Zhen Shao

The paper identifies accelerated evolution of lung-related genes in vertebrate lineages surviving end-Permian and end-Triassic mass extinctions, suggesting adaptation to hypoxia.

The paper uses CERAMIC to trace liver tumor initiation, identifying Hep_Bi-zonal cells as the origin of HCC and ICC and revealing peroxisomal metabolism and macrophage niches as key factors.

The paper uses computational modeling and fossil evidence to show a severe population bottleneck in ancient Homo around 930,000 years ago, linked to hominin dispersals and brain size increase.

The paper identifies a pre-marked enhancer, p-Enh, that primes posterior tissue development in mouse embryos through interaction with the TGF-β signaling pathway.

EAP provides a cloud-based platform for analyzing large-scale ChIP/ATAC-seq data, generating publication-ready results and enabling epigenomic analysis in cancer and therapeutic target discovery.

HyperChIP identifies hypervariable genomic regions across ChIP/ATAC-seq samples to reveal tumor heterogeneity and associated transcription factors.

This study identifies sexually dimorphic transcriptomes in mouse β cells and sex-dependent type 2 diabetes genes using scRNA-seq, highlighting sex differences in diabetes pathogenesis.

MAnorm2 is a tool for comparing ChIP-seq samples across groups, improving differential binding detection by accounting for within-group variability and outperforming existing methods.