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CPM
2007
Springer
115views Combinatorics» more  CPM 2007»
15 years 4 months ago
Two-Dimensional Range Minimum Queries
We consider the two-dimensional Range Minimum Query problem: for a static (m × n)-matrix of size N = mn which may be preprocessed, answer on-line queries of the form “where is t...
Amihood Amir, Johannes Fischer, Moshe Lewenstein
BMCBI
2010
116views more  BMCBI 2010»
14 years 10 months ago
A hybrid approach to protein folding problem integrating constraint programming with local search
Background: The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy func...
Abu Zafer M. Dayem Ullah, Kathleen Steinhöfel
BMCBI
2010
189views more  BMCBI 2010»
14 years 10 months ago
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
Background: Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly probl...
Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh,...
BMCBI
2008
214views more  BMCBI 2008»
14 years 10 months ago
Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research
Background: This paper describes techniques for accelerating the performance of the string set matching problem with particular emphasis on applications in computational proteomic...
Yoginder S. Dandass, Shane C. Burgess, Mark Lawren...
BMCBI
2010
108views more  BMCBI 2010»
14 years 10 months ago
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs
Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs ...
Fernando Garcia-Alcalde, Armando Blanco, Adrian J....