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Kedhar M, DR. M. Rajasekhara Babu, Mayank G, Abhinivesh M
Sequence alignment of two or more than two biological sequences such as protein, DNA (Deoxyribonucleic acid) or RNA (Ribonucleic acid) is called MSA (Multiple Sequence Alignment). Sequence homology can be inferred from the resulting MSA. Existing System uses dynamic programming technique which suffers from exponential growth of time as the sequence grows. A Hierarchical Expected […]
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Eric Wait, Mark Winter, Chris Bjornsson, Erzsebet Kokovay, Yue Wang, Susan Goderie, Sally Temple, Andrew Cohen
RESULTS: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and […]
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Anirban Mukhopadhyay, Chul Woo Lim, Suchendra M. Bhandarkar, Hanbo Chen, Austin New, Tianming Liu, Khaled Rasheed, Thiab Taha
Localization of cortical regions of interests (ROIs) in the human brain via analysis of Diffusion Tensor Imaging (DTI) data plays a pivotal role in basic and clinical neuroscience. In recent studies, 358 common cortical landmarks in the human brain, termed as Dense Individualized and Common Connectivity-based Cortical Landmarks (DICCCOLs), have been identified. Each of these […]
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Styliani Loukatou, Louis Papageorgiou, Paraskevas Fakourelis, Arianna Filntisi, Eleftheria Polychronidou, Ioannis Bassis, Vasileios Megalooikonomou, Wojciech Makalowski, Dimitrios Vlachakis, Sophia Kossida
Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements […]
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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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Chao Yu, Bo Yang
In this paper, we present the analysis and development of a cross-platform OpenCL parallelization of the Cellular Potts Model (CPM). In general, the evolution of the CPM is time-consuming. Using data-parallel programming model such as CUDA can accelerate the process, but it is highly dependent on the hardware type and manufacturer. Recently, OpenCL has attracted […]
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Nagaveni V, G T Raju
The main aim of string matching algorithm is to locate the appearance of a specific pattern in an array of larger size text. String matching algorithms has been used in many applications such as DNA analysis. This report introduces a new approach of string matching algorithm to detect the occurrence of several gene patterns in […]
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Yichao Zhou, Wei Xu, Bruce R. Donald, Jianyang Zeng
MOTIVATION: Structure-based computational protein design (SCPR) is an important topic in protein engineering. Under the assumption of a rigid backbone and a finite set of discrete conformations of side-chains, various methods have been proposed to address this problem. A popular method is to combine the dead-end elimination (DEE) and A* tree search algorithms, which provably […]
Yeim-Kuan Chang, De-Yu Chen
Sequence alignment is a task that calculates the degree of similarity between two sequences. Given a query sequence, finding a database sequence which is most similar to the query by sequence alignment is the first step in bioinformatics research. The first sequence alignment algorithm was proposed by Needle-man and Wunsch. They got the optimal global […]
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Yilan Liu
The next-generation sequencing technologies are pouring big data and pushing the frontier of life sciences toward new territories that were never imagined before. However, such big data impose great computational challenges to statistical analysis of these data. It is important to utilize Graphics Processing Unit (GPU)’s large throughput and massive parallelism to process large data […]
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D. Akgün, Ü. Sakoğlu, M. Mete, J. Esquivel, B. Adinoff
Intense computations in engineering and science, especially bioinformatics have been made practical by the recent advances in Graphical Processing Unit (GPU) computing technology. In this study, implementation and performance evaluations for a GPU-accelerated dynamic functional connectivity (DFC) analysis, which is an analysis method for investigating dynamic interactions among different brain networks, is presented. Open Computing […]
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Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Matteo Bellini, Giancarlo Mauri
The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing […]
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