Yafei Mao

This study introduces LGvar, a tool for cross-species detection of large structural variants, revealing distinct evolutionary dynamics in primates.

The paper identifies hidden open reading frames in plasmids using eGFP as a model, finding 6% of constructs contain hidden ORFs, mostly in the +2 frame.

The paper presents a high-accuracy T2T rhesus macaque genome assembly, identifies subtelomeric repeats as a challenge, and reveals new genomic features and functional elements in these regions.

The paper presents 320 nearly-complete East Asian genome assemblies, revealing new genetic diversity and structural variations not present in existing global pangenomes.

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

The paper develops a method to detect and analyze NUMTs in human and non-human primate genomes, revealing their genomic features, population dynamics, and evolutionary implications.

The paper identifies a human-specific genomic structure formed by a joint segmental duplication that drives transcriptional readthrough and expression fine-tuning of NPEPPS-TBC1D3.

The paper identifies three ancient segmental duplications at the human chromosome 2 fusion site, showing their differential distribution due to incomplete lineage sorting and their regulatory impact on gene expression.

VAMPIRE is a k-mer-based tool for TR discovery and analysis, revealing new insights into human and nonhuman primate centromeres and subtelomeres.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

This study presents genome assemblies and analyses of macaques to explore genetic variation, population history, and evolutionary differences between species and humans.

This study remaps Neanderthal and Denisovan genomes onto new and old references, finds improved mapping with T2T-CHM13, and identifies new introgressed sequences and population-specific archaic ancestry.

A second complete human centromere set (CHM1) plus 31 nonhuman primate centromeres reveals extensive α-satellite higher-order repeat variation, kinetochore repositioning, and saltatory emergence of new repeats.

The paper identifies structurally divergent regions in primate genomes and quantifies the impact of structural variants across multiple species.

This study compares transcriptomes between rhesus and crab-eating macaques and with humans, finding gene expression differences and overlaps with structural variants.

The paper identifies and categorizes large-scale genomic differences between the T2T-CHM13 and GRCh38 human genome assemblies, highlighting their implications for disease and evolution.

PanGenie improves variant calling by using a pangenome reference and k-mer counts, achieving higher accuracy and speed compared to traditional methods.

The paper analyzes de novo mutations in autism and developmental disorder trios to identify candidate genes and functional networks associated with neurodevelopmental disorders.

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

GenoDup detects genome duplication using the dS-based method, successfully identifying WGD in plant and animal empirical data.