Liming Cai

Dong Zhang, Xingran Xue, Russell L. Malmberg, Liming Cai: TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes. Bioinformatics 28(20): 2696-2697 (2012)

Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Ying-Wai Li, Russell L. Malmberg, Liming Cai: Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds. BMC Bioinformatics 13(S-5): S1 (2012)

Leilei Guo, Dong Zhang, Yingfeng Wang, Russell L. Malmberg, Michael J. McEachern, Liming Cai: TRFolder: computational prediction of novel telomerase RNA structures in yeast genomes. IJBRA 7(1): 63-81 (2011)

Timothy I. Shaw, Amir Manzour, Yingfeng Wang, Russell L. Malmberg, Liming Cai: Analyzing Modular RNA Structure reveals Low Global Structural Entropy in microRNA Sequence. J. Bioinformatics and Computational Biology 9(2): 283-298 (2011)

Pooya Shareghi, Yingfeng Wang, Russell L. Malmberg, Liming Cai: Simultaneous Prediction of RNA Secondary Structure and Helix Coaxial Stacking. BIBM 2011: 89-95

Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Ying-Wai Li, Russell L. Malmberg, Liming Cai: Stable stem enabled shannon entropies distinguish non-coding RNAs from random backgrounds. ICCABS 2011: 184-189

Liming Cai, Xiuzhen Huang: Fixed-Parameter Approximation: Conceptual Framework and Approximability Results. Algorithmica 57(2): 398-412 (2010)

Russell L. Malmberg, Timothy I. Shaw, Liming Cai: RNApasta: a tool for analysis of RNA structural alignments. IJBRA 6(6): 571-583 (2010)

Yingfeng Wang, Zhibin Huang, Yong Wu, Russell L. Malmberg, Liming Cai: RNATOPS-W: a web server for RNA structure searches of genomes. Bioinformatics 25(8): 1080-1081 (2009)

Liming Cai, Xuezhi Li: A note on global stability of an SEI epidemic model with acute and chronic stages. Applied Mathematics and Computation 196(2): 923-930 (2008)

Zhibin Huang, Yong Wu, Joseph Robertson, Liang Feng, Russell L. Malmberg, Liming Cai: Fast and accurate search for non-coding RNA pseudoknot structures in genomes. Bioinformatics 24(20): 2281-2287 (2008)

Liming Cai, Xiuzhen Huang, Chunmei Liu, Frances A. Rosamond, Yinglei Song: Parameterized Complexity and Biopolymer Sequence Comparison. Comput. J. 51(3): 270-291 (2008)

Liming Cai, Michael R. Fellows, David W. Juedes, Frances A. Rosamond: The Complexity of Polynomial-Time Approximation. Theory Comput. Syst. 41(3): 459-477 (2007)

Dongsheng Che, Jizhen Zhao, Liming Cai, Ying Xu: Operon Prediction in Microbial Genomes Using Decision Tree Approach. CIBCB 2007: 135-142

Jizhen Zhao, Dongsheng Che, Liming Cai: Comparative Pathway Prediction Via Unified Graph Modeling of Genomic Structure Information. ISBRA 2007: 627-637

Jizhen Zhao, Dongsheng Che, Liming Cai: Comparative Pathway Annotation with Protein-DNA Interaction and Operon Information via Graph Tree Decomposition. Pacific Symposium on Biocomputing 2007: 496-507

Yinglei Song, Chunmei Liu, Russell L. Malmberg, Congzhou He, Liming Cai: Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots. IJBRA 2(3): 289-304 (2006)

Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai: Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment. IEEE/ACM Trans. Comput. Biology Bioinform. 3(4): 423-432 (2006)

Jizhen Zhao, Liming Cai, Russell L. Malmberg: Learning the Parameters of Stochastic Grammar Models for RNA Structures with Pseudoknots. GrC 2006: 170-175

Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai: Peptide sequence tag-based blind identification of post-translational modifications with point process model. ISMB (Supplement of Bioinformatics) 2006: 307-313

Liming Cai, Xiuzhen Huang: Fixed-Parameter Approximation: Conceptual Framework and Approximability Results. IWPEC 2006: 96-108

Chunmei Liu, Yinglei Song, Bo Yan, Ying Xu, Liming Cai: Fast De novo Peptide Sequencing and Spectral Alignment via Tree Decomposition. Pacific Symposium on Biocomputing 2006: 255-266

Yinglei Song, Chunmei Liu, Russell L. Malmberg, Liming Cai: Phylogenetic Network Inferences Through Efficient Haplotyping. WABI 2006: 68-79

Jizhen Zhao, Russell L. Malmberg, Liming Cai: Rapid ab initio RNA Folding Including Pseudoknots Via Graph Tree Decomposition. WABI 2006: 262-273

Dongsheng Che, Shane T. Jensen, Liming Cai, Jun S. Liu: BEST: Binding-site Estimation Suite of Tools. Bioinformatics 21(12): 2909-2911 (2005)

Ying Xu, Liming Cai, Zhiping Weng: Preface. J. Comput. Sci. Technol. 20(4): 433 (2005)

Yinglei Song, Jizhen Zhao, Chunmei Liu, Kan Liu, Russell L. Malmberg, Liming Cai: RNA Structural Homology Search with a Succinct Stochastic Grammar Model. J. Comput. Sci. Technol. 20(4): 454-464 (2005)

Chunmei Liu, Yinglei Song, Russell L. Malmberg, Liming Cai: Profiling and Searching for RNA Pseudoknot Structures in Genomes. T. Comp. Sys. Biology 2: 37-47 (2005)

Yinglei Song, Chunmei Liu, Russell L. Malmberg, Fangfang Pan, Liming Cai: Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes. CSB 2005: 223-234

Chunmei Liu, Yinglei Song, Russell L. Malmberg, Liming Cai: Profiling and Searching for RNA Pseudoknot Structures in Genomes. International Conference on Computational Science (2) 2005: 968-975

Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai: Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment. WABI 2005: 376-388

Liming Cai, David W. Juedes: On the existence of subexponential parameterized algorithms. J. Comput. Syst. Sci. 67(4): 789-807 (2003)

Liming Cai, Russell L. Malmberg, Yunzhou Wu: Stochastic modeling of RNA pseudoknotted structures: a grammatical approach. ISMB (Supplement of Bioinformatics) 2003: 66-73

Liming Cai, David W. Juedes, Iyad A. Kanj: The inapproximability of non-NP-hard optimization problems. Theor. Comput. Sci. 289(1): 553-571 (2002)

Liming Cai, David W. Juedes: Subexponential Parameterized Algorithms Collapse the W-Hierarchy. ICALP 2001: 273-284

Liming Cai, Jianer Chen, Johan Håstad: Circuit Bottom Fan-In and Computational Power. SIAM J. Comput. 27(2): 341-355 (1998)

Liming Cai, David W. Juedes, Iyad A. Kanj: The Inapproximability of Non NP-hard Optimization Problems. ISAAC 1998: 437-446

Liming Cai, Jianer Chen, Rodney G. Downey, Michael R. Fellows: On the parameterized complexity of short computation and factorization. Arch. Math. Log. 36(4-5): 321-337 (1997)

Liming Cai, Jianer Chen, Rodney G. Downey, Michael R. Fellows: Advice Classes of Parameterized Tractability. Ann. Pure Appl. Logic 84(1): 119-138 (1997)

Liming Cai, Jianer Chen: On Fixed-Parameter Tractability and Approximability of NP Optimization Problems. J. Comput. Syst. Sci. 54(3): 465-474 (1997)

Liming Cai, Jianer Chen: On the Amount of Nondeterminism and the Power of Verifying. SIAM J. Comput. 26(3): 733-750 (1997)

Karl R. Abrahamson, Liming Cai, Steve Gordon: A Grammar Characterization of Logarithmic-Space Computation. New Trends in Formal Languages 1997: 247-255

Liming Cai, Jianer Chen, Johan Håstad: Circuit Bottom Fan-in and Computational Power. IEEE Conference on Computational Complexity 1997: 158-164

Liming Cai: The Computational Complexity of Linear PCGSs. Computers and Artificial Intelligence 15(2-3) (1996)

Liming Cai, Jianer Chen, Rodney G. Downey, Michael R. Fellows: On the Structure of Parameterized Problems in NP. Inf. Comput. 123(1): 38-49 (1995)

Liming Cai, Jianer Chen: On Input Read-Modes of Alternating Turing Machines. Theor. Comput. Sci. 148(1): 33-55 (1995)

Liming Cai, Jianer Chen: On log-Time Alternating Turing Machines of Alternation Depth k (Extended Abstract). COCOON 1995: 282-291

Liming Cai: The Computational Complexity of PCGS with Regular Components. Developments in Language Theory 1995: 209-219

Liming Cai, Jianer Chen, Rodney G. Downey, Michael R. Fellows: On the Structure of Parameterized Problems in NP (Extended Abstract). STACS 1994: 509-520

Liming Cai, Jianer Chen: On Fixed-Parameter Tractability and Approximability of NP-Hard Optimization Problems. ISTCS 1993: 118-126

Liming Cai, Jianer Chen: On the Amount of Nondeterminism and the Power of Verifying (Extended Abstract). MFCS 1993: 311-320