01
Algorithm-driven computational biology
Methods for open chromatin, enhancers, and 3D genome structure, including CharID, CharPlant, UniChrom, ETNet, TransSE, and CT-TADB.
Research details ->Computational Biology | Deep Learning
Deep learning for
genome regulation
and biomedical data
Shen Lab is based in the School of Biomedical Engineering at Anhui Medical University. We develop interpretable deep-learning methods and open-source software for 3D chromatin architecture, enhancer biology, open chromatin, and biomedical data analysis.
2022Lab established
11Listed papers
6Published codebases
About
Who we are
We combine deep learning with biomedical knowledge to build methods and software for real scientific questions.
02
Open-source published software
Code for peer-reviewed methods is released on GitHub so collaborators can reproduce analyses and extend the tools.
Browse software ->03
Training and collaboration
We welcome motivated undergraduate and graduate students in computational biology, intelligent medicine, and data science.
Join us ->Selected work
Highlighted contributions
Recent work in chromatin regulation and computational biology. Neuroscience multi-omics papers appear only on the Publications page.
CT-TADB
Predicts TAD boundaries without Hi-C by integrating DNA sequence and epigenomic features.
UniChrom
A universal deep-learning architecture for cross-scale chromatin interaction prediction.
ETNet
An interpretable transformer framework for enhancer-enhancer interaction prediction with cross-context transferability.
TransSE
Transfer learning to distinguish super-enhancers from typical enhancers across biological contexts.
Open source
Code for published papers
GitHub repositories associated with peer-reviewed articles only.
Principal investigator
Lab director
Yin Shen
Ph.D.
Associate Professor
Master's Supervisor
Dept. of Biomedical Information Engineering
School of Biomedical Engineering
Anhui Medical University
Master's Supervisor
Dept. of Biomedical Information Engineering
School of Biomedical Engineering
Anhui Medical University
Biography
Dr. Yin Shen received his Ph.D. from Huazhong Agricultural University and is currently an Associate Professor in the Department of Biomedical Information Engineering, School of Biomedical Engineering, Anhui Medical University. His research focuses on deep-learning algorithms, computational biology, and biomedical big-data analysis.
He has published more than 10 SCI papers in venues including Science Advances, Briefings in Bioinformatics, Genomics, Proteomics and Bioinformatics, BMC Genomics, npj Systems Biology and Applications, and IEEE Transactions on Computational Biology and Bioinformatics, and is PI of an NSFC Youth Science Fund project.
Education, appointments and recruitment