Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment
暂无分享,去创建一个
Russell L. Malmberg | Liming Cai | Xiuzhen Huang | Ying Xu | Chunmei Liu | Yinglei Song | Ying Xu | Chunmei Liu | Xiuzhen Huang | Yinglei Song | Liming Cai | R. Malmberg
[1] Sean R. Eddy,et al. Rfam: an RNA family database , 2003, Nucleic Acids Res..
[2] Elena Rivas,et al. Noncoding RNA gene detection using comparative sequence analysis , 2001, BMC Bioinformatics.
[3] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[4] D. Eisenberg,et al. A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.
[5] S. Bryant,et al. Statistics of sequence-structure threading. , 1995, Current opinion in structural biology.
[6] Liming Cai,et al. Protein Structure Prediction by Protein Threading , 2010, Computational Methods for Protein Structure Prediction and Modeling.
[7] Russell L. Malmberg,et al. Stochastic modeling of RNA pseudoknotted structures: a grammatical approach , 2003, ISMB.
[8] David Eppstein,et al. The Polyhedral Approach to the Maximum Planar Subgraph Problem: New Chances for Related Problems , 1994, GD.
[9] Detlef Seese,et al. Easy Problems for Tree-Decomposable Graphs , 1991, J. Algorithms.
[10] M Vihinen,et al. Modelling the structure of the calcitonin gene-related peptide. , 1994, Protein engineering.
[11] Edward C. Uberbacher,et al. Sequence-structure specificity of a knowledge based energy function at the secondary structure level , 2000, Bioinform..
[12] B. Snel,et al. Pathway alignment: application to the comparative analysis of glycolytic enzymes. , 1999, The Biochemical journal.
[13] Russell L. Malmberg,et al. Tree decomposition based fast search of RNA structures including pseudoknots in genomes , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).
[14] J. Doudna. Structural genomics of RNA , 2000, Nature Structural Biology.
[15] Hans L. Bodlaender. A linear time algorithm for finding tree-decompositions of small treewidth , 1993, STOC '93.
[16] R. Lathrop. The protein threading problem with sequence amino acid interaction preferences is NP-complete. , 1994, Protein engineering.
[17] Christian N. S. Pedersen,et al. RNA Pseudoknot Prediction in Energy-Based Models , 2000, J. Comput. Biol..
[18] Michael R. Fellows,et al. Parameterized Complexity , 1998 .
[19] Jack Snoeyink,et al. An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem , 2004, Pacific Symposium on Biocomputing.
[20] Satoshi Kobayashi,et al. Tree Adjoining Grammars for RNA Structure Prediction , 1999, Theor. Comput. Sci..
[21] S. Goebel,et al. Characterization of the RNA Components of a Putative Molecular Switch in the 3′ Untranslated Region of the Murine Coronavirus Genome , 2004, Journal of Virology.
[22] Ying Xu,et al. An Efficient Computational Method for Globally Optimal Threading , 1998, J. Comput. Biol..
[23] Guoli Wang,et al. PISCES: a protein sequence culling server , 2003, Bioinform..
[24] Kurt Mehlhorn,et al. A branch-and-cut algorithm for multiple sequence alignment , 1997, RECOMB '97.
[25] R. Durbin,et al. RNA sequence analysis using covariance models. , 1994, Nucleic acids research.
[26] S. Eddy. Computational Genomics of Noncoding RNA Genes , 2002, Cell.
[27] Stefan Arnborg,et al. Linear time algorithms for NP-hard problems restricted to partial k-trees , 1989, Discret. Appl. Math..
[28] D. Pervouchine. IRIS: intermolecular RNA interaction search. , 2004, Genome informatics. International Conference on Genome Informatics.
[29] Paul D. Seymour,et al. Graph Minors. II. Algorithmic Aspects of Tree-Width , 1986, J. Algorithms.
[30] Russell L. Malmberg,et al. Profiling and Searching for RNA Pseudoknot Structures in Genomes , 2005, International Conference on Computational Science.
[31] M Brown,et al. RNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[32] Sherif Abou Elela,et al. A Phylogenetically Based Secondary Structure for the Yeast Telomerase RNA , 2004, Current Biology.
[33] J. F. Atkins,et al. Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA. , 1999, Journal of molecular biology.
[34] Temple F. Smith,et al. Analysis and algorithms for protein sequence–structure alignment , 1998 .
[35] S. Eddy,et al. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.
[36] Jinbo Xu,et al. Rapid Protein Side-Chain Packing via Tree Decomposition , 2005, RECOMB.
[37] Jie Liang,et al. Computational Methods for Protein Structure Prediction and Modeling , 2007 .
[38] Martin Vingron,et al. A polyhedral approach to RNA sequence structure alignment , 1998, RECOMB '98.
[39] Bonnie Berger,et al. A tree-decomposition approach to protein structure prediction , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).
[40] D. Eisenberg,et al. Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.
[41] Robin Thomas,et al. On the complexity of finding iso- and other morphisms for partial k-trees , 1992, Discret. Math..
[42] Sean R. Eddy,et al. RSEARCH: Finding homologs of single structured RNA sequences , 2003, BMC Bioinformatics.
[43] Ying Xu,et al. Raptor: Optimal Protein Threading by Linear Programming , 2003, J. Bioinform. Comput. Biol..