2009 3rd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2009) Beijing, China 11 – 13 June 2009 Pages 1-605 IEEE Catalog Number: CFP0929C-PRT ISBN: 978-1-4244-2901-1 Copyright © 2009 by the Institute of Electrical and Electronic Engineers, Inc All Rights Reserved Copyright and Reprint Permissions: Abstracting is permitted with credit to the source. Libraries are permitted to photocopy beyond the limit of U.S. copyright law for private use of patrons those articles in this volume that carry a code at the bottom of the first page, provided the per-copy fee indicated in the code is paid through Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923. For other copying, reprint or republication permission, write to IEEE Copyrights Manager, IEEE Service Center, 445 Hoes Lane, Piscataway, NJ 08854. All rights reserved. ***This publication is a representation of what appears in the IEEE Digital Libraries. 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IEEE Catalog Number: CFP0929C-PRT ISBN 13: 978-1-4244-2901-1 Library of Congress No.: 2008935829 Additional Copies of This Publication Are Available From: Curran Associates, Inc 57 Morehouse Lane Red Hook, NY 12571 USA Phone: (845) 758-0400 Fax: (845) 758-2633 E-mail: [email protected] TABLE OF CONTENTS Scavenging Effects of Echinacea purpurea Extract and Active Ingredient Against Peroxynitrite...........................................................1 Yun-Jing Luo, Jing-Lin Pan, Yan-Shu Pan, Ru Gang Zhong Spatial Cluster Analysis Based on Evolutionary DNA Computing Technique ...........................................................................................5 Xiyu Liu, Hong Liu Evidence for Positive Selection in Ser/Thr Protein Kinases (STKs) Genes of Trichodesmium erythraeum ...........................................9 Chengwei Liang, Xiaowen Zhang Feature Selection for Tandem Mass Spectrum Quality Assessment via Sparse Logistical Regression..................................................13 Jiarui Ding, Fang-Xiang Wu MUI: A New Functional Similarity Measure for Gene Products Based on Gene Ontology ....................................................................17 Qiang Hu, Zheng-Guo Zhang An Information Theoretic Viewpoint on Haplotype Reconstruction from SNP Fragments ...................................................................23 Huimin Chen, Zhiyu Zhao Automatic Testing with Diagnostic Resolution for Biomedical Apparatus ...............................................................................................27 Jinhe Wang, Nan Zhang Reconstruction of Probability Phylogenetic Trees with Substitution Models ...........................................................................................31 J. F. Weng, I. Mareels, D. A. Thomas Optimization of MISCORE-Based Motif Identification Systems ...............................................................................................................35 Nung Kion Lee, Dianhui Wang KiWi: A Scalable Subspace Clustering Algorithm for Gene Expression Analysis ...................................................................................39 Obi L. Griffith, Byron J. Gao, Mikhail Bilenky, Yuliya Prychyna, Martin Ester, Steven J. M. Jones An MM-Based Optimization Algorithm for Sparse Linear Modeling on Microarray Data Analysis....................................................48 Xiaohui Chen, Raphael Gottardo Selecting Biomarkers for Ovarian Cancer Detection Using SVD and Monte Carlo Methods ................................................................52 Haifeng Lai, Bin Han, Lei Zhu, Yan Chen, Lihua Li, Rebecca Sutphen Assessing Iterative Normal Modes on Representing Protein Conformational Transitions .....................................................................56 Cheng Peng, Liqing Zhang Global Differential Gene Expression in Cancers and its Implications for Building Robust Diagnostic Classifiers..............................61 Chen Yao, Min Zhang, Jinfeng Zou, Chenguang Wang, Dong Wang, Jing Wang, Jing Zhu, Zheng Guo Novel and Homology MicroRNA Prediction by Using a Bayesian Network Based Program in Strongylocentrotus Purpuratus Genome .........................................................................................................................................................................................65 Zhenlin Wei, Xiaolin Liu, Yaqing Chang New Fast Algorithm on DNA Sequence Alignment ......................................................................................................................................69 Jing Fan, Ruili Jiao EPBC: Enhanced Possibilistic Biclustering with Application to Gene Expression Analysis...................................................................73 Mohamed A. Mahfouz, Mohamed A. Ismail DPBC: Distance Based Possibilistic Biclustering with Application to Gene Expression Analysis..........................................................79 Mohamed A. Mahfouz, Mohamed A. Ismail Modelling the Dynamics of Anti-HBV Infection Therapy with Chinese Herbs ........................................................................................83 Yongan Ye, Lequan Min Discovering New Drug in Ancient Herbal Compound Database by Unsupervised Pattern Discovery Algorithm ...............................87 Jianxin Chen, Shihuan Tang, Hongjun Yang Quantitative Structure-Activity Relationship of Sesquiterpene Lactones with Anti-Ulcerogenic Activity ...........................................91 Huajun Luo, Junzhi Wang, Yuan Zhou, Kun Zou A New Particle Swarm Optimization Based Unscented Particle Filtering ................................................................................................96 Chunhe Song, Hai Zhao, Wei Jing, Guilan Luo Mixed Using Artificial Fish - Particle Swarm Optimization Algorithm for Hyperspace Basing on Local Searching........................100 Wei Gao, Hai Zhao, Chunhe Song, Jiuqiang Xu Study on the Dynamical Behavior of Mass Attitudes.................................................................................................................................104 Jinghu Yu, Jinli Pei Mutation Patterns in Human Menin ............................................................................................................................................................108 Shaomin Yan, Guang Wu The Transient Characters of the Directed Motion of Protein Motors......................................................................................................113 Weixia Wu, Yong Zhan, Yingrong Han, Yafei Chen, Hui Zhou, Ao Zhang Computational Identification of PpsR and FnrL Regulatory Elements in Four Purple Bacteria ........................................................117 Chengwei Liang, Wei Wei, Qin Song The Identification of Human Cryptic Exons Based on SVM.....................................................................................................................122 Gang Su, Ying-Fei Sun, Jun Li An Improved Position Weight Matrix Method Based on an Entropy Measure for the Recognition of Prokaryotic Promoters ........................................................................................................................................................................................................126 Qinqin Wu, Jiajun Wang, Hong Yan Antibody Concentration Based Method for Network Security Situation Awareness.............................................................................130 Feixian Sun, Feng Xu Research on Symbiotic System of Manufacturing Enterprises and TPL Based on Symbiotic Theory ................................................134 Chouyong Chen, Lei Liu, Baoliang Hu Functional Module Analysis of Alzheimer Disease Related Genes and MicroRNAs Based on Gene Ontology Annotation.......................................................................................................................................................................................................138 Jie Zhang, Li Li, Xia Li, Haiyun Wang, Xia Li DNA Computing for Traveling Salesman Problem....................................................................................................................................142 Xikui Liu, Li Yan Three-Dimensional Simulation of Pathogen Particles Spread Around Buildings ..................................................................................146 Xue-Yi You, Peng Zhang, Wei Liu Research on Characteristic Extraction of Human Gait.............................................................................................................................150 Shan Yang, Lingjiang Kong Detection of T-Wave Alternans Based on the Maximum of T Waves ......................................................................................................154 Qun Li, Jie Zhao, Jie Tian, Yan-Na Zhao, Ji-Kui Wang, Jian-Gong Xu, Fang-Zhou Xu Integration of Medical Information Systems Based on Virtual Database and Web Services................................................................158 Yinyao Zhu, Peipei Jia, Huilong Duan, Xudong Lu SPSAS: A Segment-Based Protein Sequence Analyzing System...............................................................................................................162 Kan Liu, Fan Chen, Ping Liu, Hao Xie Compressed Pattern Matching in DNA Sequences Using Multithreaded Technology...........................................................................165 Piyuan Lin, Shaopeng Liu, Lixia Zhang, Peijie Huang Gene Expression Analysis Using Clustering................................................................................................................................................169