2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent
2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS 2009) Shang Hai, China 3 – 5 August 2009 IEEE Catalog Number: ISBN: CFP0935H-PRT 978-1-4244-4612-4 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing IJCBS 2009 Table of Contents Message from General Chair Message from Program Chairs Organizing Committee Steering Committee Program Committee Reviewers Planery Keynote Abstracts Session 1: Microarray Data Analysis Gene Selection for Microarray Expression Data with Imbalanced Sample Distributions .................................................................................................................................................................3 Abu H. M. Kamal, Xingquan Zhu, and Ramaswamy Narayanan Redundant Gene Selection Based on Particle Swarm Optimization ..................................................................10 Su-Fen Chen, Xue-Qiang Zeng, Guo-Zheng Li, Jack Y. Yang, and Mary Qu Yang Investigating Gene and MicroRNA Expression in Glioblastoma ......................................................................17 Hua Dong, Hoicheong Siu, Li Luo, Xiangzhong Fang, Li Jin, and Momiao Xiong Discovery of Biomarker Genes from Earthworm Microarray Data by Discriminant Analysis and Clustering ..............................................................................................................23 Ying Li, Nan Wang, Chaoyang Zhang, Edward J. Perkins, and Ping Gong PBC: A Software Framework Facilitating Pattern-Based Clustering for Microarray Data Analysis ..................................................................................................................................30 Dong-Guk Shin, Seung-Hyun Hong, Pujan Joshi, Rai Nori, Baikang Pei, Hsin-Wei Wang, Patrick Harrington, Lynn Kuo, Ivo Kalajzic, and David Rowe Cross-Domain Neurobiology Data Integration and Exploration ........................................................................37 Weijian Xuan, Manhong Dai, Buckner Josh, Barbara Mirel, Jean Song, Brian Athey, Stanley J. Watson, and Fan Meng Study DNA Microarray Gene Expression Data of Alzheimer’s Disease by Independent Component Analysis .....................................................................................................................44 Wei Kong, Xiaoyang Mou, and Bin Yang Probabilistic Model Based Hough Transform for Detection of Co-expression Patterns in Three-Color cDNA Microarray Data ..................................................................................................48 Peter Tino, Hongya Zhao, and Hong Yan Multiclass Gene Selection on Microarray Data Using l1-norm Least Square Regression ...................................................................................................................................................................52 Xiyi Hang Framework for Knowledge-Based Integrative Analysis of Microarray Data ..................................................56 Jiantao Shi, Kankan Wang, and Ji zhang Session 2: Genome Analysis I Genome Evolution in Malaria Parasites: I. Core Genome Components ...........................................................63 Hong Cai, Yufeng Wang, and Jianying Gu Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units ........................................................................................................................................70 Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, and Zhihong Yu Genomic Comparison of Bacterial Species Based on Metabolic Characteristics ............................................77 Gaurav Jain, Haozhu Wang, Li Liao, and E. Fidelma Boyd The Core and Pan-Genome of the Vibrionaceae ..................................................................................................84 Timothy G. Lilburn, Hong Cai, and Jianying Gu An Improved Algorithm for the Location of Heaviest Segments in Genomic Sequences ....................................................................................................................................................................91 Nikola Stojanovic GeneIndex: An Open Source Parallel Program for Enumerating and Locating Words in a Genome ...................................................................................................................................................98 Huian Li, David Hart, Matthias Mueller, Ulf Markwardt, and Craig Stewart Proteogenomic Mapping for Structural Annotation of Prokaryote Genomes ................................................103 Nan Wang, Shane Burgess, Mark Lawrence, and Susan Bridges Session 3: Genome Analysis II A Classification System for Predicting RNA Hairpin Loops ...........................................................................109 Monther Aldwairi, Rehab Duwairi, and Wafa’a Alqarqaz Layout and Post-Processing of Transcriptional Modules ..................................................................................116 Hong Sun, Tim Van den Bulcke, Bart De Moor, Karen Lemmens, Kristof Engelen, and Kathleen Marchal Mapping miRNA Regulation to Functional Gene Sets ......................................................................................122 Yidong Chen, Harry Hung-I Chen, and Yufei Huang A Primer Design Algorithm for Global Analysis of CpG Methylation ..........................................................126 Hehuang Xie, Min Wang, Yuichi Tange, Maria de F. Bonaldo, and Marcelo B. Soares Accurate Prediction of Alternatively Spliced Cassette Exons Using Evolutionary Conservation Information and Logitlinear Model ......................................................................131 Chuang Ma, Fangyuan Deng, Hui Liu, and Yanhong Zhou A Neural Network Based on Rough Set (RSNN) for Prediction of Solitary Pulmonary Nodules .................................................................................................................................................135 Hui Liu, Wei Kong, Tian-Shuang Qiu, and Guo-Li Li Variation in the Predicted Biosynthetic Capabilities of Seven Vibrionaceae ................................................139 Jennifer Neary, Yufeng Wang, and Timothy G. Lilburn Molecular Cloning and Expression of Ppdc-ldhL Fusion Gene in Zymomonas Mobilis ATCC 10988 ..............................................................................................................................................143 Nian-Fa Gao, Yong Wang, Qiang Gao, Bin-Zhe Wang, Jian Zhang, and Bo-Ya Liu Clustering of SNPs by a Structural EM Algorithm ............................................................................................147 Yulong Zhang and Liang Ji Session 4: Sequence Analysis A Parallel Algorithm for Three-Profile Alignment Method .............................................................................153 Che-Lun Hung, Chun-Yuan Lin, Yeh-Ching Chung, and Chuan Yi Tang Mapping Transcription Factors from a Model to a Non-model Organism .....................................................160 Rachita Sharma, Patricia Evans, and Virendra Bhavsar On the Design of RNA Sequences for Realizing Extended Shapes .................................................................167 Marc Hellmuth, Daniel Merkle, and Martin Middendorf Practical and Efficient Algorithms for Degenerate and Weighted Sequences Derived from High Throughput Sequencing Technologies ..............................................................................174 Pavlos Antoniou, Costas S. Iliopoulos, Laurent Mouchard, and Solon P. Pissis An Adaptive Suffix Tree Based Algorithm for Repeats Recognition in a DNA Sequence ...................................................................................................................................................................181 Hongwei Huo, Xiaowu Wang, and Vojislav Stojkovic A Bayesian Approach for Identifying miRNA Targets by Combining Sequence Prediction and Expression Profiling ...................................................................................................185 Hui Liu, Lin Zhang, Shou-Jiang Gao, and Yufei Huang Next Generation Sequence Analysis Using Genetic Algorithms on Multi-core Technology ...............................................................................................................................................................190 Kaiqi Xiong, Sang C. Suh, Jack Y. Yang, Mary Qu Yang, and Hamid Arabnia Session 5: Protein Structure and Function I Structural Domain Based Multiple Instance Learning for Predicting Gram-Positive Bacterial Protein Subcellular Localization ................................................................................195 S.Y. Mei and Wang Fei Biological Features for Sequence-Based Prediction of Protein Stability Changes upon Amino Acid Substitutions ............................................................................................................201 Shaolei Teng, Anand K. Srivastava, and Liangjiang Wang GO Semantic Similarity Based Analysis for Huaman Protein Interactions ....................................................207 Gang Chen, Jianxin Wang, and Min Li GO Semantic Similarity-Based False Positive Reduction of Protein-Protein Interactions ...............................................................................................................................................................211 Jianxing Wang, Lijian Dai, and Min Li Using Mutual Information and Models of Evolution for Improved Pattern Detection ....................................................................................................................................................................215 Stephan Kitchovitch, Ian Leung, Yuedong Song, and Pietro Liò Network Approaches for Shotgun Proteomics Data Analysis ..........................................................................222 Bing Zhang, Jing Li, David L. Tabb, and Byung-Hoon Park Session 6: Protein Structure and Function II SVM-Based Approach for Predicting DNA-Binding Residues in Proteins from Amino Acid Sequences .................................................................................................................................225 Xin Ma, Jian-Sheng Wu, Hong-De Liu, Xi-Nan Yang, Jian-Ming Xie, and Xiao Sun Putative Cell Cycle Related Genes in Plasmodium Falciparum .......................................................................230 Hong Cai, Maribel Sanchez, Yufeng Wang, and Jianying Gu Identifying New Methylated Arginines via Granular Decision Fusion with SVM Modeling ................................................................................................................................................237 Zejin Jason Ding, Yan-Qing Zhang, Nan Xie, and Yujun George Zheng A Comparative Study of Ensemble Learning Approaches in the Classification of Breast Cancer Metastasis ...................................................................................................................................242 Wangshu Zhang, Feng Zeng, Xuebing Wu, Xuegong Zhang, and Rui Jiang New Descriptors of Evolutionary Information for Accurate Prediction of DNA and RNA-Binding Residues in Protein Sequences .............................................................................................246 Liangjiang Wang and Caiyan Huang Improving Prediction of the Contact Numbers of Residues in Proteins from Primary Sequences .........................................................................................................................................251 Qiwen Dong, Shuigeng Zhou, and Jihong Guan Protein Remote Homology Detection Using Order Profiles .............................................................................255 Bin Liu, Lei Lin, Xiaolong Wang, and Xuan Wang Session 7: Protein Structure and Function III Semi-supervised Learning of Text Classification on Bacterial Protein-Protein Interaction Documents ............................................................................................................................................263 Guixian Xu, Zhendong Niu, Peter Uetz, Xu Gao, Xuping Qin, and Hongfang Liu ANN Based Protein Function Prediction Using Integrated Protein-Protein Interaction Data ........................................................................................................................................................271 Lei Shi, Young-Rae Cho, and Aidong Zhang 3D-interologs: A Protein-Protein Interacting Evolution Database across Multiple Species ..........................................................................................................................................278 Jinn-Moon Yang, Yung-Chiang Chen, and Yu-Shu Lo Assessing the Most Effective Depth for PPI Analysis .......................................................................................286 Jaine K Blayney, Huiru Zheng, Haiying Wang, and Francisco Azuaje Discovery of Motif Pairs from Protein-Protein Interaction Networks ............................................................293 Hong Zhang, Yun Xu, and Yuzhong Zhao A Systems Biology Approach to Identify Affected Regulatory and Signaling Circuits in Protein Interaction Networks ..............................................................................................................297 Ting Gong, Jianhua Xuan, Rebecca B. Reggins, and Robert Clarke Automaton Models of Computational Genetic Regulatory Networks with Combinatorial Gene-Protein Logical Interactions .....................................................................................301 Peter C.Y. Chen and Yulin Weng Session 8: Biomedical Engineering I Towards a Comprehensive HBV-Human Interaction Map ...............................................................................311 Fei Li, Yuxing Peng, Wenjian Xu, Guangchuang Yu, Peng LI, Xiaochen Bo, and Shengqi Wang Prediction of Peptides Binding to MHC Class I Alleles by Partial Periodic Pattern Mining ..........................................................................................................................................................315 Cem Meydan, Hasan Otu, and Ugur Sezerman MRI Based Fat Segmentation at 7T with Confidence Image ...........................................................................319 Yang Tang, Susan Lee, Marvin D. Nelson Jr, and Rex A. Moats An Artificial Immune System for Temporal Anomaly Detection Using Cell Activation Thresholds and Clonal Size Regulation with Homeostasis ...........................................................323 Mário J. Antunes and Manuel E. Correia Global Stochastic Contact Modeling of Infectious Diseases ............................................................................327 Armin R. Mikler, Angel Bravo-Salgado, and Courtney D. Corley Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution ..........................................331 Thomas Greve Kristensen and Christian Nørgaard Storm Pedersen Session 9: Biomedical Engineering II Analyzing Response Feasibility for Bioemergencies .........................................................................................337 Tamara Schneider, Armin R. Mikler, and Marty O'Neill II Estimation of Heart Rate Variability Changes during Different Visual Stimulations Using Non-invasive Continuous ECG Monitoring System .......................................................344 Wanqing Wu, Jungtae Lee, and Haifeng Chen A Study on Prognosis of Brain Tumors Using Fuzzy Logic and Genetic Algorithm Based Techniques .................................................................................................................................348 Arpita Das and Mahua Bhattacharya Feature Extraction and Classification of EEG Signals Using Wavelet Transform, SVM and Artificial Neural Networks for Brain Computer Interfaces ...................................................................................................................................................................352 Mohammad Reza Nazari Kousarrizi, AbdolReza Asadi Ghanbari, Mohammad Teshnehlab, Mahdi Aliyari Shorehdeli, and Ali Gharaviri A Novel Method of De-noising and Classifying on Mental EEG of Imaging Left-Right Hands Movement .................................................................................................................................356 Shaochun Wu, Duhong Song, Mingdong Li, and Lingyu Xu A Computational Framework to Study Public Health Epidemiology .............................................................360 Courtney D. Corley and Armin R. Mikler Session 10: Traditional Chinese Medicine Exploring Systems Biology Approaches to Traditional Chinese Medicine Cancer Research .......................................................................................................................................................367 Dan Xi and Jeffrey D. White Genomic Imaging: A Modern Environment for TCM Research ......................................................................371 Su-Shing Chen, Qingfeng Song, and Yu-Ping Wang YinYang Bipolar Relativity - A Unifying Theory of Nature, Agents and Life Science .......................................................................................................................................................................377 Wen-Ran Zhang Concordance of Diagnosis Based on Zangfu-Organs Syndrome Differentiation by Clinicians of Traditional Chinese Medicine ...................................................................................................384 Liu Guo-Ping, Wang Yi-Qin, Zhao Nai-Qing, Xu Zhao-Xiao, Li Fu-Feng, Dong Ying, and Qian Peng A TCM Platform for Maters' Experience Sharing ..............................................................................................388 Mingyu You, Lei Ge, Guo-Zheng Li, Liaoyu Xu, and Suying Huang Facial Complexion Acquisition and Recognition System for Clinical Diagnosis in Traditional Chinese Medicine ...........................................................................................................................392 Li Fufeng, Di Dan, Li Xiaoqiang, Wang Yiqin, Qian Peng, Zheng Xiaoyan, and Liu Guoping TCM in Innate Immunity: A YinYang-N-Element Hypothesis of the Innate Immunological System ...........................................................................................................................................397 Stefan Jaeger, Su-Shing Chen, and Wen-Ran Zhang Session 11: Systems Biology I In-Silico Effects of Mg2+ Diffusion Rates on Stochastic Event Based Simulation of the PhoPQ System ..........................................................................................................................405 Preetam Ghosh, Kalyan Basu, Sajal K. Das, and Chaoyang Zhang Global Network Features of Cancer Genes in the Human Interactome ..........................................................412 Jingchun Sun, Peilin Jia, and Zhongming Zhao A Granular Hierarchical Approach to Biophysical and Biochemical Evaluations of Transgenic Modifications ............................................................................................................417 Moshe A. Gadish, David K. Chiu, Cecil W. Forsberg, and Serguei P. Golovan Integrative Computational Identifications of the Signaling Pathway Network Related to TNF-alpha Stimulus in Vascular Endothelial Cells ........................................................................422 Jin Gu, Shao Li, Yang Chen, and Yanda Li Using Frequent Co-expression Network to Identify Gene Clusters for Breast Cancer Prognosis .....................................................................................................................................................428 Jie Zhang, Kun Huang, Yang Xiang, and Ruoming Jin A Numerical Study of Pulsatile Flow Through a Hollow Fiber Cartridge: Growth Factor-Receptor Binding and Dissociation Analysis ...........................................................................435 Changjiang Zhang, Wensheng Shen, Bing Zhao, Michael Fannon, Kimberly Forsten-Williams, and Jun Zhang Pathway and Network Analysis of Schizophrenia Candidate Genes under Meta-Analysis Linkage Peaks ....................................................................................................................442 Peilin Jia, Jingchun Sun, Leng Han, and Zhongming Zhao Enhancing Automatic Biological Pathway Generation with GO-Based Gene Similarity ...................................................................................................................................................................448 Antonio Sanfilippo, Bob Baddeley, Nat Beagley, Rick Riensche, and Banu Gopalan Session 12: Systems Biology II Estimation of Kinetic Rates of MAP Kinase Activation from Experimental Data ............................................................................................................................................................................457 Tianhai Tian Connecting Biological Themes Using a Single Human Network of Gene Associations ..............................................................................................................................................................463 Hai Fang, Ji Zhang, and Kan-Kan Wang Statistical Analysis of Discrete Dynamical System Models for Biological Networks ...................................................................................................................................................................472 Zhengyu Ouyang and Mingzhou Song Parameterized Complexity of Finding Elementary Modes in Metabolic Networks ...................................................................................................................................................................479 Hong Liu, Haodi Feng, and Daming Zhu Two Dimensional Modeling and Fractal Characterization of Tumor Vascular Network .....................................................................................................................................................................483 Radu Dobrescu and Loretta Ichim Gene Regulatory Network Inference Using Predictive Minimum Description Length Principle and Conditional Mutual Information ......................................................................................487 Vijender Chaitankar, Chaoyang Zhang, Preetam Ghosh, Edward J. Perkins, Ping Gong, and Youping Deng Dynamic Propagation Properties of Virus-Host Protein Interaction Network ...............................................491 Fei Li, Wenjian Xu, Peng LI, Xiaochen Bo, and Yuxing Peng Systematically Identifying Genes and Pathways in Multiple Cancer Types Using HGD & PSO-SVM ......................................................................................................................................494 Mahesh Visvanathan, Adagarla Bhargav Srinivas, Gerald Lushington, and Sitta Sittapalam Session 13: Novel Algorithms for Intelligent Computing I Constraint Projections for Discriminative Support Vector Machines .............................................................501 Zhao Zhang and Ning Ye Regularized Recurrent Least Squares Support Vector Machines .....................................................................508 Haini Qu, Yacine Oussar, Gerard Dreyfus, and Weisheng Xu Similarity Learning via Optimizing the Data-Dependent Kernel .....................................................................512 Huilin Xiong and Panfei Shi EasyEnsemble and Feature Selection for Imbalance Data Sets ........................................................................517 Tian-Yu Liu Genetic Algorithm Based Semi-feature Selection Method ...............................................................................521 Hualong Bu, Shangzhi Zheng, and Jing Xia Combination Forecasting Model for Mid-long Term Load Based on Least Squares Support Vector Machines and a Mended Particle Swarm Optimization Algorithm ..........................................................................................................................................525 Dongxiao Niu, Haitao Lv, and Yunyun Zhang An Improved EM-Based Semi-supervised Learning Method ...........................................................................529 Xinghua Fan, Zhiyi Guo, and Houfeng Ma A Novel Nonlinear Dimensionality Reduction Method for Robust Wood Image Recognition ...................................................................................................................................................533 Zhao Zhang and Ning Ye Designing the Self-Adaptive Fuzzy Neural Networks .......................................................................................537 Liu Fang Session 14: Novel Algorithms for Intelligent Computing II An Effective Multi-level Immune Algorithm for Graph Bipartitionin ............................................................543 Ming Leng, Lingyu Sun, and Songnian Yu A Combination Approach to Cluster Validation Based on Statistical Quantiles ...........................................549 Amparo Albalate and David Suendermann Collision Description of Clustering ......................................................................................................................556 Daniel Hsu, Ben Yang, and Shardrom Johnson A Vector Operation Based Fast Association Rules Mining Algorithm ...........................................................561 Liu Zhi, Sang Guoming, and Lu Mingyu A Quadratic Time Algorithm for Computing the Quartet Distance between Two General Trees ...................................................................................................................................565 Thomas Mailund, Jesper Nielsen, and Christian Norgaard Storm Pedersen Kalman Filtering Design Based on Real-Time Updating of Noise Matrix .....................................................569 Jiang Wei, Zhao Xia, and Chen Qijun Applying Particle Swarm Optimization to Transfer Function Specification for Direct Volume Rendering ................................................................................................................................573 Kenli Li, Rui Qi, Degui Xiao, Lei Yang, and Zhiyong Li PTS-RNSA: A Novel Detector Generation Algorithm for Real-Valued Negative Selection Algorithm ...............................................................................................................................577 Yujian Wang and Wenjian Luo Semantic Role Labeling Based on Dependency Tree with Multi-features .....................................................584 Hanxiao Shi, Guodong Zhou, Peide Qian, and Xiaojun Li Session 15: Novel Applications for Intelligent Computing A Collaborative Car Auto-Navigation Framework Based on Intelligent Trajectory Mining ....................................................................................................................................................591 Ruan Tong, Wang Zhan Quan, and Song Tao Security Data Mining in an Ontology for Vulnerability Management ............................................................597 Ju An Wang and Minzhe Guo Fingerprint Ridge Distance Estimation Based on Ridge Search ......................................................................604 Liming Zhang, Yilong Yin, and Dong Yang An Improved Asymmetric Link Bandwidth Measurement Algorithm ............................................................608 Rong Wang, Aiwang Cheng, Wei Du, and Zupeng Li The Application of Improved Immunogenetic Algorithm in Signal Timing ..................................................612 Rong Gu and Hongyun Zhang Modeling Confidentiality in a Simplified Database Access .............................................................................616 Chen-chi Shing, Marn-Ling Shing, Kuo Lane Chen, and Huei Lee RFID Dynamic Grouping Anti-collision Algorithm Based on FCM ..............................................................619 Yao-feng Xue, Hua-li Sun, and Zhi-ting Zhu Design of Obstacle Modal Discrimination System Based on the Neural Network .....................................................................................................................................................................623 Hui Liu, Jianyi Lin, and Qian Li Feature Mining and Intelligent Computing for MP3 Steganalysis ...................................................................627 Mengyu Qiao, Andrew H. Sung, and Qingzhong Liu Author Index
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