Hao Chen
Assistant Professor
Department of Computer Science
Contact
Building & Room:
SEO 1220
Address:
851 S. Morgan St., Chicago, IL 60607
Email:
Related Sites:
About
The research in the lab lies at the intersection of computational biology and AI/machine learning, with a focus on developing data-driven approaches to explore biological systems. By combining machine learning with single-cell and spatial omics data, the lab aims to uncover the dynamics of gene regulation in cellular fates and the mechanisms of cellular responses to stimuli, with implications in drug discovery and disease modeling. The group is also actively working on deep learning approaches for drug discovery, as well as genome and protein sequence modeling.
Selected Publications
- Chen H, Lee YJ, Ovando JA, Rosas L, Rojas M, Mora AL, Bar-Joseph Z, and Lugo-Martinez J. “scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics.” Cell Reports Methods, 4, 10, 2024.
- Chen H, King F, Zhou B, Wang Y, Canedy C, Hayashi J, Zhong Y, Chang M, Pache L, Wong J, Jia Y, Joslin J, Jiang T, Benner C, Chanda S, and Zhou Y. “Drug target prediction through deep learning functional representation of gene signatures.” Nature Communications, 15, 1853, 2024.
- Chen H, Li D, and Bar-Joseph Z. “SCS: cell segmentation for high-resolution spatial transcriptomics.” Nature Methods, 20, 1237–1243, 2023.
- Chen H, Li D, and Bar-Joseph Z. “Cell segmentation for high-resolution spatial transcriptomics.” Proceedings of the 27th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Istanbul, Turkey, Apr 16-19, 2023.
- Chen H, Shaw D, Bu D, and Jiang T. “FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks.” NAR Genomics and Bioinformatics, 3, lqab057, 2021.
- Chen H, Shaw D, Zeng J, Bu D, and Jiang T. “DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning.” Bioinformatics, 35, i284-i294, 2019; Proceedings of the 27th Annual International Conference on Intelligent Systems for Molecular Biology and 17th European Conference on Computational Biology (ISMB/ECCB), Basel, Switzerland, July 21-25, 2019.
Education
Postdoctoral Fellow, Carnegie Mellon University, 2024
Ph.D., University of California, Riverside, 2021