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Comparative genomics of macaques and integrated insights into genetic variation and population history.
Zhang, S., Xu, N., Fu, L., Yang, X., Li, Y., Yang, Z., …, Sun, Q.*, & Mao, Y.* (2024). bioRxiv



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


Characterization of large-scale genomic differences in the first complete human genome.

Yang, X., Wang, X., Zou, Y., Zhang, S., Xia, M., Fu, L., Vollger, M. R., Chen, N.-C., Taylor, D. J., Harvey, W. T., Logsdon, G. A., Meng, D., Shi, J., McCoy, R. C., Schatz, M. C., Li, W., Eichler, E. E., Lu, Q. & 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


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

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

Before SJTU

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

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