| 2013 | EDM | Tuned Models of Peer Assessment in MOOCs. | Chris Piech, Jonathan Huang, Zhenghao Chen, Chuong B. Do, Andrew Y. Ng, Daphne Koller |
| 2009 | ICML | Proximal regularization for online and batch learning. | Chuong B. Do, Quoc V. Le, Chuan-Sheng Foo |
| 2009 | ICML | A majorization-minimization algorithm for (multiple) hyperparameter learning. | Chuan-Sheng Foo, Chuong B. Do, Andrew Y. Ng |
| 2008 | ISMB | A max-margin model for efficient simultaneous alignment and folding of RNA sequences. | Chuong B. Do, Chuan-Sheng Foo, Serafim Batzoglou |
| 2008 | RECOMB | Automatic Parameter Learning for Multiple Network Alignment. | Jason Flannick, Antal F. Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou |
| 2008 | RECOMB | Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. | Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou |
| 2006 | ISMB | CONTRAfold: RNA secondary structure prediction without physics-based models. | Chuong B. Do, Daniel A. Woods, Serafim Batzoglou |
| 2006 | RECOMB | CONTRAlign: Discriminative Training for Protein Sequence Alignment. | Chuong B. Do, Samuel S. Gross, Serafim Batzoglou |
| 2004 | AAAI | PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. | Chuong B. Do, Michael Brudno, Serafim Batzoglou |
| 2003 | ISMB | Glocal alignment: finding rearrangements during alignment. | Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou |