Lecture Notes in Operations Research 7

Series Editors: Ding-Zhu Du and Xiang-Sun Zhang

Optimization and Systems Biology

The First International Symposium, OSB'07
Beijing, China, August 8-10, 2007

ISBN 978-7-5062-7292-6/O568

Edited by: Xiang-Sun Zhang, Luonan Chen, Ling-Yun Wu and Yong Wang



Non-unique Probe Selection with Group Testing
Ping Deng, Feng Wang, Ding-Zhu Du

Computational Systems Biology on Networks and Dynamics
Luonan Chen

Loosely Coupled Architecture for Bio-Network Reverse Engineering
Sungwon Jung, Sangwoo Kim, Doheon Lee

Optimal Finite-Horizon Control for Probabilistic Boolean Networks with Hard Constraints
Wai-Ki Ching, Shu-Qin Zhang, Yue Jiao, Tatsuya Akutsu, Alice S. Wong

Analysis of Signaling Pathway for the Differentiation of Neural Stem Cells
Wei Lu, Jiao Wang, Tieqiao Wen

An Optimization Model for Gene Regulatory Network Reconstruction with Known Biological Information
Jinshan Li, Xiang-Sun Zhang

Integrated Data Mining Strategy for Effective Metabolomic Data Analysis
Younghoon Kim, Inho Park, Doheon Lee

Numerical Modeling of the Transmission Dynamics of Influenza
Wirawan Chinviriyasit

Targeting Spatio--Temporal Patterns in Chaotic Neural Network
Manish Dev Shrimali, Guoguang He, Kazuyuki Aihara

Gene Function Prediction with the Shortest Path in Functional Linkage Graph
Xing-Ming Zhao, Luonan Chen, Kazuyuki Aihara

Establishing Protein Functional Linkage in a Systematic Way
Yong Wang, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen

Semi-synthetic Analysis toward Validating Roles of a Transcription/Translation Feedback Process for the Cyanobacterial KaiC-protein-based Circadian System in Escherichia coli
Hirokazu Tozaki, Taiichiro Kobe, Kazuyuki Aihara, Hideo Iwasaki

New Insights into Network Motif Clusters from the Views of Cellular Localizations and Signal Pathways
Guangxu Jin, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen

Detecting Community Structures in Gene Networks using Gene-Ontology Annotation
Liuhuan Dong, Winking Q. Yu, Andreas M. W. Dress

Noise-induced Robust Collective Behaviors in a Multicellular System
Ruiqi Wang, Luonan Chen, Kazuyuki Aihara

Four Examples of Phase Synchronization in Oscillator Networks
Wenqiao He, Jianhua Xu, Zengrong Liu

Qualitative Cellular Dynamics Analysis with Gene Regulatory Information and Metabolic Pathways
Hojung Nam, Kwang H. Lee, Doheon Lee

Periodic Oscillation of Piecewise Linear Three-gene Regulatory Network with Negative Feedback Loops
Yi Wang, Jian-Wei Shen, Zengrong Liu

Synchronizing Independent Gene Oscillators by Common Noisy Signaling Molecule
Tianshou Zhou, Yanbin Zhang, Anlong Xu, Luonan Chen

Robust Impulsive Synchronization of Delayed Dynamical Networks and Its Applications
Lan Xiang, Zengrong Liu, Jin Zhou

Missing Enzyme Identification Using Reversible-Jump Markov-Chain-Monte-Carlo Learning Approach
Bo Geng, Xiaobo Zhou, Jinmin Zhu, Y. S. Hung, Stephen Wong

Local Similarities and Clustering of Biological Sequences: New Insights from N-local Decoding
Eduardo Corel, Ramzi El Fegalhi, Fanny G\'erardin, Mark Hoebeke, Marc Nadal, Alexandre Grossmann, Claudine Devauchelle

Analyzing Protein Sequences Using Quantitative Association Rule
Meng Ma, Shuangping Chen, Junqing Niu, Xufa Wang

An Approach for Clustering Protein Pockets into Similar Groups
Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen

Large Validation of Anti-learnable Signature in Classification of Response to Chemoradiotherapy in Esophageal Adenocarcinoma Patients
Adam Kowalczyk, Danielle M. Greenawalt, Justin Bedo, Cuong Duong, Garvesh Raskutti, Robert J. S. Thomas, Wayne A. Phillips

Peak Detection with Chemical Noise Removal Using Short-Time FFT for a Kind of MALDI Data
Shu-Qin Zhang, Xiaobo Zhou, Honghui Wang, Anthony Suffredini, Denise Gonzales, Wai-Ki Ching, Michael K. Ng, Stephen Wong

Reducing Error of Tumor Classification by Using Dimension Reduction with Feature Selection
Hua-Long Bu, Guo-Zheng Li, Xue-Qiang Zeng

Two Improvments of NMF Used for Tumor Clustering
Zhong-Yuan Zhang, Xiang-Sun Zhang

A Discriminate Multidimensional Mapping for Small Sample Database
Xiaoqin Hu, Ling Jing, Qian Li

Robust Measurement Selection for Biochemical Pathway Experimental Design
Martin Brown, Fei He, Lam Fat Yeung

Solving Large Double Digestion Problems for DNA Restriction Mapping by Using Branch-and-Bound Integer Linear Programming
Zhijun Wu, Yin Zhang

Weighted Local Least Squares Imputation Method for Missing Value Estimation
Wai-Ki Ching, Kwai-Wa Cheng, Li-Min Li, Nam-Kiu Tsing, Alice S. Wong

Integer Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis
Morihiro Hayashida, Fuyan Sun, Sachiyo Aburatani, Katsuhisa Horimoto, Tatsuya Akutsu

Linkage Disequilibrium Map by Unidimensional Nonnegative Scaling
Michael K. Ng, Eric S. Fung, Hai-Yong Liao

Two Phase Evolutionary Method for Multiple Sequence Alignments
Farhana Naznin, Morikazu Nakamura, Takeo Okazaki, Yumiko Nakajima

Assessing Distance Measures for Protein Structure Comparison
Zikai Wu, Yong Wang, Enmin Feng, Luonan Chen

Second Order Cone Programming Formulations for Robust Support Vector Ordinal Regression Machine
Zhi-Xia Yang, Ying-Jie Tian, Nai-Yang Deng

SVM-based Automatic Classification for Protein Structural Domain
Xiao-Jian Shao, Ying-Jie Tian, Nai-Yang Deng

An MPEC Model for Selecting Optimal Parameter in Support Vector Machines
Yu-Lin Dong, Zun-Quan Xia, Ming-Zheng Wang

Decremental Learning Algorithms for Nonlinear Langrangian and Least Squares Support Vector Machines
Hua Duan, Hua Li, Guoping He, Qingtian Zeng

Remodelling of the Inverse DEA Model: A Prediction Tool for Not-for-profit Organizations
Jin-Chuan Cui, Xiang-Sun Zhang, Xiao-Ya Li

The Optimum Method of Prior Parameters in Survival Analysis
Ming Han

A New T-F Function Theory and Algorithm for Nonlinear Integer Programming
Wei-Xiang Wang, You-Lin Shang, Lian-Sheng Zhang

A Framework of Optimization Method for Classification
Juliang Zhang, Yong Shi

Extra Resource Allocation Problem with the Most Compromise Common Weights Based on DEA
Xiao-Ya Li, Jin-Chuan Cui

A Trust Region Algorithm Model With Radius Bounded Below for Minimization of Locally Lipschitzian Functions
Houchun Zhou, Dexue Zhang, Wenyu Sun

Vehicle Routing for Medical Supplies in Large-Scale Emergencies
Degang Liu, Jiye Han, Jianming Zhu

A Posteriori Error Estimator for Linear Elliptic Problem
S. Chinviriyasit

A Quadratic Programming Model for Political Districting Problem
Zhenping Li, Rui-Sheng Wang, Yong Wang

The Auxiliary Problem Algorithm for Generalized Linear Complementarity Problem Over a Polyhedral Cone
Dexue Zhang, Hongchun Sun

The Incidence Chromatic Number of 2-connected 1-trees
Hua Duan, Qingtian Zeng, Congying Han, Wenjun Lian

Parallel Simulation of Compressible Fluid Dynamics Using Lattice Boltzmann Method
Bing He, Wei-Bing Feng, Wu Zhang, Yu-Ming Cheng

Harvesting from a Population in a Stochastic Crowded Environment with Harvesting Cost
Jihong Yuan, Kunhui Liu

Author Index