12759
Quan Zhou, Wenlin Chen, Shiji Song, Jacob R. Gardner, Kilian Q. Weinberger, Yixin Chen
The past years have witnessed many dedicated open-source projects that built and maintain implementations of Support Vector Machines (SVM), parallelized for GPU, multi-core CPUs and distributed systems. Up to this point, no comparable effort has been made to parallelize the Elastic Net, despite its popularity in many high impact applications, including genetics, neuroscience and systems […]
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Guillaume Chapuis
The exponential growth in bioinformatics data generation and the stagnation of processor frequencies in modern processors stress the need for efficient implementations that fully exploit the parallel capabilities offered by modern computers. This thesis focuses on parallel algorithms and implementations for bioinformatics problems. Various types of parallelism are described and exploited. This thesis presents applications […]
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Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi
Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines […]
J. Li, S. Ranka, S. Sahni
We develop novel single-GPU parallelizations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignment score as well as the actual alignment. Experimental results demonstrate an order of magnitude reduction in run time relative […]
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R.P. Souto, C. Osthoff, A.T.R. de Vasconcelos, D.A. Augusto, P.L. da Silva Dias, A. Rodriguez, O. Trelles, M. Ujaldon
High-density oligonucleotide microarrays allow several millions of genetic markers in a single experiment to be observed. Current bioinformatics tools for gene expression quantile data normalization are unable to process such huge data sets. In parallel with this reality, the huge volume of molecular data produced by current high-throughput technologies in modern molecular biology has increased […]
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Guillaume Chapuis
The exponential growth in bioinformatics data generation and the stagnation of processor frequencies in modern processors stress the need for efficient implementations that fully exploit the parallel capabilities offered by modern computers. This thesis focuses on parallel algorithms and implementations for bioinformatics problems. Various types of parallelism are described and exploited. This thesis presents applications […]
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Sungin Park, Soo-Yong Shin, Kyu-Baek Hwang
BACKGROUND: Multidimensional scaling (MDS) is a widely used approach to dimensionality reduction. It has been applied to feature selection and visualization in various areas. Among diverse MDS methods, the classical MDS is a simple and theoretically sound solution for projecting data objects onto a low dimensional space while preserving the original distances among them as […]
Syed Faraz Mahmood
Advances in sequencing technologies have revolutionized the field of genomics by providing cost effective and high throughput solutions. In this paper, we develop a parallel sequence assembler implemented on general purpose graphic processor units (GPUs). Our work was largely motivated by a growing need in the genomic community for sequence assemblers and increasing use of […]
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Tony Kam-Thong
Recent advances in sequencing technology and automated phenotyping render it possible to study the relationship between genotype and phenotype at an unprecedented level of detail. While mapping phenotypes to single loci in the genome is a standard technique in Statistical Genetics, the problem of epistasis search, that is mapping phenotypes to pairs of loci, remains […]
Jiadong Wu, Bo Hong, Takako Takeda, Jun-tao Guo
BACKGROUND: Protein-DNA docking is a very challenging problem in structural bioinformatics and has important implications in a number of applications, such as structure-based prediction of transcription factor binding sites and rational drug design. Protein-DNA docking is very computational demanding due to the high cost of energy calculation and the statistical nature of conformational sampling algorithms. […]
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David Seide
This project focuses on using GPGPUs for solving the inexact alignment of short-reads with respect to a reference indexed using the Burrows-Wheeler Transform. To be more specific we dealt with a solution of an alignment that allows up to one error.
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Pooya Zandevakili, Ming Hu, Zhaohui Qin
Computational detection of TF binding patterns has become an indispensable tool in functional genomics research. With the rapid advance of new sequencing technologies, large amounts of protein-DNA interaction data have been produced. Analyzing this data can provide substantial insight into the mechanisms of transcriptional regulation. However, the massive amount of sequence data presents daunting challenges. […]
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