| 2025 | RECOMB | An Adversarial Scheme for Integrating Multi-modal Data on Protein Function. | Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan |
| 2019 | RECOMB | Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. | Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng |
| 2018 | PSB | Annotating gene sets by mining large literature collections with protein networks. | Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker |
| 2018 | RECOMB | Deciphering Signaling Specificity with Deep Neural Networks. | Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng |
| 2013 | PSB | Session Introduction. | Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader |
| 2007 | ISMB | SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. | Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan |
| 2006 | PSB | Discovering Regulated Networks During HIV-1 Latency and Reactivation. | Sourav Bandyopadhyay, Ryan M. Kelley, Trey Ideker |
| 2005 | RECOMB | Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. | Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan |
| 2005 | RECOMB | Comparison of Protein-Protein Interaction Confidence Assignment Schemes. | Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker |
| 2004 | PSB | Session Introduction. | Trey Ideker, Erik K. Neumann, Vincent Schchter |
| 2004 | RECOMB | Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. | Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp |
| 2002 | ISMB | Discovering regulatory and signalling circuits in molecular interaction networks. | Trey Ideker, Owen Ozier, Benno Schwikowski, Andrew F. Siegel |