| DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays Z Chen, J Zhang, J Liu, Y Dai, D Lee, MR Min, M Xu, M Gerstein Bioinformatics 37 (Supplement_1), i280-i288, 2021 | 8 | 2021 |
| iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease Z Duan, Y Dai, A Hwang, C Lee, K Xie, C Xiao, M Xu, MJ Girgenti, ... PLOS Computational Biology 19 (9), e1011444, 2023 | 1 | 2023 |
| Translator: A Transfer Learning Approach to Facilitate Single-Cell ATAC-Seq Data Analysis from Reference Dataset S Xu, M Skarica, A Hwang, Y Dai, C Lee, MJ Girgenti, J Zhang Journal of Computational Biology 29 (7), 619-633, 2022 | 1 | 2022 |
| Single-cell genomics and regulatory networks for 388 human brains PS Emani, JJ Liu, D Clarke, M Jensen, J Warrell, C Gupta, R Meng, ... bioRxiv, 2024.03. 18.585576, 2024 | | 2024 |
