A5057593998- Pancreatic function and diabetes
- Single-cell and spatial transcriptomics
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Machine Learning in Bioinformatics
- Cancer Genomics and Diagnostics
- Retinal Development and Disorders
- Venomous Animal Envenomation and Studies
- Complex Network Analysis Techniques
- Genomics and Phylogenetic Studies
- Cellular transport and secretion
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Metabolism, Diabetes, and Cancer
- Opinion Dynamics and Social Influence
- Data Visualization and Analytics
- Molecular Biology Techniques and Applications
Shanghai Jiao Tong University
2023-2025
Ministry of Education of the People's Republic of China
2025
University of Chinese Academy of Sciences
2023
National Center for Mathematics and Interdisciplinary Sciences
2023
Academy of Mathematics and Systems Science
2023
Chinese Academy of Sciences
2023
Anhui Normal University
2021
McGill University
2015
Blindness due to retinal degeneration affects millions of people worldwide, but many disease-causing mutations remain unknown. PNPLA6 encodes the patatin-like phospholipase domain containing protein 6, also known as neuropathy target esterase (NTE), which is toxic organophosphates that induce human paralysis severe axonopathy large neurons. Mutations in cause spastic paraplegia characterized by motor neuron degeneration. Here we identify childhood blindness seven families with degeneration,...
Abstract Due to the similarity human hepatocytes, porcine hepatocytes play an important role in hepatic research and drug evaluation. However, once were cultured vitro, it was often prone dedifferentiate, resulting loss of their characteristic features normal functions, which impede application liver transplantation hepatotoxic drugs Up now, this process has yet be thoroughly investigated from single‐cell resolution multi‐omics perspective. In study, we utilized 10× multiome technology...
Abstract Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of state alterations and response mechanisms under chemical perturbations, which plays a crucial role drug discovery screening processes. Considering that experimental measurements need substantial time cost, we developed deep learning-based method called Molecule-induced Transcriptional Change Predictor (MiTCP) to predict (CTPs) 978 landmark genes...
Here we present stFormer, a foundation model which incorporates ligand genes within spatial niches into Transformer encoders of single-cell transcriptomics. We demonstrate that despite moderate pretraining data size, the spatially informed gene representations generated by stFormer more consistently cluster cells, accurately encode hierarchy and membership receptor-dependent networks, remarkably boost identification ligand-receptor interaction pairs, could simulate perturbation effects...
Pancreatic islet failure is a key characteristic of type 2 diabetes besides insulin resistance. To get molecular insights into the pathology islets in diabetes, we developed computational approach to integrating expression profiles Goto-Kakizaki and Wistar rat from designed experiment with those human an observational study. A principal gene-eigenvector characterized by up-regulated angiogenesis down-regulated oxidative phosphorylation was identified conserved across two species. In case...
Abstract The pathogenesis of diseases is closely associated with genes, and the discovery disease genes holds significant importance for understanding mechanisms designing targeted therapeutics. However, biological validation all expensive challenging. In this study, we propose DGP-AMIO, a computational method based on graph attention networks, to rank unknown identify potential novel by integrating multi-omics gene interaction networks from multiple data sources. DGP-AMIO outperforms other...
Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges the existing gap-closing methods, based on either k-mer representation by de Bruijn graph or overlap-layout-consensus paradigm. Besides, chimeric reads will cause erroneous k-mers former false overlaps of latter.We propose a novel local assembly approach gap closing, called RegCloser. It represents read coordinates their respectively parameters observations...
Community structure is one of the important features in networks to understand complex systems. Detecting community often formulated as an optimization problem recent years. The nature-inspired methods have been used deal with this problem. However, these algorithms are facing challenges when they applied solve detection problems a large-scale social network. In paper, we propose Hierarchical Cooperative Social Spider Algorithm (HCSSA), novel method reveal structures networks. spider...