y.* & Satoh, N.
iScience
2018
The roles of introgression and climate change in the rise to dominance of Acropora corals
Mao, Y.*, Economo, E.P., & Satoh, N.
Current Biology