Shilong Zhang

TE-Dee integrates TE knowledge, expression, and genetic associations to provide a structured resource for TE biology and AI model training.

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

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.

mirCCC infers microRNA-mediated cell-cell communication from single-cell RNA sequencing by detecting coordinated gene expression changes and models miRNA activity and transfer capacity.

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.

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 benchmarks APA detection tools in single-cell and spatial transcriptomes, finding SCAPE and scAPAtrap perform best across multiple metrics.

This study systematically analyzes single-cell data to show how transposable elements dynamically regulate the endothelial-to-hematopoietic transition through epigenetic changes and inflammatory signaling.

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.