Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai
An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental...
Parameterized Complexity and Biopolymer Sequence Comparison (2008)
Liming Cai, Xiuzhen Huang, Chunmei Liu, Frances Rosamond, Yinglei Song
The article surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence,...
doi:10.1093/comjnl/bxm035 Parameterized Complexity and Biopolymer Sequence Comparison (2008)
Liming Cai, Xiuzhen Huang, Chunmei Liu, Frances Rosamond, Yinglei Song
The paper surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence,...
Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai
doi:10.1093/bioinformatics/btl226 Peptide sequence tag-based blind identification of
Phylogenetic Network Inferences through Efficient (2008)
Yinglei Song, Chunmei Liu, Russell L. Malmberg, Liming Cai
Abstract. The genotype phasing problem is to determine the haplotypes of diploid individuals from their genotypes where linkage relationships are not known. Based on the model of perfect phylogeny,...
Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots (2008)
Yinglei Song, Chunmei Liu, Russell L. Malmberg
*Corresponding authors Abstract: Stochastic Context-Free Grammars (SCFG) has been shown to be effective in modelling RNA secondary structure for searches. Our previous work (Cai et al., 2003) in...
Efficient Annotation of Non-coding RNA Structures Including Pseudoknots via Automated Filters (2008)
Chunmei Liu, Yinglei Song, Ping Hu, Russell L. Malmberg, Liming Cai
Computational search of genomes for RNA secondary structure is an important approach to the annotation of non-coding RNAs. The bottleneck of the search is sequence-structure alignment, which is often...
Exact Algorithms for Finding the Minimum Independent Dominating Set in Graphs (2008)
Abstract. In this paper, we consider the Minimum Independent Dominating Set problem and develop exact exponential algorithms that break the trivial O(2 |V | ) bound. A simple O ∗ ( √ 3 |V | )...
Parameterized Complexity and Biopolymer Sequence Comparison (2008)
Cai, Liming, Huang, Xiuzhen, Liu, Chunmei, Rosamond, Frances, Song, Yinglei
The paper surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence,...
Liu, Chunmei, Yan, Bo, Song, Yinglei, Xu, Ying, Cai, Liming
An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental...
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment (2005)
Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Abstract. Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify...
Profiling and searching for RNA pseudoknot structures (2005)
Chunmei Liu, Yinglei Song, Russell L. Malmberg, Liming Cai
Abstract. We developed a new method that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent...
Tree decomposition based fast search of RNA structures including pseudoknots in genomes (2005)
Yinglei Song, Russell Malmberg, Liming Cai, Chunmei Liu, Fangfang Pan
Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for...
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment (2005)
Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Abstract. Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify...
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment (2005)
Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Abstract—Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify...
Mutter, George L, Zahrieh, David, Liu, Chunmei, Neuberg, Donna, Finkelstein, David, Baker, Heather E, ...
Abstract Background Primary human tissues are an invaluable widely used tool for discovery of gene expression patterns which characterize disease states. Tissue processing methods remain...