Yafei Mao

Cross-species discovery of large structural variants reveals distinct evolutionary dynamics in primates

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

An alarm system for biomedical construct design: a lesson from the unintended protein product of eGFP

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.

A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias

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.

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

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

Multidimensional variation and population stratification across 8000 complete human centromeres

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.

A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA

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.

Joint Segmental Duplication Co-option Drives Human-specific Transcriptional Readthrough and Expression Fine-tuning of NPEPPS-TBC1D3

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.

Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation

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: Analyzing variation and motif pattern in tandem repeats

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

Complete sequencing of ape genomes

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.

Comparative genomics of macaques and integrated insights into genetic variation and population history

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

A Refined Analysis of Neanderthal-Introgressed Sequences in Modern Humans with a Complete Reference Genome

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.

The variation and evolution of complete human centromeres

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.

Structurally divergent and recurrently mutated regions of primate genomes

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

Comparative transcriptome in rhesus macaques and crab-eating macaques

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

A refined characterization of large-scale genomic differences in the first complete human genome

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.

Pangenome-based genome inference

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

Integrated gene analyses of de novo mutations from 46,612 trios with autism and developmental disorders

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

The structure, function, and evolution of a complete human chromosome 8

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 Pipeline: a tool to detect genome duplication using the dS-based method

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