2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2010) Chengdu, China 18 – 20 June 2010 Volume 1 Pages 1-509 IEEE Catalog Number: CFP1029C-PRT ISBN: 978-1-4244-4712-1 1/14 TABLE OF CONTENTS SIMULATION AND ANALYSIS OF THE NETWORK MODEL OF THE QUORUM SENSING PROCESS DURING BIOFILM CREATION ....................................................................................................................................................................1 Ruixuan Zhao, Mingzhi Mao A CELLULAR AUTOMATON MODEL FOR THE TRANSMISSION DYNAMICS OF SCHISTOSOMIASIS................................5 Yun Liu, Kai Chu, Xiaoli Xu, Haiwei Wu, Cheng Wan THREE-DIMENSIONAL NUMERICAL MODELING FOR WIND-DRIVEN CIRCULATION AND POLLUTANT TRANSPORT IN A LARGE-SCALE LAKE .......................................................................................................................9 Zhuo Zhang, Zhi-Yao Song MULTI-TISSUE TETRAHEDRAL MESH GENERATION FROM MEDICAL IMAGES..................................................................16 Ping Hu, Hui Chen, Wen Wu, Pheng-Ann Heng NUCLEOTIDE FLUCTUATION ANALYSIS OF DIM-LIGHT VISION RHODOPSIN GENE AND MRNA SEQUENCES IN VERTEBRATES ...............................................................................................................................................................20 Todd Holden, Ni. Gadura, E. Cheung, J. Rada, P. Schneider, G. Tremberger Jr., D. Sunil, D. Lieberman, T. Cheung EXTRACTING BIOMARKER INFORMATION APPLYING NATURAL LANGUAGE PROCESSING AND MACHINE LEARNING..................................................................................................................................................................................24 Md. Tawhidul Islam, Mostafa Shaikh, Abhaya Nayak, Shoba Ranganathan CONSTRAINING AND SUMMARIZING OPTIMAL RISK AND PREVENTIVE PATTERNS IN MEDICAL DATA.................................................................................................................................................................................................................28 Junpeng Zhang, Jianfeng He, Jiuyong Li, Lei Ma THE MORPHOLOGY PREDICTION OF LYSOZYME CRYSTALS DEDUCED FROM THE BFDH LAW AND ATTACHMENT ENERGY MODEL BASED ON THE INTERMOLECULAR INTERACTION.......................................................32 Zhanzhong Wang, Pingping Jiang, Leping Dang USVM: SELECTION OF SNPS IN DISEASES ASSOCIATION STUDY USING UMDA AND SVM................................................36 Bin Wei, Qinke Peng, Jing Li, Xuejiao Kang, Chenyao Li BIAS OF PHENOTYPE SIMILARITY SCORES BETWEEN DISEASES .............................................................................................41 Jing Wang, Xianxiao Zhou, Jing Zhu, Zheng Guo PROGNOSTIC MODEL FOR THE PATIENTS WITH SEVERE LIVER DISEASE...........................................................................45 Wenfang Wu, Jing Zhang, Binrong Ma, Jinqiu He, Lunli Zhang, Chunyi Zou, Shaojie Xin, Changyan Lin A LOW-LOAD ARCHITECTURE OF PICTURE AUTOMATIC ARCHIVING AND COMMUNICATION SYSTEM............................................................................................................................................................................................................50 Yue Zhao, Zhiqiong Wang, Ying Han, Shijia Guo, Jianzhao Cao RELATIONSHIPS BETWEEN INHIBITION CONSTANTS, TYPES OF INHIBITION AND IC50: CALCULATION AND COMPARISON ON IC50 OF TWO MODEL TYROSINASE INHIBITORS ................................................54 Hairong Mao, Jiangang Xie, Qimeng Zhang, Xinyu Lü, Shubai Li INFERRING PROTEIN ANNOTATION FROM TOPOLOGICAL STRUCTURAL ANALYSIS ON PROTEIN INTERACTION NETWORK.........................................................................................................................................................................58 Dengdi Sun, Jin Fan, Haifeng Zhao, Bin Luo VAMA: A VERSATILE WEB-BASED TOOL FOR VARIABILITY ANALYSIS IN MULTIPLY-ALIGNED AMINO ACID SEQUENCES: VAMA: VARIABILITY ANALYSIS OF MULTIPLE ALIGNMENTS .............................................62 Aditi Gupta, Aridaman Pandit, Somdatta Sinha AN ONLINE SYSTEM FOR FUNCTIONAL RELATIONSHIP ANALYSIS OF GENOME-WIDE GENE PRODUCTS ......................................................................................................................................................................................................66 Qiang Hu, Zheng-Guo Zhang QUALITATIVE ANALYSIS OF A DELAYED AND STAGE-STRUCTURED PREDATOR-PREY SYSTEM................................70 Lingshu Wang, Guanghui Feng MONTE CARLO SIMULATIONS OF SPATIAL PATTERNS OF THE DEGREE OF POLARISATION FOR BACKSCATTERING LIGHTS IN TURBID MEDIA WITH BIREFRINGENCE.................................................................................74 Yinqi Feng, Yaoqin Liu, Zheng Chang CADVIST: VISUALIZATION TOOL FOR BLAST ALIGNMENT OF DENGUE VIRUS SEQUENCES ........................................79 Boonyarat Viriyasaksathian, Yodchanan Wongsawat, Prapat Suriyaphol SEARCHING SINGLE NUCLEOTIDE POLYMORPHISM MARKERS TO COMPLEX DISEASES USING GENETIC ALGORITHM FRAMEWORK AND A BOOSTMODE SUPPORT VECTOR MACHINE .............................................83 Khantharat Anekboon, Suphakant Phimoltares, Chidchanok Lursinsap, Sissades Tongsima, Suthat Fucharoen NIPAH VIRUS CLASSIFICATION VIA FRACTAL DIMENSION & SHANNON ENTROPY..........................................................87 Todd Holden, N. Gadura, E. Cheung, P. Schneider, G. Tremberger Jr., N. Elham, D. Sunil, D. Lieberman, T. Cheung BROILER GROWTH PERFORMANCE ANALYSIS: FROM CORRELATION ANALYSIS, MULTIPLE LINEAR REGRESSION, TO NEURAL NETWORK.................................................................................................................................91 Meiyan Xiao, Peijie Huang, Piyuan Lin, Shangwei Yan STEEPER ACTION POTENTIAL DURATION RESTITUTION SLOPE INCREASES RISK OF VENTRICULAR FIBRILLATION: A SIMULATION STUDY................................................................................................................95 Yi Zheng, Daming Wei, Zuxiang Fang MULTI-OBJECTIVE OPTIMIZATION RESEARCH FOR EFFECTIVE CONSTITUENTS OF QILIQIANGXIN CAPSULE OF CHINESE FORMULA...........................................................................................................................99 Hongtao Wang, Jiming Jia, Siwen Tang, Dengfeng Xu, Yajie Zheng, Huixin Zhang, Yiling Wu, Renquan Liu A CO-CLUSTERING TECHNIQUE FOR GENE EXPRESSION DATA USING BI-PARTITE GRAPH APPROACH....................................................................................................................................................................................................102 Suvendu Kanungo, Gadadhar Sahoo, Manoj Madhava Gore COMPLEXITY ANALYSIS OF SLEEP EEG SIGNAL...........................................................................................................................107 Ling Li, Ruiping Wang BIOSORPTION CHARACTERISTICS OF EXTRACELLULAR POLYMERIC SUBSTANCE (EPS) PRODUCED BY RHIZOBIUM RADIOBACTER FOR REMOVAL OF CU (II) AND MN (II) IONS FORM AQUEOUS SOLUTIONS..............................................................................................................................................................................110 Li-Li Wang, Fang Ma, Shan-Shan Feng, De-Zhi Sun, Bing Yu, Jie Xing USING SPECTRAL COMPONENTS FOR PREDICTING TREATMENT EFFECTS ON TIME SERIES MICROARRAY GENE EXPRESSION PROFILES.................................................................................................................................114 Qian Xu, Hong Xue, Qiang Yang MODELING OF MUTANT CYSTATHIONINE BETA-SYNTHASE WITH SEVERITY OF ITS DEFICIENCY.........................119 Shaomin Yan, Guang Wu ANALYSIS OF THE CHLOROPHYLL α FLUORESCENCE TRANSIENT OF SPIRODELA POLYRHIZA BY JIP-TEST.........................................................................................................................................................................................................123 Hongtao Li, Yu Zhao, Ke Zhu, Jinju Wang, Qingdai Liu, Hongjie An CONSTRUCTION OF A SEQUENCE- AND BACKBONE-DEPENDENT ROTAMER LIBRARY BY HIDDEN- MARKOV MODEL .......................................................................................................................................................................................127 Wei Wen, Qiang Lü, Peng Yang, Lingyun Yang, Jinzhen Wu, Xu Huang A NEW METHOD FOR IDENTIFICATION POTENTIAL SNP RELATING TO TRAIT ON HIGHLY POLYMORPHIC GENE SEQUENCE COMBINATION NCBI DATABASE AND MULTI-SEQUENCE ALIGNMENT SOFTWARE.........................................................................................................................................................................131 Hongbin Lee, Bo Wang A NEW PARAMETER SET FOR CLUBFOOT CLASSIFICATION ....................................................................................................135 Cong Liu, Lei Wang, Teng Zhang, Tiexiang Wen A NETWORK-BASED APPROACH FOR PROTEIN FUNCTIONS PREDICTION USING LOCALLY LINEAR EMBEDDING .................................................................................................................................................................................................139 Haifeng Zhao, Dengdi Sun, Rifeng Wang, Bin Luo AN EFFECTIVE ELECTROPORATION PROTOCOL FOR BACILLUS ALCALOPHILUS TCCC11004...................................143 Kun Cheng, Fuping Lu, Xiaomei Liang HYDRODYNAMIC EFFECTS ON MICROBIAL GROWTH: A CASE STUDY ON