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

LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference. - Carolyn J. Lawrence; Christian M. Zmasek; R. Kelly Dawe; Russell L. Malmberg (Bioinform., 2004)

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

Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment. - Yinglei Song; Chunmei Liu; Xiuzhen Huang; Russell L. Malmberg; Ying Xu 001; Liming Cai (WABI, 2005)

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

Profiling and Searching for RNA Pseudoknot Structures in Genomes. - Chunmei Liu; Yinglei Song; Russell L. Malmberg; Liming Cai (Trans. Comp. Sys. Biology, 2005)

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

Phylogenetic Network Inferences Through Efficient Haplotyping. - Yinglei Song; Chunmei Liu; Russell L. Malmberg; Liming Cai (WABI, 2006)

Rapid ab initio RNA Folding Including Pseudoknots Via Graph Tree Decomposition. - Jizhen Zhao; Russell L. Malmberg; Liming Cai (WABI, 2006)

Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots. - Yinglei Song; Chunmei Liu; Russell L. Malmberg; Congzhou He; Liming Cai (Int. J. Bioinform. Res. Appl., 2006)

Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment. - Yinglei Song; Chunmei Liu; Xiuzhen Huang; Russell L. Malmberg; Ying Xu 001; Liming Cai (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Fast and accurate search for non-coding RNA pseudoknot structures in genomes. - Zhibin Huang; Yong Wu; Joseph Robertson; Liang Feng; Russell L. Malmberg; Liming Cai (Bioinform., 2008)

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

RNApasta: a tool for analysis of RNA structural alignments. - Russell L. Malmberg; Timothy I. Shaw; Liming Cai (Int. J. Bioinform. Res. Appl., 2010)

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

TRFolder: computational prediction of novel telomerase RNA structures in yeast genomes. - Leilei Guo; Dong Zhang; Yingfeng Wang; Russell L. Malmberg; Michael J. McEachern; Liming Cai (Int. J. Bioinform. Res. Appl., 2011)

Analyzing Modular RNA Structure reveals Low Global Structural Entropy in microRNA Sequence. - Timothy I. Shaw; Amir Manzour; Yingfeng Wang; Russell L. Malmberg; Liming Cai (J. Bioinform. Comput. Biol., 2011)

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

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

Protein Closed Loop Prediction from Contact Probabilities. - Liang Ding 007; Joseph Robertson; Russell L. Malmberg; Liming Cai (ISBRA, 2013)

Patterns of Chromatin-Modifications Discriminate Different Genomic Features in Arabidopsis. - Anuj Srivastava; Xiaoyu Zhang; Sal LaMarca; Liming Cai; Russell L. Malmberg (ISBRA, 2013)

Ab initio Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model. - Liang Ding 007; Xingran Xue; Sal LaMarca; Mohammad Mohebbi; Abdul Samad; Russell L. Malmberg; Liming Cai (CMSR@ECCB, 2014)

Stochastic k-Tree Grammar and Its Application in Biomolecular Structure Modeling. - Liang Ding 007; Abdul Samad; Xingran Xue; Xiuzhen Huang; Russell L. Malmberg; Liming Cai (LATA, 2014)

Accurate prediction of RNA nucleotide interactions with backbone k-tree model. - Liang Ding 007; Xingran Xue; Sal LaMarca; Mohammad Mohebbi; Abdul Samad; Russell L. Malmberg; Liming Cai (Bioinform., 2015)

Genome-wide identification and evolutionary analysis of long non-coding RNAs in cereals. - Ying Sun; Willie L. Rogers; Katrien M. Devos; Liming Cai; Russell L. Malmberg (ICCABS, 2016)

Efficient Learning of Optimal Markov Network Topology with k-Tree Modeling. - Liang Ding 007; Di Chang; Russell L. Malmberg; Aaron Martínez; David Robinson; Matthew Wicker; Hongfei Yan; Liming Cai (CoRR, 2018)

Accurate prediction of human miRNA targets via graph modeling of the miRNA-target duplex. - Mohammad Mohebbi; Liang Ding 007; Russell L. Malmberg; Cory Momany; Khaled Rasheed; Liming Cai (J. Bioinform. Comput. Biol., 2018)

A Multi-hypothesis Learning Algorithm for Human and Mouse miRNA Target Prediction. - Mohammad Mohebbi; Liang Ding 007; Russell L. Malmberg; Liming Cai (ICCABS, 2019)

Human MicroRNA Target Prediction via Multi-Hypotheses Learning. - Mohammad Mohebbi; Liang Ding 007; Russell L. Malmberg; Liming Cai (J. Comput. Biol., 2021)