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CSB
2005
IEEE
182views Bioinformatics» more  CSB 2005»
14 years 1 months ago
Bacterial Whole Genome Phylogeny Using Proteome Comparison and Optimal Reversal Distance
Traditional phylogenetic tree reconstruction is based on point mutations of a single gene. This approach is hardly suitable for genomes whose genes are almost identical and hardly...
Noppadon Khiripet
SC
2005
ACM
14 years 1 months ago
Integrated Loop Optimizations for Data Locality Enhancement of Tensor Contraction Expressions
A very challenging issue for optimizing compilers is the phase ordering problem: In what order should a collection of compiler optimizations be performed? We address this problem ...
Swarup Kumar Sahoo, Sriram Krishnamoorthy, Rajkira...
WABI
2007
Springer
14 years 1 months ago
Topology Independent Protein Structural Alignment
Abstract. Protein structural alignment is an indispensable tool used for many different studies in bioinformatics. Most structural alignment algorithms assume that the structural ...
Joe Dundas, T. Andrew Binkowski, Bhaskar DasGupta,...
FUN
2010
Springer
230views Algorithms» more  FUN 2010»
13 years 11 months ago
O(1)-Time Unsorting by Prefix-Reversals in a Boustrophedon Linked List
Conventional wisdom suggests that O(k)-time is required to reverse a substring of length k. To reduce this time complexity, a simple and unorthodox data structure is introduced. A ...
Aaron Williams
COMBINATORICS
2006
121views more  COMBINATORICS 2006»
13 years 7 months ago
Permutation Reconstruction from Minors
We consider the problem of permutation reconstruction, which is a variant of graph reconstruction. Given a permutation p of length n, we delete k of its entries in each possible w...
Mariana Raykova