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Lecture Notes in Operations Research 11
Series Editors: Ding-Zhu Du and Xiang-Sun Zhang Optimization and Systems Biology The Third International Symposium, OSB'09 ISBN 978-7-5100-0549-7/O764 Edited by: Luonan Chen, Xiang-Sun Zhang, Ling-Yun Wu and Yong Wang |
Plenary Sessions
The Prediction of Protein Post-translational Modification Sites
Naiyang Deng, Ling-Yun Wu, Xiaobo Wang
Modeling the Roles of miRNA164 in Determining the Age-dependent Cell Death in Plant Leaves
Hye Ryun Woo, Seungmin Han, Jin Hee Kim, Il-Hwan Lee, Daehee Hwang, Hong Gil Nam
Systems Biology of Cell Signaling
Qing Nie
Next Generation DNA Sequencing and Bioinformatics: Bottlenecks and Opportunities
Kwok-Wing Stephen Tsui
Exploring the Design Principle of Emergent Properties in Biological Systems
Kwang-Hyun Cho
Parallel Sessions
Voting for the Prediction of Protein Secondary Structure and Its Evaluation
Ying-Song Dong, Zhi-Song He, Zi-Liang Qian, Yu-Dong Cai
A Study of Network-based Kernel Methods on Protein-Protein Interaction for Protein Functions Prediction
Wai-Ki Ching, Limin Li, Yat-Ming Chan, Hiroshi Mamitsuka
Finite-Horizon Control of Genetic Regulatory Networks with Multiple Hard-Constraints
Wai-Ki Ching, Yang Cong
NMF-based Models for Tumor Clustering: A Systematic Comparison
Zhong-Yuan Zhang
Extracting Community Structure of Complex networks by Self-Organizing Maps
Zhenping Li, Rui-Sheng Wang, Luonan Chen
Consensus of A Modified Time-Delayed Vicsek Model
Yao Chen, Jinhu L\"u
New Approaches for Computer-Assisted Skin Cancer Diagnosis
M. J. Ogorza\l ek, G. Sur\'{o}wka, L. Nowak, C. Merkwirth
Shrunken Dissimilarity Measure for Genome-wide SNP Data Classification
Haiyong Liao, Yang Liu, Michael K. Ng
Exponential Stability Analysis for Impulsive Neural Networks with Time-varying Delays
Shui-Ming Cai, Feng-Dan Xu, Wei-Xing Zheng, Zeng-Rong Liu
A General Analysis of Single IP$_3$ Receptors Modulated by Cytosolic Ca$^{2+}$ and IP$_3$
Chen Jia, Yihan Li, Minping Qian
Understanding the Biological Functions of DCF1 Based on Molecular Interaction Network
Xing-Ming Zhao, Renhong Qian, Xiangchun Ju, Tieqiao Wen
Discovering Transcriptional Regulation by Integrating Protein-Protein Interaction, Gene Expression and Transcriptional Interaction Data
Fei Luo, Jinyan Li
Density Clustering Based SVM and Its Application to Polyadenylation Signals
Yuanhai Shao, Yining Feng, Jing Chen, Naiyang Deng
Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Spaces
Zheng Xia, Xiaobo Zhou, Youxian Sun, Ling-Yun Wu
Evolving Additive Trees for Modeling Biochemical Systems
Yuehui Chen, Bin Yang, Yaou Zhao, Qingfang Meng
A Constrained Optimization Method for Community Detection
Ji-Guang Wang, Lin Wang, Yu-Qing Qiu, Yong Wang, Xiang-Sun Zhang
Prediction of Protein-Protein Interaction Based Only on Coding Sequences
Yongcui Wang, Ji-Guang Wang, Zhi-Xia Yang, Naiyang Deng
Cross-species Comparison for Identifying Orthologous Simple Sequence Repeats of Disease Genes
Chih-Chia Chen, Tsan-Huang Shih, Chien-Ming Chen, Chin-Hua Hu, Wen-Shyong Tzou, Tun-Wen Pai
Comparing Biological Networks via Graph Compression
Morihiro Hayashida, Tatsuya Akutsu
Steady-state Optimization Model and Algorithm of Glycerol Bioconversion to 1,3-Propanediol in Continuous Culture
An Li, En-Min Feng, Pei-Jun Guo, Jian-Xiong Ye
A Parallel Algorithm of Constructing Gene Regulatory Networks
Mei Xiao, Luwen Zhang, Bing He, Jiang Xie, Wu Zhang
Prediction of Conformational Epitopes by Geometrical Affinity and Chemical Propensity Approaches
Cheng-Ying Tang, Wei-Kuo Wu, Yu-Ping Hsu, Hsin-Wei Wang, Tun-Wen Pai, Hao-Teng Chang
Protein-Protein Interaction Detection By SVM From Sequence Information
Hong-Wei Liu
A Network-Based Approach for Identifying Effective Drug Combination
Zikai Wu, Luonan Chen
Global Synchronization for General Delayed Dynamical Networks
Jianhua Xu, Zengrong Liu, Xiao Chang
Mathematical Modeling of Signaling Pathways Leading to Type I IFN Gene Expression
Xiufen Zou, Xueshuang Xiang, Yan Chen, Zishu Pan
Detection of Horizontal Gene Transfer in Bacterial Genomes
Hui Ning, Bing Yang, Jun Cui, Ling Jing
A Novel SVM-RFE for Gene Selection
Jun-Yan Tan, Zhi-Xia Yang, Naiyang Deng
Parameter Optimization in Network Dynamics Including Unmeasured Variables by the Symbolic-numeric Approach
Masahiko Nakatsui, Katsuhisa Horimoto
Protein Subcellular Localization Prediction for \textsl {Fusarium graminearum}
Chenglei Sun, Wei-Hua Tang, Luonan Chen, Xing-Ming Zhao
Prediction of Differentiation-ralated Pathways Induced by Rho-GDI$\gamma $
Jiao Wang, Xiao Li, Tieqiao Wen
A Robust Clustering Technique for Grouping Biological Data: an Illustrative Study in Gene Expression Data
Xuemei Ning, Shihua Zhang
Stochastic Synchronization of Circadian Rhythms
R. K. Brojen Singh, Ram Ramaswamy
Crosstalk of Dysfunctional Pathways in Alzheimer's Disease Brains
Zhi-Ping Liu, Luonan Chen
Align Protein Surface Structures to Identify Evolutionally and Structurally Conserved Residues
Lin Wang, Ji-Guang Wang, Luonan Chen
Markov Model of Biological Networks
Cai-Feng Du, Fu-Zhou Gong
The Potent Chinese Herbs for Inhibiting Cytotoxicity of Eosinophil Cationic Protein
Louis J. Tseng, Blacky T. Kao, Wei-Yong Lin, Margaret Dah-Tsyr Chang, Tun-Wen Pai, Ying-Chen Huang, Hao-Teng Chang
Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks
Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang
Inverse Eigenvalue Problems and Their Associated Approximation Problems for Matrices with $J$-(Skew) Centrosymmetry
Zhong-Yun Liu, You-Cai Duan, Yun-Feng Lai, Yu-Lin Zhang
A Linear Projection Approach for Resolving Community Structure
Xiaoping Liao, Wei Ren, Guiying Yan
Kernel Regularized Multiple Criteria Linear Programming
Wen-Jing Chen, Ying-Jie Tian
Modularized Random Walk with Restart for Candidate Disease Genes Prioritization
Xing Chen, Guiying Yan, Wei Ren, Ji-Bin Qu
Maximizing Modularity Density for Exploring Modular Organization of Protein Interaction Networks
Shihua Zhang, Xuemei Ning, Chris Ding
Analysis of Transcriptome of Rice Anther
Wenjuan Zhang, Wei-Hua Tang, Jiguang Wang, Zhiping Liu, Xing-Ming Zhao, Luonan Chen
Nonlinear Coupling for Improved Stochastic Network Model: A Study of Schnakenberg Model
Youfang Cao, Jie Liang
An Information and Combinatorial Theories-based Supervised Learning Framework for Integrative Inference and Analysis of Genetic Regulatory Networks
Binhua Tang, Xuechen Wu, Ge Tan, Su-Shing Chen, Qing Jing, Bairong Shen
ChemIME: An Input Method Engine for Chemical Compounds
Haruka Takeuchi, Xu Yang, Shin-ya Takane
Response Time and Its Role in Noise Filtering
Dengyu Liu, Xiao Chang, Ruiqi Wang
A Weighted Parsimony Model for Community Detection in Complex Networks
Junhua Zhang, Xiang-Sun Zhang
Actions of Excitement and Fast Inhibition in Neuron Net
Tao Ren, Dunyuan Hao
Analysis for Stimuli to Shoot Genes of Arabidopsis Thaliana Based on Logical Relationships
Shudong Wang, Yan Chen, Qingyun Wang, Eryan Li, Yansen Su, Dazhi Meng
A Random Iterative Algorithm for Community Detection
Junhua Zhang, Shihua Chen
Study on Multilocus Interactions for Hypertension by an Information Theoretic Method
Junhua Zhang, Wentao Huang, Zhiyuan Zhao, Biao Li, Yuelan Wang, Dongfeng Gu, Guoying Li, Runsheng Chen
A Novel Approach for Pathway Inference Based on Network Flow
Xianwen Ren, Xiang-Sun Zhang
Stochastic Hybrid System for Chemical Master Equation
Luonan Chen, Ruiqi Wang, Kazuyuki Aihara