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Article
Open AccessIdentifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU
Despite decades of research, effective treatments for most cancers remain elusive. One reason is that different instances of cancer result from different combinations of multiple genetic mutations (hits). Ther...
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Article
Open AccessAuthor Correction: Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
Open AccessDifferentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations
Cancer is known to result from a combination of a small number of genetic defects. However, the specific combinations of mutations responsible for the vast majority of cancers have not been identified. Current...
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Article
Open AccessmuBLASTP: database-indexed protein sequence search on multicore CPUs
The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utili...
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Article
Open AccessHigh-performance biocomputing for simulating the spread of contagion over large contact networks
Many important biological problems can be modeled as contagion diffusion processes over interaction networks. This article shows how the EpiSimdemics interaction-based simulation system can be applied to the g...
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Article
Open AccessMulti-dimensional characterization of electrostatic surface potential computation on graphics processors
Calculating the electrostatic surface potential (ESP) of a biomolecule is critical towards understanding biomolecular function. Because of its quadratic computational complexity (as a function of the number of at...
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Article
Open AccessMissing genes in the annotation of prokaryotic genomes
Protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. However there have been reports that prokaryotic gene finder programs hav...
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Chapter and Conference Paper
Dynamic Right-Sizing: An Automated, Lightweight, and Scalable Technique for Enhancing Grid Performance
With the advent of computational grids, networking performance over the wide-area network (WAN) has become a critical component in the grid infrastructure. Unfortunately, many high-performance grid application...
