Cache-Oblivious Dynamic Programming for Bioinformatics
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[2] V. Ramachandran,et al. The Cache-Oblivious Gaussian Elimination Paradigm: Theoretical Framework, Parallelization and Experimental Evaluation , 2010, Theory of Computing Systems.
[3] Vijaya Ramachandran,et al. Oblivious algorithms for multicores and network of processors , 2010, 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS).
[4] Vijaya Ramachandran,et al. Cache-efficient dynamic programming algorithms for multicores , 2008, SPAA '08.
[5] Josef Weidendorfer,et al. Valgrind 3.3 - Advanced Debugging and Profiling for Gnu/Linux Applications , 2008 .
[6] Maxime Crochemore,et al. Algorithms on strings , 2007 .
[7] Rezaul Alam Chowdhury,et al. Algorithms and data structures for cache-efficient computation: theory and experimental evaluation , 2007 .
[8] Hai-Son Le,et al. Efficient Cache-oblivious String Algorithms for Bioinformatics , 2007 .
[9] Vijaya Ramachandran,et al. The cache-oblivious gaussian elimination paradigm: theoretical framework and experimental evaluation , 2006, SPAA '06.
[10] Vijaya Ramachandran,et al. Cache-oblivious dynamic programming , 2006, SODA '06.
[11] Hai-Son Le. Algorithms for Identification of Patterns in Biogeography and Median Alignment of Three Sequences in Bioinformatics , 2006 .
[12] Craig A. Stewart,et al. Introduction to computational biology , 2005 .
[13] Volker Strumpen,et al. Cache oblivious stencil computations , 2005, ICS '05.
[14] Éva Tardos,et al. Algorithm design , 2005 .
[15] C. Pandu Rangan,et al. A linear space algorithm for the LCS problem , 2004, Acta Informatica.
[16] Bjarne Knudsen,et al. Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree , 2003, WABI.
[17] Nancy F. Hansen,et al. Comparative analyses of multi-species sequences from targeted genomic regions , 2003, Nature.
[18] T. Z. DeSantis,et al. Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA , 2003, Bioinform..
[19] Gad M. Landau,et al. A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices , 2003, SIAM J. Comput..
[20] T. Speed,et al. Biological Sequence Analysis , 1998 .
[21] Nan Yu,et al. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.
[22] Clifford Stein,et al. Introduction to Algorithms, 2nd edition. , 2001 .
[23] L. Allison,et al. Fast, optimal alignment of three sequences using linear gap costs. , 2000, Journal of theoretical biology.
[24] L. Bergroth,et al. A survey of longest common subsequence algorithms , 2000, Proceedings Seventh International Symposium on String Processing and Information Retrieval. SPIRE 2000.
[25] Tatsuya Akutsu,et al. Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots , 2000, Discret. Appl. Math..
[26] Christian N. S. Pedersen,et al. RNA Pseudoknot Prediction in Energy-Based Models , 2000, J. Comput. Biol..
[27] Matteo Frigo,et al. Cache-oblivious algorithms , 1999, 40th Annual Symposium on Foundations of Computer Science (Cat. No.99CB37039).
[28] E Rivas,et al. A dynamic programming algorithm for RNA structure prediction including pseudoknots. , 1998, Journal of molecular biology.
[29] Elen aRiva san. A Dynamic Programming Algorithm for RNA Structure Prediction Including Pseudoknots , 1999 .
[30] Dan Gusfield,et al. Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .
[31] Richard Hughey,et al. Reduced space sequence alignment , 1997, Comput. Appl. Biosci..
[32] Dan Gusfield,et al. Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .
[33] Alberto Apostolico,et al. Fast Linear-Space Computations of Longest Common Subsequences , 1992, Theor. Comput. Sci..
[34] Alok Aggarwal,et al. The input/output complexity of sorting and related problems , 1988, CACM.
[35] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[36] Eugene W. Myers,et al. Optimal alignments in linear space , 1988, Comput. Appl. Biosci..
[37] Bruce W. Erickson,et al. Optimal sequence alignment using affine gap costs , 1986 .
[38] S. Altschul,et al. Optimal sequence alignment using affine gap costs. , 1986, Bulletin of mathematical biology.
[39] O. Gotoh. An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.
[40] H. T. Kung,et al. I/O complexity: The red-blue pebble game , 1981, STOC '81.
[41] Mike Paterson,et al. A Faster Algorithm Computing String Edit Distances , 1980, J. Comput. Syst. Sci..
[42] David Maier,et al. The Complexity of Some Problems on Subsequences and Supersequences , 1978, JACM.
[43] Daniel S. Hirschberg,et al. An Information-Theoretic Lower Bound for the Longest Common Subsequence Problem , 1977, Inf. Process. Lett..
[44] Alfred V. Aho,et al. Bounds on the Complexity of the Longest Common Subsequence Problem , 1976, J. ACM.
[45] Daniel S. Hirschberg,et al. A linear space algorithm for computing maximal common subsequences , 1975, Commun. ACM.