The Research page highlights chromatin regulation, enhancer modeling, and biomedical data applications. Neuroscience-related papers are fully listed here and can be filtered above. Corresponding authors are marked with *.

2026

npj Systems Biology and Applications TAD / 3D Genome

CT-TADB predicts TAD boundaries without Hi-C by integrating DNA sequences and epigenomic features

Chen T, Wang S, Jin Y, Yuan Y, Liang Z, Shen Y

BMC Genomics Chromatin Interaction

UniChrom: a universal deep learning architecture for cross-scale chromatin interaction prediction

Wang S, Chen T, Yang Z, Xu X, Shen Y

IEEE Transactions on Computational Biology and Bioinformatics Super Enhancer

TransSE: A Transfer Learning-Based Predictive Model for Distinguishing Super Enhancers and Typical Enhancers

Shen Y, Xu X, Wang S, Chen T, Zhang Z, Sun Q, Sun X, Liang Z, Gao J

Neural Regeneration Research Neuro / Multi-omics

Genetic and pathway complexity in Alzheimer's disease: Insights from multi-omic data about the immune response and mitochondrial function

Xu X, Li J, Wang F, Xue K, He J, Meng X, Shen Y

2025

Briefings in Bioinformatics Enhancer Interaction

ETNet: an interpretable transformer framework for enhancer-enhancer interaction prediction with cross-context transferability

Wang S, Chen T, Yang Z, Liang Z, Shen Y

CNS Neuroscience and Therapeutics Neuro / Multi-omics

Integrated Multi-Omics Analysis and Cross-Model Validation Reveal Mitochondrial Signatures in Alzheimer's Disease

Xu X, Fan SS, Li J, Wu H, He J, He Y, Meng XY, Shen Y

Molecular Neurobiology Neuro / Multi-omics

Systematic Identification of Mitochondrial Signatures in Alzheimer's Disease and Inflammatory Bowel Disease

Wang F, Wang J, Chen T, Wang S, Meng X, Shen Y, Xu X

Frontiers in Aging Neuroscience Neuro / Multi-omics

Deciphering novel mitochondrial signatures: multi-omics analysis uncovers cross-disease markers and oligodendrocyte pathways in Alzheimer's disease and glioblastoma

Xu X, Wang J, Chen T, Wang S, Wang F, He J, Meng XY, Shen Y

2022

Briefings in Bioinformatics Open Chromatin

CharID: a two-step model for universal prediction of interactions between chromatin accessible regions

Shen Y, Zhong Q, Liu T, Wen Z, Shen W, Li L*

2021

Genomics, Proteomics and Bioinformatics Plant Genomics

CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes

Shen Y, Chen LL, Gao J*

2020

Science Advances Genome

The genome of jojoba (Simmondsia chinensis): A taxonomically isolated species that directs wax ester accumulation in its seeds

Sturtevant D+, Lu S+, Zhou ZW+, Shen Y+, et al. Chen LL*, Chapman KD*, Guo L*

2019

Carcinogenesis Deep Learning

A deep learning model based on sparse auto-encoder for prioritizing cancer-related genes and drug target combinations

Chang JW, Ding Y, Tahir ul Qamar M, Shen Y, Gao J*, Chen LL*

This page is a maintained list aligned with ORCID and PubMed. For corrections, email shenyin@ahmu.edu.cn.