| 2014 | ECCB | Ab initio Prediction of RNA Nucleotide Interactions with Backbone | Liang Ding, Xingran Xue, Sal LaMarca, Mohammad Mohebbi, Abdul Samad, Russell L. Malmberg, Liming Cai |
| 2014 | LATA | Stochastic k-Tree Grammar and Its Application in Biomolecular Structure Modeling. | Liang Ding, Abdul Samad, Xingran Xue, Xiuzhen Huang, Russell L. Malmberg, Liming Cai |
| 2007 | CIBCB | Operon Prediction in Microbial Genomes Using Decision Tree Approach. | Dongsheng Che, Jizhen Zhao, Liming Cai, Ying Xu |
| 2007 | PSB | Comparative Pathway Annotation with Protein-DNA Interaction and Operon Information via Graph Tree Decomposition. | Jizhen Zhao, Dongsheng Che, Liming Cai |
| 2006 | GRC | Learning the Parameters of Stochastic Grammar Models for RNA Structures with Pseudoknots. | Jizhen Zhao, Liming Cai, Russell L. Malmberg |
| 2006 | ISMB | Peptide sequence tag-based blind identification of post-translational modifications with point process model. | Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai |
| 2006 | PSB | Fast De novo Peptide Sequencing and Spectral Alignment via Tree Decomposition. | Chunmei Liu, Yinglei Song, Bo Yan, Ying Xu, Liming Cai |
| 2006 | WABI | Phylogenetic Network Inferences Through Efficient Haplotyping. | Yinglei Song, Chunmei Liu, Russell L. Malmberg, Liming Cai |
| 2006 | WABI | Rapid | Jizhen Zhao, Russell L. Malmberg, Liming Cai |
| 2005 | ICCS | Profiling and Searching for RNA Pseudoknot Structures in Genomes. | Chunmei Liu, Yinglei Song, Russell L. Malmberg, Liming Cai |
| 2005 | WABI | Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment. | Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai |
| 2003 | ISMB | Stochastic modeling of RNA pseudoknotted structures: a grammatical approach. | Liming Cai, Russell L. Malmberg, Yunzhou Wu |
| 2001 | ICALP | Subexponential Parameterized Algorithms Collapse the W-Hierarchy. | Liming Cai, David W. Juedes |
| 2000 | CEC | Evolutionary computation techniques for multiple sequence alignment. | Liming Cai, David Juedes, Evgueni Liakhovitch |
| 1998 | ISAAC | The Inapproximability of Non NP-hard Optimization Problems. | Liming Cai, David W. Juedes, Iyad A. Kanj |
| 1995 | COCOON | On log-Time Alternating Turing Machines of Alternation Depth k (Extended Abstract). | Liming Cai, Jianer Chen |
| 1995 | DLT | The Computational Complexity of PCGS with Regular Components. | Liming Cai |
| 1994 | STACS | On the Structure of Parameterized Problems in NP (Extended Abstract). | Liming Cai, Jianer Chen, Rodney G. Downey, Michael R. Fellows |
| 1993 | MFCS | On the Amount of Nondeterminism and the Power of Verifying (Extended Abstract). | Liming Cai, Jianer Chen |