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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