Liming Cai

发表

Graph Tree Decomposition Based Fast Peptide Sequencing and Spectral Alignment ①

Ying Xu, Chunmei Liu, Yinglei Song, 2008 .

Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families

J. Mrázek, A. Srivastava, Liming Cai, 2011, PloS one.

Analyzing Modular RNA Structure reveals Low Global Structural Entropy in microRNA Sequence

Russell L. Malmberg, Liming Cai, Yingfeng Wang, 2011, J. Bioinform. Comput. Biol..

Optimal learning of Markov k-tree topology

Hongfei Yan, Liming Cai, R. Malmberg, 2022, Journal of Computational Mathematics and Data Science.

Comparative Pathway Prediction with Structural Genomic Information via a Unified Graph Model

Liming Cai, Dongsheng Che, Jizhen Zhao, 2007 .

Genome-wide identification and evolutionary analysis of long non-coding RNAs in cereals

Russell L. Malmberg, Liming Cai, Ying Sun, 2016, ICCABS.

α-HMMand optimal decoding higher-order structures on sequential data

Liming Cai, David Robinson, F. R. Dastjerdi, 2022, Journal of Computational Mathematics and Data Science.

Simultaneous prediction of RNA secondary structure and helix coaxial stacking

Yingfeng Wang, Liming Cai, R. Malmberg, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

TRFolder: computational prediction of novel telomerase RNA structures in yeast genomes

Liming Cai, Dong Zhang, Yingfeng Wang, 2011, Int. J. Bioinform. Res. Appl..

Accurate prediction of human miRNA targets via graph modeling of miRNA-target duplex

Liang Ding, Russell L. Malmberg, Liming Cai, 2016, ICCABS.

Protein Structure Prediction by Protein Threading

Liming Cai, Ying Xu, Dong Xu, 2010, Computational Methods for Protein Structure Prediction and Modeling.

Peptide sequence tag-based blind identification of post-translational modifications with point process model

Bo Yan, Liming Cai, Ying Xu, 2006, ISMB.

Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition

Liming Cai, Russell L Malmberg, Liming Cai, 2007, Journal of mathematical biology.

Rapid ab initio RNA Folding Including Pseudoknots Via Graph Tree Decomposition

Russell L. Malmberg, Liming Cai, Jizhen Zhao, 2006, WABI.

RNApasta: a tool for analysis of RNA structural alignments

Russell L. Malmberg, Liming Cai, Timothy I. Shaw, 2010, Int. J. Bioinform. Res. Appl..

Transcriptome Analysis of Sarracenia, an Insectivorous Plant

Russell L. Malmberg, Liming Cai, Anuj Srivastava, 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

Patterns of Chromatin-Modifications Discriminate Different Genomic Features in Arabidopsis

Russell L. Malmberg, Liming Cai, Xiaoyu Zhang, 2013, ISBRA.

Fast and accurate search for non-coding RNA pseudoknot structures in genomes

Russell L. Malmberg, Liming Cai, Yong Wu, 2008, Bioinform..

Fixed-Parameter Approximation: Conceptual Framework and Approximability Results

Liming Cai, Xiuzhen Huang, Xiuzhen Huang, 2010, Algorithmica.

Fixed-Parameter Approximation: Conceptual Framework and Approximability Results

Liming Cai, Xiuzhen Huang, Xiuzhen Huang, 2006, IWPEC.

Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds

Russell L. Malmberg, Liming Cai, Yingfeng Wang, 2011, BMC Bioinformatics.

Overproduction and purification of highly active recombinant Pseudomonas aeruginosa str. PAO1 RNA polymerase holoenzyme complex.

Liming Cai, C. Momany, Derrick Afful, 2019, Protein expression and purification.

BEST: Binding-site Estimation Suite of Tools

Liming Cai, Dongsheng Che, Shane T. Jensen, 2005, Bioinform..

Stochastic k-Tree Grammar and Its Application in Biomolecular Structure Modeling

Liang Ding, Russell L. Malmberg, Liming Cai, 2014, LATA.

Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment

Russell L. Malmberg, Liming Cai, Xiuzhen Huang, 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Parameterized Complexity and Biopolymer Sequence Comparison

Liming Cai, Xiuzhen Huang, Frances A. Rosamond, 2008, Comput. J..

TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes

Russell L. Malmberg, Liming Cai, Dong Zhang, 2012, Bioinform..

A Novel Structural Measure Separating Non-Coding RNAs from Genomic Backgrounds

Russell L. Malmberg, Yingfeng Wang, Liming Cai, 2015 .

Human MicroRNA Target Prediction via Multi-Hypotheses Learning

Liang Ding, Russell L Malmberg, Mohammad Mohebbi, 2020, J. Comput. Biol..

Stochastic modeling of RNA pseudoknotted structures: a grammatical approach

Russell L. Malmberg, Liming Cai, Yunzhou Wu, 2003, ISMB.

Efficient Learning of Optimal Markov Network Topology with k-Tree Modeling pdf

Liang Ding, Di Chang, Russell L. Malmberg, 2018, ArXiv.

Sequence analysis BEST : Binding-site Estimation Suite of Tools

Jun S. Liu, Liming Cai, Dongsheng Che, 2005 .

Accurate prediction of RNA nucleotide interactions with backbone k-tree model

Liang Ding, Russell L. Malmberg, Liming Cai, 2015, Bioinform..

Ab initio Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model

Liang Ding, Russell L. Malmberg, Liming Cai, 2014, CMSR@ECCB.

Polynomial kernels collapse the W-hierarchy pdf

Liang Ding, Liming Cai, Xiuzhen Huang, 2013, ArXiv.

Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm

Yu Zhang, Liming Cai, Jason H. Moore, 2015, BioData Mining.

A Multi-hypothesis Learning Algorithm for Human and Mouse miRNA Target Prediction

Russell L. Malmberg, Liming Cai, Mohammad Mohebbi, 2019, ICCABS.

A New Graph Theoretic Approach for Protein Threading

Liming Cai, Ying Xu, Junfeng Qu, 2014, Fundam. Informaticae.

Comparative Pathway Annotation with Protein-DNA Interaction and Operon Information via Graph Tree Decomposition

Liming Cai, Dongsheng Che, Jizhen Zhao, 2006, Pacific Symposium on Biocomputing.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes

Russell L. Malmberg, Liming Cai, Chunmei Liu, 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

RNAV : NON-CODING RNA SECONDARY STRUCTURE VARIATION SEARCH VIA GRAPH HOMOMORPHISM

Liming Cai, A. U.S, R. Malmberg, 2010 .