A refined characterization of large-scale genomic differences in the first complete human genome.
Yang X, Wang X, Zou Y,… & Mao, Y.* (2022). bioRxiv, 2022: 2022.12. 17.520860.

A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics.
Mao, Y.*, & Zhang, G. (2022). Nature Methods, 19 (6), 635-638.

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, 54, 518–525. 

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, 594 (7861), 77-81.

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, 593 (7857), 101-107.

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, 12 (1), 1-14.

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, 2020;20:832–840.

Genomic insights into hybridization of reef corals.
Mao, Y.* (2020). Coral Reefs, 39 (1), 61-67.

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, 370(6523).

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, 21(1), 1-35.

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, 30(11), 1680-1693.

A likely ancient genome duplication in the speciose reef-building coral genus, Acropora.
Mao, Y.*, & Satoh, N. (2019). iScience, 13, 20-32.

GenoDup Pipeline: a tool to detect genome duplication using the dS-based method.
Mao, Y.* (2019). PeerJ, 7, e6303.

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, 28(21), 3373-3382.

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, 101(6), 362-367.

NOTE: *Corresponding author