Publications
Preprints
A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA
Fu, L.*, Chen, J., Lian, D., Du, S., Wu, D., Yang, C., Wang, Z., Li, Z., ... Yang, X., ... Zhang, G.*, Ma, K.* & Mao, Y.*
bioRxiv (Accepted) 2026
Joint segmental duplication co-option drives human-specific transcriptional readthrough and expression fine-tuning of NPEPPS-TBC1D3
Ma, K.*, Yang, Z., Li, Z., Guo, J., Lian, D., Wang, Z., Ma, H., Zhang, S., Fu, L., ... Jiang, X., Xie, Q., Li, G., Yang, C., Chen, J., Zhang, J., ... Yang, X., ... & Mao, Y.*
bioRxiv (Under Review) 2026
Complex subtelomeric architectures in a complete rhesus macaque reference genome
Zhang, S., Xu, N., Lu, Y., Nie, Y., Li, Z., de Gennaro, L., ... Li, Z., ... Fu L., Zhang, Z., Chen, J., Ma, K., Yang, X., Zhang, J., ... Sun, Q.* & Mao, Y.*
bioRxiv (Accepted) 2026
VAMPIRE: Analyzing variation and motif pattern in tandem repeats
Yang, Z., Zhang, S., Logsdon, G. A. & Mao, Y.*
bioRxiv (In Revision) 2025
Tibetan near-complete pangenome reveals complex variants underlying high-altitude adaptation
He, Y.*, Liu, K., Mao, L., Zhou, F., Song, J., Qi, X., ... Han, J., Fu, L., ... Mao, Y.* & Su, B.*
bioRxiv (Under Review) 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 analysis between rhesus macaques (Macaca mulatta) and crab-eating macaques (M. fascicularis).
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., ... Ruan, J.* & 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
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., Gillentine, M. A., Henning, B., Mao, Y., ... & Eichler, E. E.*
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.*
Nature Genetics
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.*
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.*
Nature Communications
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.*
Nature
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
Genomic insights into hybridization of reef corals
Mao, Y.*
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., ... Rogers, J.* & Eichler, E.E.*
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.*
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.*
Genome Research
A likely ancient genome duplication in the speciose reef-building coral genus, Acropora
Mao, Y.* & Satoh, N.
iScience
GenoDup Pipeline: a tool to detect genome duplication using the dS-based method
Mao, Y.*
PeerJ
The roles of introgression and climate change in the rise to dominance of Acropora corals
Mao, Y.*, Economo, E.P., & Satoh, N.
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.*
Genomics