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

Polynomial kernels collapse the W-hierarchy. - Liang Ding 007; Abdul Samad; Xingran Xue; Xiuzhen Huang; Liming Cai (CoRR, 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)

Maximum spanning k-trees. - Liang Ding 007 (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)