| 2011 | IUI | How to serve soup: interleaving demonstration and assisted editing to support nonprogrammers. | Melinda T. Gervasio, Will Haines, David N. Morley, Thomas J. Lee, C. Adam Overholtzer, Shahin Saadati, Aaron Spaulding |
| 2009 | IAAI | Learning by Demonstration to Support Military Planning and Decision Making. | Thomas D. Garvey, Melinda T. Gervasio, Thomas J. Lee, Karen L. Myers, Carl Angiolillo, Matthew E. Gaston, Janette Knittel, Jake Kolojejchick |
| 2008 | ISMB | Annotation-based inference of transporter function. | Thomas J. Lee, Ian T. Paulsen, Peter D. Karp |
| 2005 | AAAI | Online Query Relaxation via Bayesian Causal Structures Discovery. | Ion Muslea, Thomas J. Lee |
| 1999 | AAAI | Generating qualitatively Different Plans througt Metatheoretic Biases. | Karen L. Myers, Thomas J. Lee |
| 1998 | ICML | Bayesian Network Classification with Continuous Attributes: Getting the Best of Both Discretization and Parametric Fitting. | Nir Friedman, Moiss Goldszmidt, Thomas J. Lee |
| 1997 | ISMB | Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity. | Marie desJardins, Peter D. Karp, Markus Krummenacker, Thomas J. Lee, Christos A. Ouzounis |