| 2009 | SAC | Construct anticancer drug-drug correlation network. | Jiao Li, Pamela Crowell, Jake Yue Chen |
| 2008 | SAC | Towards an integrative human pathway database for systems biology applications. | Harini N. Kasamsetty, Xiaogang Wu, Jake Yue Chen |
| 2008 | SAC | Mining disease-specific molecular association profiles from biomedical literature: a case study. | Jiao Li, Xiaoyan Zhu, Jake Yue Chen |
| 2006 | PSB | Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data. | Jake Yue Chen, Changyu Shen, Andrey Y. Sivachenko |
| 2006 | SAC | An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies. | Jake Yue Chen, Sarah L. Pinkerton, Changyu Shen, Mu Wang |
| 2005 | SAC | A complex biological database querying method. | Jake Yue Chen, John V. Carlis, Ning Gao |
| 2004 | KDD | High-throughput Protein Interactome Data: Minable or Not? | Jake Yue Chen, Andrey Y. Sivachenko, Lang Li |
| 2004 | SAC | Editorial message: special track on bioinformatics. | Warren T. Jones, Mathew J. Palakal, Jake Yue Chen |
| 2003 | SAC | Similar_Join: Extending DBMS with a Bio-specific Operator. | Jake Yue Chen, John V. Carlis |