| 2025 | AIME | Generating Novel Linker Structures in Antibody-Drug Conjugates with Diffusion Models. | April Cao, Jake Y. Chen |
| 2025 | KDD | 24 | Da Yan, Truong-Son Hy, Jake Y. Chen, Mohammed J. Zaki |
| 2024 | KDD | 23 | Da Yan, Ahmed Abdeen Hamed, Jake Y. Chen, Mohammed J. Zaki |
| 2024 | KDD | Health Day: Building Health AI Ecosystem: From Data Harmonization to Knowledge Discovery. | Jake Y. Chen, Peipei Ping |
| 2023 | KDD | 22nd International Workshop on Data Mining in Bioinformatics (BIOKDD 2023). | Da Yan, Ariful Azad, Jie Hou, Jake Y. Chen, Mohammed J. Zaki |
| 2023 | WWW | Cross-Team Collaboration and Diversity in the Bridge2AI Project. | Huimin Xu, Chitrank Gupta, Zhandos Sembay, Swathi Thaker, Pamela Payne-Foster, Jake Y. Chen, Ying Ding |
| 2022 | EGPGV | GraphWaGu: GPU Powered Large Scale Graph Layout Computation and Rendering for the Web. | Landon Dyken, Pravin Poudel, Will Usher, Steve Petruzza, Jake Y. Chen, Sidharth Kumar |
| 2022 | KDD | 21th International Workshop on Data Mining in Bioinformatics (BIOKDD 2022). | Da Yan, Catia Pesquita, Carsten Grg, Jake Y. Chen, Mohammed J. Zaki |
| 2021 | AMIA | PAGER-CoV-Run: An online interactive analytical platform for COVID-19 functional genomic downstream analysis. | Zongliang Yue, Nishant Batra, Hui-Chen Hsu, John Mountz, Jake Y. Chen |
| 2021 | KDD | 20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021). | Da Yan, Steve Qin, Debswapna Bhattacharya, Jake Y. Chen, Mohammed J. Zaki |
| 2020 | IRI | Empowering Team Science Across the Translational Spectrum with the UAB Biomedical Research Infrastructure Technology Enhancement (U-BRITE). | James J. Cimino, Wayne H. Liang, Jelai Wang, Dongmei Sun, John David Osborne, Amy Y. Wang, S. Louis Bridges, Matthew C. Wyatt, Jake Y. Chen |
| 2016 | CIKM | DTMBIO 2016: The Tenth International Workshop on Data and Text Mining in Biomedical Informatics. | Sangwoo Kim, Jake Y. Chen, Vincenzo Cutello, Doheon Lee |
| 2009 | CBMS | A neural network approach to multi-biomarker panel development based on LC/MS/MS proteomics profiles: A case study in breast cancer. | Fan Zhang, Jake Y. Chen |