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检索条件"任意字段=IEEE Computational Systems Bioinformatics Conference"

共 879 条记录，以下是91-100 订阅

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computational grid-based 3-tier ART1 data mining for bioinformatics applications

引用

3rd International conference on Fuzzy systems and Knowledge Discovery

作者： Cho, Kyu Cheol Park, Da Hye Lee, Jong Sik Inha Univ Sch Comp Sci & Engn Nam Ku Inchon 402751 South Korea

ISBN: (纸本)3540459162

computational Grid technology has been noticed as an issue to solve large-scale bioinformatics-related problems and improves data accuracy and processing speed on multiple computation platforms with distributed bioDATA sets. This paper focuses on a GPCR data mining processing which is an important bioinformatics application. This paper proposes a Grid-based 3-tier ART1 classifier which operates an ART1 clustering data mining using grid computational resources with distributed GPCR data sets. This Grid-based 3-tier ART1 classifier is able to process a large-scale bioinformatics application in guaranteeing high bioDATA accuracy with reasonable processing resources. This paper evaluates performance of the Grid-based ART1 classifier in comparing to the ART1-based classifier and the ART1 optimum classifier. The data mining processing time of the Grid-based ART1 classifier is 18% data mining processing time of the ART1 optimum classifier and is the 12% data mining processing time of the ART1-based classifier. And we evaluate performance of the Grid-based 3-tier ART1 classifier in comparing to the Grid-based ART1 classifier. As data sets become larger, data mining processing time of the Grid-based 3-tier ART1 classifier more decrease than that of the Grid-based ART1 classifier. computational Grid in bioinformatics applications gives a great promise of high performance processing with large-scale and geographically distributed bioDATA sets.

关键词： Data mining

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I/O induced scalability limits of bioinformatics applications

I/O induced scalability limits of bioinformatics application...

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7th ieee International conference on bioinformatics and Bioengineering, BIBE

作者： Henschel, Robert Müller, Matthias S. 01062 Dresden Germany

ISBN: (纸本)1424415098

The growing size of sequence, protein and other biological databases results in an increased computational complexity of the analysis process. Often parallelization is the only solution to limit the turnaround time within reasonable limits. Most scalability studies focus on the parallel algorithm and the resulting communication and synchronization patterns of the implementations. In this paper we examine to what extend I/O bottlenecks limit the scalability on current and future architectures. We study the behavior of two different bioinformatics applications (THREADER, HMMER) and show that these applications are representatives of two different classes with distinct I/O profiles and demands. ©2007 ieee.

关键词： Scalability

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Genome wide computational identification of regulatory RNAs in rice plant pathogen Xanthomonas oryzae

Genome wide computational identification of regulatory RNAs ...

引用

International conference on bioinformatics and systems Biology (BSB)

作者： Kumari, Priyanka Som, Anup Univ Allahabad Ctr Bioinformat Inst Interdisciplinary Studies Allahabad 211002 Uttar Pradesh India

ISBN: (纸本)9781538664346

Xanthomonas oryzae is a gram negative bacterial phytopathogen which causes leaf blight disease of rice plant, posing serious threat to the plants and their yield. Regulatory RNAs are heterogeneous functional RNA molecules which modulate/regulate gene expression, thus controlling a wide variety of physiological functions. As an effort to understand the role of regulatory RNAs in the physiology and pathogenesis of Xanthomonas oryzae, we identified candidate regulatory RNAs, such as riboswitches (Cobalamin, FMN, Glycine, SAM, TPP, crcB), small RNAs (asX1, asX3, asX4, sX2, sX5, sX6, sX7, sX9, sX11, sX12, sX13, sX14, Xoo1, Xoo2, Xoo5, Xoo8) and ribozyme (RNaseP_arch), using in silico approach. We also identified the genes regulated by these regulatory RNAs and their role.

关键词： Xanthomonas oryzae Regulatory RNAs:(II.) Ribozymes Riboswitches sRNA phytopathogen bioinformatics

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Toward a realistic model for gene network evolution

Toward a realistic model for gene network evolution

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7th ieee International conference on bioinformatics and Bioengineering, BIBE

作者： Chen, Wenhai Jiang, Tianzi Xia, Tian Gu, Xun National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Science Beijing 100080 China Center for Bioinformatics and Computational Biology Iowa State University Ames IA 50011 United States Center for Bioinformatics and Biological Statistics Department of Genetics Development and Cell Biology Iowa State University Ames IA 50011 United States

We investigated how to establish a realistic model for the evolutionary emergence of gene network that is scale-free. After theoretical analysis and compute simulation, we have demonstrated the evolutionary principles... 详细信息

ISBN: (纸本)1424415098

关键词： Genes

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Efficient basin hopping in the protein energy surface 2012

Efficient basin hopping in the protein energy surface

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2012 ieee International conference on bioinformatics and Biomedicine, BIBM2012

作者： Olson, Brian Shehu, Amarda Department of Computer Science George Mason University Fairfax VA 22030 United States Department of Bioinformatics and Computational Biology George Mason University Fairfax VA 22030 United States Department of Bioengineering George Mason University Fairfax VA 22030 United States

ISBN: (纸本)9781467325585

The vast and rugged protein energy surface can be effectively represented in terms of local minima. The basin-hopping framework, where a structural perturbation is followed by an energy minimization, is particularly suited to obtaining this coarse-grained representation. Basin hopping is effective for small systems both in locating lower-energy minima and obtaining conformations near the native structure. The efficiency decreases for large systems. Our recent work improves efficiency on large systems through molecular fragment replacement. In this paper, we conduct a detailed investigation of two components in basin hopping, perturbation and minimization, and how they work in concert to affect the sampling of near-native local minima. We show that controlling the magnitude of perturbation jumps is related to the ability to effectively steer the exploration towards conformations near the protein native state. In minimization, we show that a simple greedy search is just as effective as Metropolis Monte Carlo-based minimization. Finally, we show that an evolutionary-inspired approach based on the Pareto front is particularly effective in reducing the ensemble of sampled local minima and obtains a simpler representation of the probed energy surface. © 2012 ieee.

关键词： Proteins

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Accelerating Needleman-Wunsch Global Alignment Algorithm with GPUs 12

Accelerating Needleman-Wunsch Global Alignment Algorithm wit...

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12th ieee/ACS International conference of Computer systems and Applications (AICCSA)

作者： Fakirah, Maged Shehab, Mohammed A. Jararweh, Yaser Al-Ayyoub, Mahmoud Jordan Univ Sci & Technol Irbid Jordan

ISBN: (纸本)9781509004782

Over the recent decades, bioinformatics has acquired a major concern due to the rapid growth in biological data that includes protein structures and genome sequences. Many considerable efforts have been conducted by computer scientists, mathematicians and biologists to coup with complex biological problems such as sequence alignment problem, using several techniques to formulate/model the targeted biological problems as computational problems and design algorithms to solve them in an accurate and efficient manner. NeedlemanWunsch algorithm as well as other alignment algorithms have been the subject of many studies to improve their performance due to their importance and the large scale of the data they have to handle (e.g., aligning strings of hundreds of thousands of characters). Approaches included a mixture of different parallel implementations using specialized hardware such as Graphical Processing Units (GPUs) and a vectorized approach of reading and processing the input data. In this work, a parallel implementation of NW algorithm is presented using GPU due to its efficiency and high speed, to solve the slowness problem associated with this algorithm when processing large data sets, as well as to enhance the performance of the algorithm especially when processing vectors of adjacent cells parallel to the matrix miner diagonal. The experiments show that the proposed implementation improves the performance of the algorithm by 99%.

关键词： bioinformatics

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Gene teams with relaxed proximity constraint

Gene teams with relaxed proximity constraint

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2005 ieee computational systems bioinformatics conference, CSB 2005

作者： Kim, Sun Choi, Jeong-Hyeon Yang, Jiong School of Informatics Center for Genomics and Bioinformatics Indiana University IN 47408 United States School of Informatics Indiana University IN 47408 United States EECS Case Western Reserve Univ. OH 44106 United States

ISBN: (纸本)0769523447

Functionally related genes co-evolve, probably due to the strong selection pressure in evolution. Thus we expect that they are present in multiple genomes. Physical proximity among genes, known as gene team, is a very useful concept to discover functionally related genes in multiple genomes. However, there are also many gene sets that do not preserve physical proximity. In this paper, we generalized the gene team model, that looks for gene clusters in a physically clustered form, to multiple genome cases with relaxed constraint. We propose a novel hybrid pattern model that combines the set and the sequential pattern models. Our model searches for gene clusters with and/or without physical proximity constraint. This model is implemented and tested with 97 genomes (120 replicons). The result was analyzed to show the usefulness of our model. Especially, analysis of gene clusters that belong to B. subtilis and E. coli demonstrated that our model predicted many experimentally verified operons and functionally related clusters. Our program is fast enough to provide a sevice on the web at http://***/platcom/. Users can select any combination of 97 genomes to predict gene teams. © 2005 ieee.

关键词： Genes

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Signal processing in bioinformatics 14

Signal processing in bioinformatics

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14th International conference on Digital Signal Processing (DSP 2002)

作者： Costa, LD Univ Sao Paulo Inst Fis Sao Carlos BR-13560970 Sao Carlos SP Brazil

ISBN: (纸本)0780375033

The ongoing reunification of the several biological areas - especially genetics, evolution, development and ecology - into a coherent whole will rely increasingly on the application of mathematic-computational concepts and techniques, which characterizes the new area of bioinformatics. The current article addresses such a tendency from the specific perspective of signal/image processing and analysis, outlining the main problems of interest and their specific demands. Among the several related approaches, special attention is focused on DNA chip image analysis, 3D gene expression characterization, the dynamical evolution of biological shapes, and dynamic systems models.

关键词： bioinformatics

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Nucleotide composition bias in high throughput gene expression measurement methods 13

Nucleotide composition bias in high throughput gene expressi...

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13th ieee International conference on Signal Processing and Communication systems (ICSPCS)

作者： Jaksik, Roman Lalik, Anna Puszynski, Krzysztof Silesian Tech Univ Inst Automat Control Gliwice Poland

ISBN: (纸本)9781728121949

Studies of gene expression levels are known to be affected by biases related to the experimental procedure. Nucleotide composition of the studied genes significantly affects the efficiency of biochemical reactions used to prepare the material for study which translates to the measured expression levels. Data pre-processing methods aim at reducing such differences and the use of replicate samples is expected to increase the data quality, however all commonly used methods suffer from the reproducibility problems. In this work we utilize information provided by over two thousand experiments in order to explain the origin of nucleotide composition bias, highlight the magnitude of the problem and show its consequences for the interpretation of gene expression studies. We show that despite data standardization and the use of sample replicates the effect can have significant impact on the detection of differentially expressed genes between analyzed conditions, affecting interpretation of results from such studies.

关键词： RNA sequencing oligonucleotide microarrays detection of differentially expressed genes bioinformatics

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Generating Peptide Sequence Tags for Peptide Identification via Tandem Mass Spectrometry

Generating Peptide Sequence Tags for Peptide Identification ...

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9th ieee International conference on bioinformatics and BioEngineering

作者： Yu, Changyong Wang, Guoren Zhao, Yuhai Mao, Keming Wu, Junjie Zhai, Wendan Northeastern Univ Minist Educ Key Lab Med Image Comp Shenyang 110004 Peoples R China Northeastern Univ Sch Informat Sci & Engn Shenyang 110004 Peoples R China

ISBN: (纸本)9781424442942

Large scale, rapid and accurate protein identification is the crucial basis for further protein analysis in computational proteomics. Searching protein database by use of the protein tandem mass spectra has been a standard solution for solving this problem. Though several algorithms have been proposed, more sensitive and accurate approaches are still needed. In this paper, an effective database search approach is proposed. Prior to searching sequence database, an approach based on a graph-theoretic model is proposed to infer the peptide sequence tag (PST) from the tandem mass spectra data which is the partial sequence of the peptide. Also, an index approach for the protein sequence database is proposed for speeding up the database search and filtering out the incorrect protein sequences. Then, a novel scoring method for evaluating the match between the peptide sequence tag and the protein sequence is proposed for improving the accuracy of the database search result. Finally, we develop an algorithm for solving the problem and implement it as a computer program Pep Check. All the results of Pep Check are compared with those of the famous algorithms. Experimental results demonstrate that Pep Check is as accurate as or more accurate than them with the test datasets.

关键词： Peptides Mass spectroscopy Databases Large-scale systems bioinformatics Biomedical engineering Proteomics Protein sequence Amino acids Spine

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