Detailed Arrangement of Oral Presentations
O-3-PM-1-B: Novel Algorithms for Intelligent Computing I
Chair: Ning Ye
1:30 pm – 3:30 pm, Aug. 3, 2009, Room B
136 Constraint Projections for Discriminative Support Vector Machines
zhao zhang, ning ye
125 Regularized Recurrent Least Squares Support Vector Machines
Haini Qu, Yacine Oussar, Gerard Dreyfus, Weisheng Xu
115 Similarity learning via optimizing the data-dependent kernel
Huilin Xiong, Panfei Shi
73 EasyEnsemble and Feature Selection for Imbalance Data Sets
Tian-Yu Liu
135 A Novel Nonlinear Dimensionality Reduction Method for Robust Wood Image Recognition
zhao zhang, ning ye
83 Designing the Self-Adaptive Fuzzy Neural Networks
liu fang
O-3-PM-1-C: Genome Analysis I
Chair: Yufeng Wang
1:30 pm – 3:30 pm, Aug. 3, 2009, Room C
146 Genome Evolution in Malaria Parasites: I. Core Genome Components
Hong Cai, Yufeng Wang, Jianying Gu
19 Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units
Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, Zhihong Yu
30 Genomic Comparison of Bacterial Species Based on Metabolic Characteristics
Gaurav Jain, Haozhu Wang, Li Liao, E. Fidelma Boyd
129 The core and pan-genome of the Vibrionaceae
Timothy G. Lilburn, Hong Cai, Jianying Gu
63 GeneIndex: an open source parallel program for enumerating and locating words in a genome
Huian Li, David Hart, Matthias Mueller, Ulf Markwardt, Craig Stewart
161 Proteogenomic Mapping for Structural Annotation of Prokaryote Genomes
Nan Wang, Shane Burgess, Mark Lawrence, Susan Bridges
144 Mathematical Modeling of Macrophage Driven Left Ventricular Remodeling
Yufang Jin, Dennis Jordan, Jamie Berger, Qiuxia Dai, G. Patricia Escobar, Merry L. Lindsey
O-3-PM-1-D: Workshop on Traditional Chinese Medicine I (in Chinese)
Chair: Su-Shing Chen
1:30 pm – 3:30 pm, Aug. 3, 2009, Room D
Invited talk From:
Nevin Zhang
Dan Xi
Liaoyu Xu
Wenran Zhang
O-3-PM-1-E: Protein Structure and Function I
Chair: Bing Zhang
1:30 pm – 3:30 pm, Aug. 3, 2009, Room E
74 Structural Domain Based Multiple Instance Learning for Predicting Gram-Positive Bacterial Protein Subcellular Localization
S.Y. Mei,Wang Fei
41 Biological Features for Sequence-Based Prediction of Protein Stability Changes upon Amino Acid Substitutions
Shaolei Teng, Anand K. Srivastava, Liangjiang Wang
108 GO semantic similarity based analysis for huaman protein interactions
Gang Chen, Jianxin Wang, Min Li
107 GO semantic similarity-based false positive reduction of protein-protein interactions
Lijian Dai,Jianxing Wang,Min Li
121 Using Mutual Information and Models of Evolution for improved pattern detection
Stephan Kitchovitch, Ian Leung, Yuedong Song, Pietro Lio'
210 Network approaches for shotgun proteomics data analysis
Bing Zhang, Jing Li, David L. Tabb, Byung-Hoon Park
104 Statistical Potential Function Design Based on Genetic Algorithm
Xin Geng, Jihong Guan, Qiwen Dong and Shuigeng Zhou
O-3-PM-2-B: Novel Algorithms for Intelligent Computing II
Chair: Lei Wang
3:40 pm – 5:40 pm, Aug. 3, 2009, Room B
131 A Combination approach to Cluster Validation Based on Statistical Quantiles
Amparo Albalate, David Suendermann
120 Collision Description of Clustering
Daniel Hsu, Ben Yang, Shardrom Johnson
28 A Vector Operation Based Fast Association Rules Mining Algorithm
Liu Zhi, Sang Guoming, Lu Mingyu
160 A quadratic time algorithm for computing the quartet distance
Thomas Mailund, Jesper Nielsen, Christian Norgaard Storm Pedersen
155 Kalman filtering design based on real-time updating of noise matrix
jiangwei,zhaoxia,chenqijun
103 PTS-RNSA: A Novel Detector Generation Algorithm for Real-Valued Negative Selection Algorithm
Yujian Wang,Wenjian Luo
117 Semantic Role Labeling based on dependency Tree with multi-features
Guodong Zhou, Peide Qian, Xiaojun Li
O-3-PM-2-C: Genome Analysis II
Chair: Monther Aldwairi
3:40 pm – 5:40 pm, Aug. 3, 2009, Room C
141 A Classification System for Predicting RNA Hairpin Loops
Monther Aldwairi, Rehab Duwairi and Wafa’a Alqarqaz
29 Layout and Post-Processing of Transcriptional Modules
Hong Sun, Karen Lemmens, Tim Van den Bulcke, Kristof Engelen, Bart De Moor, Kathleen Marchal
148 A Primer Design Algorithm for Global Analysis of CpG Methylation
Hehuang Xie, Min Wang, Yuichi Tange, Maria de F. Bonaldo, Marcelo B. Soares
35 A neural network based on rough set(RSNN) for prediction of solitary pulmonary nodules
Hui Liu,Wei Kong,Tian-Shuang Qiu,Guo-Li Li
57 Variation in the predicted biosynthetic capabilities of seven Vibrionaceae
Jennifer Neary, Yufeng Wang, Timothy G. Lilburn
100 Clustering of SNPs by a structural EM algorithm
Yulong Zhang, Liang Ji
O-3-PM-2-D: Workshop on TCM II (in Chinese)
Chair: Dan Xi
3:40 pm – 5:00 pm, Aug. 3, 2009, Room D
Invited talk from:
Su-Shing Chen
Fufeng Li
Guo-Zheng Li
165 Exploring Systems Biology Approaches to Traditional Chinese Medicine Cancer Research
Dan Xi, Jeffrey D. White
152 Genomic Imaging: A Modern Environment for TCM Research
Su-Shing Chen, Qingfeng Song, Yu-Ping Wang
155 Concordance of Diagnosis Based on Zangfu-organs Syndrome Differentiation by Clinicians of Traditional Chinese Medicine
Liu Guo-Ping, Wang Yi-Qin,Zhao Nai-Qing,Xu Zhao-Xiao,Li Fu-Feng,Dong Ying
154 A TCM Platform for Maters’ Experience Sharing
Mingyu You, Lei Ge, Guo-Zheng Li, Liaoyu Xu, Suying Huang
157 Facial complexion acquisition and recognition system for clinical diagnosis
LI Fufeng, DI Dan, LI Xiaoqiang, WANG Yiqin, QIAN Peng, ZHENG Xiaoyan, LIU Guoping
147 TCM in Innate Immunity
Stefan Jaeger, Su-Shing Chen, Wen-Ran Zhang
13 YinYang Bipolar Relativity - A Unifying Theory of Nature, Agents and Life Science
Wen-Ran Zhang
O-3-PM-2-E: Protein Structure and Function II
Chair: Liangjiang Wang
3:40 pm – 5:40 pm, Aug. 3, 2009, Room E
33 SVM-based Approach for Predicting DNA-binding Residues in Proteins from Amino Acid Sequences
Xin Ma, Jian-Sheng Wu, Hong-De Liu, Xi-Nan Yang, Jian-Ming Xie ,Xiao Sun
145 Putative Cell Cycle Related Genes in Plasmodium falciparum
Hong Cai, Maribel Sanchez, Yufeng Wang, Jianying Gu
162 Identifying new Methylated Arginines via Granular Decision Fusion with SVM Modeling
Zejin Ding, Nan Xie, Yan-Qing Zhang, Yujun Zheng
90 A comparative study of ensemble learning approaches in the classification of breast cancer metastasis
Wangshu Zhang, Feng Zeng, Xuebing Wu, Xuegong Zhang, Rui Jiang
40 New Descriptors of Evolutionary Information for Accurate Prediction of DNA and RNA-Binding Residues in Protein Sequences
Liangjiang Wang, Caiyan Huang
43 Improving prediction of the contact numbers of residues in proteins from primary sequences
Qiwen Dong; Shuigeng Zhou; Jihong Guan
105 Protein remote homology detection using order profiles
Bin Liu, Lei Lin, Xiaolong Wang, Xuan Wang
O-4-AM-1-B: Novel Applications for Intelligent Computing
Chair: Tong Ruan
8:00 am – 10:00 am, Aug. 4, 2009, Room B
54 A Collaborative Car Auto-navigation Framework Based On Intelligent Trajectory Mining
Ruan Tong, Wang Zhan Quan, Song Tao
36 Fingerprint Ridge Distance Estimation Based on Ridge Search
Liming Zhang, Yilong Yin, Dong Yang
31 The Application of Improved Immunogenetic Algorithm in Signal Timing
Rong Gu, Hongyun Zhang
62 Modeling Confidentiality in a Simplified Database Access
Chen-chi Shing, Marn-Ling Shing, Kuo Lane Chen,, Huei Lee
55 RFID Dynamic Grouping Anti-collision Algorithm Based on FCM
yaofeng xue, huali sun, zhiting zhu
67 Feature Mining and Intelligent Computing for MP3 Steganalysis
Mengyu Qiao, Andrew H. Sung, Qingzhong Liu
60 Security Data Mining in an Ontology for Vulnerability Management
Ju An Wang, Minzhe Guo
O-4-AM-1-C: Microarray Data Analysis
Chair: Wei Kong
8:00 am – 10:00 am, Aug. 4, 2009, Room C
153 Gene Selection for Microarray Expression Data with Imbalanced Sample Distributions
Abu H. M. Kamal, Xingquan Zhu, Ramaswamy Narayanan
119 Redundant Gene Selection based on Particle Swarm Optimization
Su-Fen Chen, Xue-Qiang Zeng, Guo-Zheng Li, Jack Y. Yang, Mary Qu Yang
34 Investigating Gene and MicroRNA Expression in Glioblastoma
Hua Dong, Hoicheong Siu, Li Luo, Xiangzhong Fang, Li Jin, Momiao Xiong
61 PBC: A Software Framework Facilitating Pattern-Based Clustering for Microarray Data Analysis
Dong-Guk Shin, Seung-Hyun Hong, Pujan Joshi, Rai Nori, Baikang Pei, Hsin-Wei Wang, Patrick Harrington, Lynn Kuo, Ivo Kalajzic, David Rowe
42 Study DNA microarray gene expression data of Alzheimer disease by independent component analysis
Wei Kong,Xiaoyang Mou,Bin Yang
96 Probabilistic Model Based Hough Transform for Detection of Co-expression Patterns in Three-Color cDNA Microarray Data
Peter Tino, Hongya Zhao, Hong Yan
212 Discovery of Biomarker Genes from Earthworm Microarray Data by Discriminant Analysis and Clustering
Ying Li, Nan Wang, Edward J. Perkins, Ping Gong
O-4-AM-1-D: Systems Biology I
Chair: Zhongming Zhao
8:00 am – 10:00 am, Aug. 4, 2009, Room D
101 In-silico effects of Mg2+ diffusion rates on stochastic event based simulation of the PhoPQ system
Preetam Ghosh, Kalyan basu, Sajal K Das, Chaoyang Zhang
150 Global Network Features of Cancer Genes in the Human Interactome
Jingchun Sun, Peilin Jia, Zhongming Zhao
132 A Granular Hierarchical Approach to Biophysical and Biochemical Evaluations of Transgenic Modifications
Moshe A. Gadish, David K. Chiu, Cecil W. Forsberg, Serguei P. Golovan
124 Integrative Computational Identifications of the Signaling Pathway Network Related to TNF-alpha Stimulus in Vascular Endothelial Cells
Jin Gu, Shao Li, Yang Chen, Yanda Li
149 Using Frequent Co-expression Network to Identify Gene Clusters for Breast Cancer Prognosis
Jie Zhang, Yang Xiang, Ruoming Jin, Kun Huang
39 A Numerical Study of Pulsatile Flow Through a Hollow Fiber Cartridge: Growth Factor-Receptor Binding and Dissociation Analysis
Changjiang Zhang, Wensheng Shen, Bing Zhao, Michael Fannon, Kimberly Forsten-Williams, Jun Zhang
156 Pathway and Network Analysis of Schizophrenia Candidate Genes under Meta-analysis Linkage Peaks
Peilin Jia, Jingchun Sun, Leng Han, Zhongming Zhao
O-4-AM-1-E: Protein Structure and Function III
Chair: Jason Xuan
8:00 am – 10:00 am, Aug. 4, 2009, Room E
66 Semi-Supervised Learning of Text Classification on Bacterial Protein-Protein Interaction documents
Guixian Xu, Zhendong Niu, Peter Uetz, Xu Gao, Xuping Qin, Hongfang Liu
45 ANN Based Protein Function Prediction Using Integrated Protein-Protein Interaction Data
Lei Shi, Young-Rae Cho, Aidong Zhang
52 3D-interologs: A protein-protein interacting evolution database across multiple species
Jinn-Moon Yang, Yung-Chiang Chen, Yu-Shu Lo
51 Assessing the Most Effective Depth for PPI Analysis
Jaine K Blayney, Huiru Zheng, Haiying Wang, Francisco Azuaje
58 A Systems Biology Approach to Identify Affected Regulatory and Signaling Circuits in Protein Interaction Networks
Ting Gong, Jianhua (Jason) Xuan, Rebecca B. Reggins, Robert Clarke
176 Automaton Models of Computational Genetic Regulatory Networks with Combinatorial Gene-Protein Logical Interactions
Peter C. Y. Chen, Yulin Weng
116 Prediction Of Peptides Binding To MHC Class I Alleles By Partial Periodic Pattern Mining
Cem Meydan, Hasan Otu, Ugur Sezerman
O-4-AM-2-B: Biomedical Engineering
Chair: Armin R Mikler
10:10 am – 12:10 am, Aug. 4, 2009, Room B
64 An Artificial Immune System for Temporal Anomaly Detection Using Cell Activation Thresholds and Clonal Size Regulation with Homeostasis
Mário João Gonçalves Antunes, Manuel E. Correia
122 Global Stochastic Contact Modeling of Infectious Diseases
Armin R Mikler, Angel Bravo-Salgado, Courtney D Corley
72 A Study on Prognosis of Brain Tumors Using Fuzzy Logic and Genetic Algorithm Based Techniques
Arpita Das, Mahua Bhattacharya
164 Optimal Overlay of Ligands with Flexible Bonds using Differential Evolution
Thomas Greve Kristensen, Christian Nørregård Storm Pedersen
126 Analyzing Response Feasibility for Bioemergencies
Tamara Schneider, Armin R. Mikler, Marty O'Neill II
80 Estimation of Heart Rate Variability Changes during Different Visual Stimulations Using Non-invasive Continuous ECG Monitoring System
Wanqing Wu, Jungtae Lee, Haifeng Chen
143 A Novel Method of De-noising and Classifying on Mental EEG of Imaging Left-Right Hands MoveMent
Shaochun Wu, Duhong Song, Mingdong Li, Lingyu XU
102 A Computational Framework to Study Public Health Epidemiology
Courtney D Corley, Armin R Mikler
O-4-AM-2-C: Sequence Analysis
Chair: Ruixin Zhu
10:10 am – 12:10 am, Aug. 4, 2009, Room C
159 A Parallel Algorithm for Three-Profile Alignment Method
Che-Lun Hung, Chun-Yuan Lin, Yeh-Ching Chung, Chuan Yi Tang
111 Mapping Transcription Factors from a Model to a non-Model Organism
Rachita Sharma, Patricia Evans, Virendra Bhavsar
59 On the Design of RNA Sequences for Realizing Extended Shapes
Marc Hellmuth,Daniel Merkle,Martin Middendorf
99 Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies
Pavlos Antoniou, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis
65 Cross-Domain Neurobiology Data Integration and Exploration
Weijian Xuan, Manhong Dai, Buckner Josh, Barbara Mirel, Jean Song, Brian Athey, Stanley J. Watson, Fan Meng
130 Multiclass Gene Selection on Microarray Data using l1-norm Least Square Regression
Xiyi Hang
O-4-AM-2-D: Systems Biology II
Chair: Preetam Ghosh
10:10 am – 12:10 am, Aug. 4, 2009, Room D
106 Estimation of Kinetic Rates of MAP kinase Activation from Experimental Data
Tianhai Tian
68 Statistical Analysis of Discrete Dynamical System Models for Biological Networks
Zhengyu Ouyang, Mingzhou Song
27 Two Dimensional Modeling and Fractal Characterization of Tumor Vascular Network
Radu Dobrescu, Loretta Ichim
110 Dynamic Propagation Properties of Virus-Host Protein Interaction Network
Fei Li, Wenjian Xu, Peng LI, Xiaochen Bo, Yuxing Peng
71 Finding Common Genes & Pathways for Multiple Cancer Types Using Hyper Geometric Distribution and Particle Swarm Optimization - Support Vector Machine
Mahesh Visvanathan, Adagarla, Bhargav Srinivas, Sitta Sittapalam, Gerald H Lushington
213 Gene Regulatory Network Inference Using Predictive Minimum Description Length Principle and Conditional Mutual Information
Vijender Chaitankar, Chaoyang Zhang, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng
133 Enhancing Automatic Biological Pathway Generation with GO-based Gene Similarity
Antonio Sanfilippo, Bob Baddeley, Nat Beagley, Rick Riensche, Banu Gopalan
O-4-AM-2-E: Workshop on Methods and Applications of Systems Biology
Chair: Yidong Chen, Yufei Huang, Ji Zhang
10:10 am – 12:10 am, Aug. 4, 2009, Room E
163 Framework for knowledge-based integrative analysis of microarray data - software for integrative analysis and application
Jiantao Shi, Kankan Wang, Ji zhang
167 Connecting biological themes using a single human network of gene associations
Hai Fang, Ji Zhang, Kan-Kan Wang
211 Mapping miRNA regulation to Functional Gene Sets
Yidong Chen, Harry Hung-I Chen, Yufei Huang
168 A Bayesian Approach for Identifying miRNA Targets by Combining Sequence Prediction and Expression Profiling
Hui Liu, Shou-Jiang Gao, Yufei Huang
214 Multiscale genomic imaging with wavelets signal analysis
Yu-Ping Wang, Qiang Wu, and Su-Shing Chen
215 Time varying Gene Regulatory Networks Revealed by Integrating Gene Expression Data and Existing Knowledge
Jia Meng, Hui Liu, Shou-Jiang Gao, and Yufei Huang
216 Accurate LC Peak Detection and Quatification
Jianqiu Zhang, and Willam Haskins
|