| 2025 | ICLR | Learning to Discover Regulatory Elements for Gene Expression Prediction. | Xingyu Su, Haiyang Yu, Degui Zhi, Shuiwang Ji |
| 2025 | RECOMB | Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data. | Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang |
| 2025 | WABI | An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. | Ahsan Sanaullah, Degui Zhi, Shaojie Zhang |
| 2022 | AMIA | Pancreatic cancer risk prediction using recurrent neural network models trained on electronic health records and claims data. | Laila Rasmy, Peter Beshara, Bijun S. Kannadath, Degui Zhi |
| 2022 | AMIA | Explainability versus Accuracy to Engender Trust. | Angela Ross, Laila Rasmy, Degui Zhi, Kathleen McGrow |
| 2022 | AMIA | Combining Transfer Learning with Graph Attention Models for HIV Risk Prediction. | Evan Yu, Cui Tao, Jingcheng Du, Degui Zhi, Yang Xiang, Kayo Fujimoto, Xi Luo, John A. Schneider |
| 2022 | WABI | Haplotype Threading Using the Positional Burrows-Wheeler Transform. | Ahsan Sanaullah, Degui Zhi, Shaoije Zhang |
| 2021 | AMIA | Generalizable Gated Recurrent Neural Network based model to predict COVID-19 patient outcomes on admission. | Laila Rasmy, Bijun S. Kannadath, Masayuki Nigo, Ziqian Xie, Bingyu Mao, Khush A. Patel, Yujia Zhou, Xiao Dong, Hua Xu, Degui Zhi |
| 2021 | AMIA | CovRNN: predicting outcomes of COVID-19 patients on admission using their electronic health records with minimal data processing. | Laila Rasmy, Masayuki Nigo, Bijun S. Kannadath, Ziqian Xie, Bingyu Mao, Khush A. Patel, Wanheng Zhang, Yujia Zhou, Angela Ross, Hua Xu, Degui Zhi |
| 2021 | WABI | Efficient Haplotype Block Matching in Bi-Directional PBWT. | Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi |
| 2020 | RECOMB | d-PBWT: Dynamic Positional Burrows-Wheeler Transform. | Ahsan Sanaullah, Degui Zhi, Shaojie Zhang |
| 2018 | AMIA | Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data. | Jing An, Mandana Salimi, Anupama E. Gururaj, Cui Tao, Degui Zhi, Hua Xu |
| 2018 | AMIA | Asthma Onset Prediction Using Structured EMR Data. | Yang Xiang, Jun Xu, Jingcheng Du, Degui Zhi, Cui Tao |
| 2017 | AMIA | Clinical Named Entity Recognition Using Deep Learning Models. | Yonghui Wu, Min Jiang, Jun Xu, Degui Zhi, Hua Xu |
| 2017 | RECOMB | Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform. | Ardalan Naseri, Xiaoming Liu, Shaojie Zhang, Degui Zhi |
| 2007 | WABI | Alignment-Free Local Structural Search by Writhe Decomposition. | Degui Zhi, Maxim Shatsky, Steven E. Brenner |