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Russell L. Malmberg 的论文(28) 排序方式:
Stochastic modeling of RNA pseudoknotted structures: a grammatical approach  
Motivation: Modeling RNA pseudoknotted structures remains challenging. Methods have previously been developed to model RNA stem-loops successfully using stochastic context-free grammars (SCFG) adapted......
Intelligent Systems in Molecular Biology  2003
25次引用 0 0
Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes  
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 acc......
IEEE Computer Society Bioinformatics Conference  2005
11次引用 0 0
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment  
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 the......
Algorithms in Bioinformatics  2005
6次引用 0 0
Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment  
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 the structure......
IEEE/ACM Transactions on Computational Biology and Bioinformatics  2006
4次引用 0 0
Profiling and Searching for RNA Pseudoknot Structures in Genomes  
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 Covariance......
International Conference on Computational Science  2005
4次引用 0 0
Fast and accurate search for non-coding RNA pseudoknot structures in genomes  
Motivation: Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective b......
Bioinformatics/computer Applications in The Biosciences  2008
3次引用 0 0
Rapid ab initio RNA Folding Including Pseudoknots via Graph Tree Decomposition  
Abstract. The prediction of RNA secondary structure including pseudoknots remains a challenge due to the intractable computation of the sequence conformation from intriguing nucleotide interactions. O......
Algorithms in Bioinformatics  2006
3次引用 0 0
RNA Structural Homology Search with a Succinct Stochastic Grammar Model  
An increasing number of structural homology search tools, mostly based on profile stochastic context-free grammars (SCFGs) have been recently developed for the non-coding RNA gene identification. SCFG......
Journal of Computer Science and Technology  2005
1次引用 0 0
LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference  
Summary: LumberJack is a phylogenetic tool intended to serve two purposes: to facilitate sampling treespace to find likely tree topologies quickly, and to map phylogenetic signal onto regions of an al......
Bioinformatics/computer Applications in The Biosciences  2004
1次引用 0 0
Phylogenetic Network Inferences Through Efficient Haplotyping  
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, the genotype......
Algorithms in Bioinformatics  2006
0次引用 0 0

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