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Lecture Notes in Operations Research 9
Series Editors: Ding-Zhu Du and Xiang-Sun Zhang Optimization and Systems Biology The Second International Symposium, OSB'08 ISBN 978-7-5062-9289-4/O639 Edited by: Xiang-Sun Zhang, Luonan Chen, Ling-Yun Wu and Yong Wang |
Model Identification: A Key Challenge is Computational Systems Biology
Eberhard O. Voit
Optimization analysis of modularity measures for network community detection
Xiang-Sun Zhang, Rui-Sheng Wang
Some Infection Models for the Development of AIDS
Wai-Ki Ching, Yang Cong, Tuen-Wai Ng, Zheng-Jian Bai
A Genetic Algorithm for Optimal Control of Probabilistic Boolean Networks
Wai-Ki Ching, Ho-Yin Leung, Nam-Kiu Tsing, Shu-Qin Zhang
Parameter estimation and Stability of equilibrium of Gene Regulatory Network by Piecewise Multi-affine approach
Jianwei Shen, Yi Wang, Zengrong Liu, Rongling Lang
Periodic Oscillation of Gene Networks with Forcing and Delay
Yi Wang, Zhongjun Ma, Jianwei Shen
A Multi-class Algorithm Model Based on p-class Support Vector Ordinal Regression Machine
Zhi-Xia Yang
MicroRNA-mediated Incoherent Deedforward Motifs Are Robust
Feng-dan Xu, Zengrong Liu, Jian-wei Shen
Analysis of the Special Structure of the Suprachiasmatic Nucleus
Ying Li, Jian-Bao Zhang
Uncovering Differentially Expressed Pathways with Protein Interaction and Gene Expression Data
Yu-Qing Qiu, Shihua Zhang
A New Algorithm for Sequential and Non-sequential Protein Multiple Structure Alignment
Lin Wang, Wen-Juan Zhang
On Distribution and Enumeration of Attractors in Probabilistic Boolean Networks
Morihiro Hayashida, Takeyuki Tamura, Tatsuya Akutsu, Wai-Ki Ching
Identification of Intracellular Kinetic Parameters in Continuous Bioconversion of Glycerol by Klebsiella pneumoniae
En-min Feng, Chong-yang Liu, Zhao-hua Gong, Ya-qin Sun
Phase Shifts of Circadian Transcripts in Rat Suprachiasmatic Nucleus
Ryoko Morioka, Masanori Arita, Katsuhiko Sakamoto, Soshi Kawaguchi, Hajime Tei, Katsuhisa Horimoto
Motif based Identification of Pathogenic Patterns for Filamentous Fungi
Xing-Ming Zhao, Weihua Tang, Luonan Chen
Stability of Stochastic Genetic Regulatory Networks
Yonghui Sun, Gang Feng
Rho-GDI gamma Inhibits the Proliferation of Human Glioma Cells
Jiao Wang, Xiao Li, Xing-Ming Zhao, Tieqiao Wen
The Imbalanced Problem in Mass-spectrometry Data Analysis
Hao-Hua Meng, Guo-Zheng Li, Rui-Sheng Wang, Xing-Ming Zhao, Luonan Chen
The Network Biomarker Discovery in Prostate Cancer from Both Genomics and Proteomics Levels
Guangxu Jin, Xiaobo Zhou, Kemi Cui, Stephen T.C. Wong
A Hybrid Feature Selection Algorithm: Combination of Symmetrical Uncertainty and Genetic Algorithms
Bai-Ning Jiang, Xiang-Qian Ding, Lin-Tao Ma, Ying He, Tao Wang, Wei-Wei Xie
Effects of Multiple Parameter Variations on Biological System Behaviors
Xiao Chang, Deng-Yu Liu, Ruiqi Wang
Distinguishing Enzymes from Non-enzymes via Support Vector Machine
Yongcui Wang, Yingjie Tian, Naiyang Deng
Dynamics of the Mixed Feedback Loop Integrated with MicroRNA
Ge Wang, Jin Zhou
Mass Flow Model and Essentiality of Enzymes in Metabolic Networks
Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang
Fault Diagnosis by Using Selective Ensemble Learning Based on Mutual Information
Tian-Yu Liu, Guo-Zheng Li
Time Series Segmentation for Gene Regulatory Process with Time-Window-Extension Technique
Zhi-Yong Zhang, Katsuhisa Horimoto, Zengrong Liu
Identify SSR Regulators for Functional Gene Sets through Cross-Species Comparison
Chien-Ming Chen, Meng-Chang Hsiao, Tun-Wen Pai, Ronshan Cheng, Wen-Shyong Tzou, Margaret Dah-Tsyr Chang
Improved Approach for Haplotype Inference Based on Markov Chain
Ling-Yun Wu, Ji-Hong Zhang, Raymond Chan
Model Based Probe Fitting and Selection for SNP Array
Ling-Yun Wu, Xiaobo Zhou, Chung-Che Chang, Stephen T.C. Wong
Analysis of Domain Interactions Among Gamma-secretase Substrates
Zhi-Ping Liu, Weiming Xia, Luonan Chen
Analysis of Network Dynamics Including Hidden Variables by Symbolic-numeric Approach
Daisuke Tominaga, Yasuhito Tokumoto, Masahiko Nakatsui, Fuyan Sun, Jun Miyake, Katsuhisa Horimoto
An Algorithm and its Application of Multi-stage Identification Model of Nonlinear Dynamical System
Caixia Gao, En-min Feng
An Algebraic-Numeric Algorithm for the Model Selection in Network Motifs in Escherichia coli
Masahiko Nakatsui, Hiroshi Yoshida, Katsuhisa Horimoto
Clustering Parameter Values for Differential Equation Models of Biological Pathways
Dong-Soo Kahng, Doheon Lee
A Heuristic Method for Generating Probabilistic Boolean Networks from a Prescribed Transition Probability Matrix
Wai-Ki Ching, Xi Chen, Nam-Kiu Tsing, Ho-Yin Leung
Accurate Prediction of Translation Initiation Sites by Universum SVM
Tingting Gao, Yingjie Tian, Xiaojian Shao, Naiyang Deng
Predicting Non-protein-coding RNA Genes in Escherichia Coli Using SVM with Signature Descriptor
Hong-Wei Liu
Comparative Study on A Class of Evaluation Indices for Community Detection
Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang
Biclustering Based on Self-multiplication of Matrix
Ru-Xin Qin, Ying-Jie Tian, Jing Chen, Naiyang Deng
Inferring Gene Regulatory Networks by Incremental Evolution and Network Decomposition
Wei-Po Lee, Yu-Ting Hsiao
Sensitivity Analysis of a Cis-Regulatory Input Function
Ai-Min Chen, Tian-Shou Zhou
Condition Specific Subnetwork Identification Using an Optimization Model
Yong Wang, Yu Xia
Revealing Disease Related Interactions by Correlation Analysis
Zi-Kai Wu, Zhi-Yong Zhang, Lv-Wen Zhang, Katsuhisa Horimoto
Incorporating Gene Similarity into Support Vector Machine for Microarray Classification and Gene Selection
Jun-Yan Tan, Zhi-Xia Yang
Ensemble Non-negative Matrix Factorization for Clustering Biomedical Documents
Shanfeng Zhu, Wei Yuan, Fei Wang
Identifying Differentially Activated Pathways by Augmenting Activities of Transcription Factor Target Genes
Hyunchul Jung, Eunjung Lee, Jongwon Kim, Doheon Lee
Solving Drug Enzyme-Target Identification Problem Using Genetic Algorithm
Yu-Ying Zhao, Xue-Mei Ning
Simpson's Rule Based FFT Method to Compute Densities of Stable Distribution
Li Wang, Ji-Hong Zhang
Regulation of Cell Signaling Cascades by Influenza A Virus
Yu-Li Wan, Hui Zhong, Cheng-Jun Wu, Yao-Wu Yang, Jian-Wei Wang, Tao Hong
Structure-based Functional Annotation of Protein Sequences Guided by Comparative Models
Daron. M. Standley, Akira R. Kinjo, Miesko Lis, Mark van der Giezen, Haruki Nakamura