Minglei Shi

Sequential-GAM constructs the single-cell geometric 3D genome structure

Sequential-GAM constructs the single-cell geometric 3D genome structure by estimating radial positions and hierarchical organization of chromosomes and genes.

Long-Range Enhancer Networks Gradually Emerge as Key Regulators During Human Cortical Neurogenesis

The paper maps long-range enhancer networks in human, macaque, and mouse fetal cortex, showing human-specific enhancers and neuropsychiatric disorder-linked SNPs regulate gene expression during neurogenesis.

MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data

MarkovHC is a clustering algorithm that identifies cell types, trajectories, and critical points in single-cell omics data by reconstructing a pseudo-energy landscape based on metastability theory.

MyoD is a structure organizer of 3D genome architecture in muscle cells

The paper shows MyoD organizes 3D genome architecture in muscle cells and demonstrates H3K27ac is insufficient for MyoD-induced chromatin loops.

Deep-learning enables proteome-scale identification of phase-separated protein candidates from immunofluorescence images

The paper uses deep learning to identify phase-separated protein candidates from immunofluorescence images by classifying spherical droplet structures.

3D Genome Analysis Identifies Enhancer Hijacking Mechanism for High-Risk Factors in Human T-Lineage Acute Lymphoblastic Leukemia

The paper identifies 3D genome alterations and enhancer hijacking mechanisms in T-lineage acute lymphoblastic leukemia (T-ALL) using integrated analyses of 18 patients and 4 controls.

HBP: an integrative and flexible pipeline for the interaction analysis of Hi-C dataset

HBP is a pipeline for analyzing Hi-C data to infer 3D genome structure and chromatin interactions, with confidence estimation and integration capabilities for other datasets.