bioRxiv

VAMPIRE: Analyzing variation and motif pattern in tandem repeats.
Yang, Z., Zhang, S., Logsdon, G. A. & Mao, Y.* (2025). bioRxiv

A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias.
Zhang, S., Xu, N., Lu, Y., Nie, Y., Li, Z., Gennaro, L. d., ... Sun, Q.* & Mao, Y.* (2025). bioRxiv

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.* (2024). bioRxiv

2025

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.* (2025). Cell Genomics

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. (2025). Nature

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. (2025). Genome Biology

2024

Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies.

Ma, K., Yang, X., Mao, Y*. (2024). Trends in Genetics

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.* (2024). Cell

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.* (2024). Zoological Research

The variation and evolution of complete human centromeres.

Logsdon, G.A., Rozanski, A.N., Ryabov, F., … Mao, Y., ... & Eichler, E. E.* (2024). Nature

2023

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.* (2023). Genome Biology

Exploring the primate genome: Unraveling the mysteries of evolution and human disease.

He, Y.*, & Mao, Y.* (2023). The Innovation

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.* (2023). Nature Communications

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.* (2023). Zoological 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.* (2023). Genome Research

The complete and fully-phased diploid genome of a male Han Chinese.

Yang, C., Zhou, Y., Song, Y., ... Zhang, S., ... Mao, Y., ... & Zhang, G.* (2023). Cell Research

2022

A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics.
Mao, Y.*, & Zhang, G. (2022). Nature Methods

Before SJTU

Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders.
Wang, T., Kim, C. N., Bakken, T. E., ... Mao, Y., ... & Eichler, E. E. (2022). Proceedings of the National Academy of Sciences

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes.
Ebler, J., Ebert, P., Clarke, W. E., Rausch, T., Audano, P. A., Houwaart, T., Mao, Y., ... & Marschall, T. (2022). Nature Genetics

A high-quality bonobo genome refines the analysis of hominid evolution.
Mao, Y., Catacchio, C.R., Hillier, L.W., Porubsky, D., Li, R., Sulovari, A., ... & Eichler, E.E. (2021). Nature

The structure, function and evolution of a complete human chromosome 8.
Logsdon, G.A., Vollger, M.R., Hsieh, P., Mao, Y., Liskovykh, M.A., Koren, S., ... & Eichler, E.E. (2021). 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., Huang, T.H., Dishuck, P.C., ... & Eichler, E.E. (2021). Nature Communications

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. (2020). Molecular Ecology Resources

Genomic insights into hybridization of reef corals.
Mao, Y. (2020). Coral Reefs

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.
Warren, W.C., Harris, R.A., Haukness, M., Fiddes, I.T., Murali, S.C., Fernandes, J., … Mao, Y., ... & Eichler, E.E. (2020). Science

An evolutionary driver of interspersed segmental duplications in primates.
Cantsilieris, S., Sunkin, S.M., Johnson, M.E., Anaclerio, F., Huddleston, J., Baker, C., … Mao, Y., ... & Eichler, E.E. (2020). Genome Biology

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.
Maggiolini, F.A.M., Sanders, A.D., Shew, C.J., Sulovari, A., Mao, Y., Puig, M., ... & Antonacci, F. (2020). Genome Research

A likely ancient genome duplication in the speciose reef-building coral genus, Acropora.
Mao, Y.* & Satoh, N. (2019). iScience

GenoDup Pipeline: a tool to detect genome duplication using the dS-based method.
Mao, Y.* (2019). PeerJ

The roles of introgression and climate change in the rise to dominance of Acropora corals.
Mao, Y., Economo, E.P., & Satoh, N. (2018). Current Biology

Non-random arrangement of synonymous codons in archaea coding sequences.
Zhang, Y., Shao, Z., Yang, L., Sun, X., Mao, Y., Chen, J. & Wang, B. (2013). Genomics

NOTE: Corresponding author

bioRxiv

2025

​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.* (2025). Cell Genomics

​

​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.* (2025). Nature

​​

​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.* (2025). Genome Biology