Sheng Zhong

scLong is a billion-parameter foundation model that captures long-range gene context in scRNA-seq by modeling all genes and integrating gene knowledge, outperforming existing models in various tasks.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The paper identifies AD-associated changes in m6A methylation on promoter antisense RNAs and shows their role in regulating gene expression and neuronal survival in Alzheimer's disease.

The paper identifies stable RNA-chromatin interactions in human embryonic stem cells using RNase treatment and reveals their genomic localization and association with transcription factors and histone modifications.

PRIM-seq maps RNA-protein interactions by generating chimeric DNA sequences, revealing over 350,000 RNA-protein pairs in human cells.

The paper identifies mitochondrial RNAs (mtRNAs) as chromatin-associated RNAs (caRNAs) that regulate nuclear transcription in response to stress and disease.

This study investigates how chromatin-associated RNA interacts with 3D genome organization in human cells, revealing a feedback loop between RNA distribution and chromatin structure.

The paper introduces MUSIC, a technique to profile chromatin interactions, gene expression, and RNA-chromatin associations in single cells, revealing age-related changes and disease associations in human brain samples.

The paper shows PHGDH expression increases sequentially with AD pathology and symptoms in mice and humans, correlating with cognitive decline and suggesting PHGDH as a potential biomarker and caution for L-serine therapy.

The paper investigates how RNA-chromatin interactions change in endothelial cells under high-glucose and TNF treatment, showing their role in inflammation and endothelial dysfunction.

EpiAlignment aligns genomic regions using DNA sequence and epigenomic data from two species, providing semi-global alignments based on combined sequence and epigenome similarity.

The paper identifies a correlation between RNA-DNA interactions in normal cells and fusion RNA pairs in cancer, suggesting a mechanism for fusion transcript formation.

GITAR provides a software tool for Hi-C data analysis, including preprocessing, normalization, visualization, and TADs analysis, with a library of processed datasets.

Rainbow-seq combines lineage tracing with single-cell RNA-seq to track cell division history and reveal transcriptome differences in mouse embryos.

GIVE provides a library for creating personalized genome browsers on personal websites without needing system administration.

The paper identifies genomic regions proximal to nuclear speckles using noncoding RNAs and MARGI assay, showing nsaRNAs interact with specific genomic sites.

The paper develops a joint evolutionary model for genome and epigenome data to infer dependencies between sequence mutations and epigenomic variations across species.

The paper outlines the goals and structure of the 4D Nucleome Project, which aims to map the spatial and temporal dynamics of the genome in human and mouse cells.