Yi Qin Gao

GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles

GenoME predicts genomic profiles and perturbations using ATAC-seq and DNA sequence, generalizing to new cell types and identifying enhancer-promoter connections.

Information Network Flux interprets the importance of regulatory circuits in the protein and gene spaces

The paper introduces INF, an algorithm that integrates protein and gene level information to analyze regulatory circuits and their role in cellular responses and identity.

Assisting and Accelerating NMR Assignment with Restrained Structure Prediction

This paper introduces RASP, a deep learning model that improves structure prediction with restraints, and FAAST, a pipeline that accelerates NMR NOESY peak assignment and structure ensemble generation.

Hierarchical prediction and perturbation of chromatin organization reveal how loop domains mediate higher-order architectures

HiCGen predicts and perturbs chromatin organization, revealing loop domains' role in higher-order structures like TADs and compartments.

Integrating various Experimental Information to Assist Protein Complex Structure Prediction by GRASP

GRASP improves protein complex structure prediction by integrating experimental restraints, outperforming existing tools in accuracy and flexibility.

Tokenizing Foldable Protein Structures with Machine-Learned Artificial Amino-Acid Vocabulary

This paper introduces ProTokens, artificial amino-acid tokens that enable efficient compression and processing of protein structures for design and analysis.

Characterization of network hierarchy reflects cell-state specificity in genome organization

The paper analyzes Hi-C data to show that chromatin contact networks in cancer and leukemia have reduced information transmission efficiency and shallower hierarchy compared to normal tissues.

Computational Enhanced Hi-C data reveals the function of structural geometry in genomic regulation

The paper develops CTG, a diffusion-based method to improve Hi-C data reliability and reveal structural genomic regulation.

Understanding gene regulatory mechanisms based on gene classification

This study examines how CpG density distribution around transcription start sites influences gene transcription and regulation patterns in human genes.

Progressive domain segregation in early embryonic development and underlying correlation to genetic and epigenetic changes

The paper examines chromatin structural changes and epigenetic reprogramming during mouse and human embryonic development, showing domain segregation correlates with genetic and epigenetic changes.

Toward an understanding of the relation between gene regulation and 3D genome organization

The paper quantifies the relationship between 3D chromatin structure and gene regulation by analyzing domain segregation and gene expression patterns in different tissues.