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2010 International conference on Life System Modeling and Simulation & 2010 International conference on Intelligent Computing for Sustainable Energy and Environment

作者： Yanliang Cai, Jiangsheng Yu , and Hanpin Wang Keylaboratory of High Confidence Software Technologies, Ministry of Education School of Electronic Engineering and Computer Science, Peking University, China

Protein-protein interaction (PPI) plays an important role in the living organisms, and a major goal of proteomics is to determine the PPI networks for the whole organisms. So both experimental and computational approaches to predict PPIs are urgently needed in the field of proteomics. In this paper, four distinct protein encoding methods are proposed, based on the biological significance extracted from the categories of protein subcellular and functional localizations. And then, some classifiers are tested to prediction PPIs. To show the robustness of classification and ensure the reliability of results, each classifier is examined by many independent random experiments of 10-fold cross validations. The model of random forest achieves some promising performance of PPIs.

关键词： Prediction of Protein-Protein Interactions Using Subcellular and Functional Localizations

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Advances in neural networks research: An introduction

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NEURAL NETWORKS 2009年第5-6期22卷 489-490页

作者： Kozma, Robert Bressler, Steven Perlovsky, Leonid Venayagamoorthy, Ganesh Kumar Univ Memphis FedEx Inst Technol Memphis TN 38152 USA Florida Atlantic Univ Boca Raton FL 33431 USA Harvard Univ Cambridge MA 02138 USA Missouri Sci & Technol Univ Rolla MO USA

The present Special Issue "Advances in Neural Networks Research: IJCNN2009" provides a state-of-art overview of the field of neural networks. It includes 39 papers from selected areas of the 2009 International joint conference on Neural Networks (IJCNN2009). IJCNN2009 took place on June 14-19, 2009 in Atlanta, Georgia, USA, and it represents an exemplary collaboration between the International Neural Networks Society and the ieee computational Intelligence Society. Topics in this issue include neuroscience and cognitive science, computational intelligence and machine learning, hybrid techniques, nonlinear dynamics and chaos, various soft computing technologies, intelligent signal processing and pattern recognition, bioinformatics and biomedicine, and engineering applications. (C) 2009 Elsevier Ltd. All rights reserved.

关键词： Neuroscience Cognition Machine Learning Hybrid systems Soft Computing Dynamic systems Image Processing bioinformatics Robotics Power systems

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Using Clouds for Metagenomics: A Case Study

Using Clouds for Metagenomics: A Case Study

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ieee International conference on Cluster Computing (Cluster 2009)

作者： Wilkening, Jared Wilke, Andreas Desai, Narayan Meyer, Folker Argonne Natl Lab Div Math & Comp Sci Argonne IL 60439 USA

ISBN: (纸本)9781424450114

Cutting-edge sequencing systems produce data at a prodigious rate;and the analysis of these datasets requires significant computing resources. Cloud computing provides a tantalizing possibility for on-demand access to computing resources. However, many open questions remain. We present here a performance assessment of BLAST on real metagenomics data in a cloud setting, in order to determine the viability of this approach. BLAST is one of the premier applications in bioinformatics and computational biology and is assumed to consume the vast majority of resources in that area.

关键词： bioinformatics

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A Classification System for Predicting RNA Hairpin Loops

A Classification System for Predicting RNA Hairpin Loops

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International Joint conference on bioinformatics, systems Biology and Intelligent Computing

作者： Aldwairi, Monther Duwairi, Rehab Algarqaz, Wafa'a Jordan Univ Sci & Technol Dept Comp Engn Irbid Jordan

ISBN: (纸本)9780769537399

RiboNucleic Acid (RNA) molecules fold back over themselves to form secondary structures which determine the RNA's functionality in living cells. RNA secondary structure can be determined in laboratory by X-ray diffraction and nuclear magnetic resonance (NMR) techniques. However, these techniques are slow and expensive. Therefore, computational approaches are used to predict the secondary structure of RNA molecules. A new approach. RNA-SSP, for predicting RNA secondary structure elements is proposed. It combines computational approaches and machine learning classifiers to predict individual structure elements using a new search heuristic. The approach is implemented and tested for hairpin loops and a methodology for extending the approach to predict the remaining secondary structure elements is proposed. The experiments showed a significant improvement in prediction accuracy to 95% for stem regions and 80% for loops. The overall weighted-average accuracy for predicting hairpin loop sub-structure is 89% with a sensitivity of 85.29%.

关键词： bioinformatics RNA Secondary Structure Prediction computational RNA

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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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Decimal Transforming Operations in Spiking Neural P systems

Decimal Transforming Operations in Spiking Neural P Systems

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2nd International conference on Biomedical Engineering and Informatics (BMEI)

作者： Chen, Haizhu Gao, Xi Chongqing Univ Coll Comp Sci Chongqing 400044 Peoples R China Guilin Univ Elect Technol Sch Comp Sci Guilin 541004 Peoples R China

ISBN: (纸本)9781424441334

Spiking neural P systems are a new computing model incorporating the ideas of spiking neurons into membrane computing. It has been shown that they have powerful computational capability and potential capability in solving computationally hard problems. The paper proved the possibility to perform transforming operations between decimal number and n-base number in spiking neural P system, and gave transforming models and an effective method to implement transforming operations.

关键词： bioinformatics

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Image and Signal Analysis in Molecular Biology and Personalized Medicine

Image and Signal Analysis in Molecular Biology and Personali...

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6th International Multi-conference on systems, Signals and Devices

作者： Pham, Tuan D. Univ New S Wales ADFA Sch Informat Technol & Elect Engn Canberra ACT 2600 Australia

ISBN: (纸本)9781424443451

This paper addresses recent advances in computational tools for analysis of molecular imaging, medical imaging, and mass spectrometry data in cancer and cardiovascular diseases. These recently developed methods based on the principles of linear prediction, geostatistics, and fuzzy-set theory appear to be very useful sources of information for understanding the interactions and behaviors of complex biological networks and the development of predictive medicine.

关键词： Bioimaging Medical imaging bioinformatics Linear prediction Geostatistics Fuzzy sets

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A graph theoretic algorithm for removing redundant protein sequences

A graph theoretic algorithm for removing redundant protein s...

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3rd International conference on bioinformatics and Biomedical Engineering, iCBBE 2009

作者： Pengfei, Liu Zhenbing, Zeng Ziliang, Qian KaiYan, Feng Yudong, Cai Software Engineering Institute of East China Normal University 3663 North Zhongshan Road Shanghai 200062 China CAS-MPG Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yueyang Road Shanghai 200031 China Bioinformatics Center Key Lab. of Systems Biology Shanghai Institutes for Biological Sciences 320 Yueyang Road Shanghai 200031 China Graduate School of the Chinese Academy of Sciences 19 Yuquan Road Beijing 100039 China Division of Imaging Science and Biomedical Engineering University of Manchester Stopford Building M13 9PT United Kingdom Institute of System Biology Shanghai University 99 ShangDa Road Shanghai 200244 China

ISBN: (纸本)9781424429028

Many biological sequence databases have redundant sequences which are not helpful to statistical analysis and require more computational time and resources to process. This lead us to design a new and fast program to generate a non-redundant sequence set. A graph theoretic algorithm was designed to process BLAST output and remove redundant proteins from a protein sequence database. We have developed a program named BlastCuller which can be used to generate a non-redundant protein database. BlastCuller is a flexible program with a parameter of sequence similarity cutoff, which can be a decimal from 0.0 to 1.0. This program can be downloaded from http://***/BlastCuller. html. ©2009 ieee.

关键词： Graph theory

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RiboSW - A web server for identifying RNA riboswitches

RiboSW - A web server for identifying RNA riboswitches

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2009 9th ieee International conference on bioinformatics and BioEngineering, BIBE 2009

作者： Chang, Tzu-Hao Liu, Baw-Jhiune Wu, Li-Ching Huang, Hsien-Da Yeh, Chi-Ta Horng, Jorng-Tzong Chang, Cheng-Wei Department of Computer Science and Information Engineering National Central University Jhongli 320 Taiwan Department of Computer Science and Engineering Yuan Ze University Jhongli 320 Taiwan Institute of Systems Biology and Bioinformatics National Central University Jhongli 320 Taiwan Department of Biological Science and Technology Institute of Bioinformatics National Chiao-Tung University Hsinchu 300 Taiwan Department of Computer Science and Information Engineering National Central University Jhongli Taiwan Department of Bioinformatics Asia University Wufeng Taiwan Department of Information Management Hsing Wu College LinKou 224 Taiwan

ISBN: (纸本)9780769536569

Riboswitches are cis-acting genetic regulatory elements within a specific mRNA, and can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, more and more riboswitches were identified and investigated about their roles in regulatory functions in different species. Both of the sequence contexts and structural conformations are important characteristics of riboswitches. None of previous developed tools, such Covariance Models (CMs), Riboswitch finder, and RibEx, provides a web server for efficiently searching homologous instances to known riboswitches and considers two crucial characteristics of each riboswitch, such as structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method to identify twelve kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. RiboSW is now available on the web at http://***/RiboSW/. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction. That makes it possible to have an accurate and convenient web server for biologists to obtain their analyzing results in a given mRNA sequence. The supplementary data is available on the web at http://***/ RiboSW/***. © 2009 ieee.

关键词： RNA

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A hybrid intelligent system for estimating a load margin to saddle node bifurcation point of voltage stability

A hybrid intelligent system for estimating a load margin to ...

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2009 15th International conference on Intelligent System Applications to Power systems, ISAP '09

作者： Mori, Hiroyuki Ishibashi, Naoto Department of Electronics and Bioinformatics Meiji University Kawasaki 214-8571 Japan

ISBN: (纸本)9781424450985

This paper proposes a hybrid intelligent system for estimating a load margin to the saddle node bifurcation point of voltage stability. The proposed method is based on the integration of Regression Tree (RT) and Artificial Neural Network (ANN). Voltage stability analysis is one of the main concerns in power system operating and planning. Voltage stability analysis aims at evaluating the saddle node bifurcation point on PV or QV carves. So, it is necessary to estimate a load margin to the saddle node bifurcation point of voltage stability efficiently. In this paper, a new method is proposed to estimate the load margin with the hybrid method of RT and ANN. RT is used to classify data into terminal nodes and extract rules from each terminal node. ANN is constructed to estimate the load margin to the bifurcation points at each terminal node. Also, a new method for generating power system conditions is presented to consider the correlation of the nodal specified values. The proposed method is successfully applied to the ieee 30-bus system in terms of computational accuracy and computational time. © 2009 ieee.

关键词： Data mining

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