Xuemei Lu

A multi-tissue epigenomic atlas links the sheep non-coding genome to domestication and complex traits

SheepEpimap combines 516 histone CUT&Tag, ATAC-seq and RNA-seq datasets from 43 sheep tissues to annotate 2.93 million cis-regulatory elements and 145,407 allele-specific variants for trait interpretation.

Long-read RNA-seq resolves isoform-level and context-specific regulatory architecture of complex traits in cattle

The paper uses long-read RNA-seq to uncover isoform-level and context-specific regulatory effects in cattle, improving the resolution of molecular atlases and GWAS loci.

Genomes of Wiebesia fig wasps reveal the adaptation and codiversification in fig-fig wasp mutualism

This study analyzes the genomes of Wiebesia fig wasps to understand how codiversification with fig hosts influences their evolutionary trajectories and adaptation to host-specific traits.

Sex-specific Genetic Regulatory Effects in Chickens

The paper identifies sex-specific genetic regulatory effects in chickens using whole-genome sequencing and transcriptomes, revealing sex-dependent gene regulation and structural variants.

A multi-tissue atlas of genetic regulatory effects in sheep

The paper presents a multi-tissue sheep atlas identifying regulatory variants and their effects on molecular phenotypes, revealing allelic heterogeneity and evolutionary patterns.

Elevated EGR1 Binding at Enhancers in Excitatory Neurons Correlates with Neuronal Subtype-Specific Epigenetic Regulation

The paper identifies EGR1 binding at enhancers in excitatory neurons and shows its correlation with subtype-specific epigenetic regulation and gene pathways.

Genomic Evidence for Males of Exceptional Reproductive Output (ERO) in Apes and Humans

The paper uses genomic diversity data to estimate the variance ratio of reproductive output in males and females across apes and humans, finding evidence for exceptional reproductive output in some males.

CircAge: A Comprehensive Resource for Aging-Associated Circular RNAs Across Species and Tissues

circAge compiles aging-associated circRNA data from 7 species and 21 tissues, identifying 413,378 unique circRNAs and their conservation, interactions, and coding potential.

On the discovered Cancer Driving Nucleotides (CDNs)-Distributions across genes, cancer types and patients

This study identifies Cancer Driving Nucleotides (CDNs) across cancer types and patients, finding that most remain unidentified and highlights the need for larger sample sizes to improve detection.

Rapid evolution of fine-scale recombination during domestication: a perspective from population genomics

The paper constructs a fine-scale recombination map in domestic chickens to study rapid evolutionary changes in recombination rates during domestication.

The theory of massively repeated evolution and full identifications of Cancer Driving Nucleotides (CDNs)

This study develops a theory to identify Cancer Driving Nucleotides (CDNs) by analyzing mutation recurrence across large cancer datasets, finding that mutations recurring at least three times are likely CDNs.

Molecular Parallelisms and Divergences Between Human and Canine Mammary Cancer

This study compares genomic and transcriptomic differences between human and canine mammary cancers, revealing both similarities and divergences in mutation patterns and selective pressures.

Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity

The paper studies chromosomal evolution in cancer cell lines, finding that cells lose sex chromosomes and gain autosomes, leading to a 2:3 X:A ratio that may enhance fitness.

Further genetic diversification in multiple tumors and an evolutionary perspective on therapeutics

The study analyzes genetic diversity in multiple hepatocellular carcinomas, finding that low-frequency mutations pre-exist and contribute to drug resistance, presenting challenges and opportunities for cancer therapeutics.