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2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS)

Aug. 3 2009 to Aug. 5 2009

Shanghai

Table of Contents

Papers
Planery Keynote AbstractsFreely available from IEEE.pp. xxv-xxxvii
Papers
Message from Program ChairsFreely available from IEEE.pp. xvi
Papers
Title Page iFreely available from IEEE.pp. i
Papers
Title Page iiiFreely available from IEEE.pp. iii
Papers
[Copyright notice]Freely available from IEEE.pp. iv
Papers
Table of contentsFreely available from IEEE.pp. v-xiv
Papers
Message from General ChairFreely available from IEEE.pp. xv
Papers
Organizing CommitteeFreely available from IEEE.pp. xvii
Papers
Steering CommitteeFreely available from IEEE.pp. xviii-xix
Papers
Program CommitteeFreely available from IEEE.pp. xx-xxii
Papers
list-reviewerFreely available from IEEE.pp. xxiii-xxiv
Papers
Gene Selection for Microarray Expression Data with Imbalanced Sample DistributionsFull-text access may be available. Sign in or learn about subscription options.pp. 3-9
by Abu H. M. Kamal, Xingquan Zhu, Ramaswamy Narayanan
Redundant Gene Selection Based on Particle Swarm OptimizationFull-text access may be available. Sign in or learn about subscription options.pp. 10-16
by Su-Fen Chen, Xue-Qiang Zeng, Guo-Zheng Li, Jack Y. Yang, Mary Qu Yang
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Investigating Gene and MicroRNA Expression in GlioblastomaFull-text access may be available. Sign in or learn about subscription options.pp. 17-22
by Hua Dong, Hoicheong Siu, Li Luo, Xiangzhong Fang, Li Jin, Momiao Xiong
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Discovery of Biomarker Genes from Earthworm Microarray Data by Discriminant Analysis and ClusteringFull-text access may be available. Sign in or learn about subscription options.pp. 23-29
by Ying Li, Nan Wang, Edward J. Perkins, Ping Gong
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PBC: A Software Framework Facilitating Pattern-Based Clustering for Microarray Data AnalysisFull-text access may be available. Sign in or learn about subscription options.pp. 30-36
by Dong-Guk Shin, Seung-Hyun Hong, Pujan Joshi, Rai Nori, Baikang Pei, Hsin-Wei Wang, Patrick Harrington, Lynn Kuo, Ivo Kalajzic, David Rowe
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Cross-Domain Neurobiology Data Integration and ExplorationFull-text access may be available. Sign in or learn about subscription options.pp. 37-43
by Weijian Xuan, Manhong Dai, Buckner Josh, Barbara Mirel, Jean Song, Brian Athey, Stanley J. Watson, Fan Meng
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Study DNA Microarray Gene Expression Data of Alzheimer's Disease by Independent Component AnalysisFull-text access may be available. Sign in or learn about subscription options.pp. 44-47
by Wei Kong, Xiaoyang Mou, Bin Yang
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Probabilistic Model Based Hough Transform for Detection of Co-expression Patterns in Three-Color cDNA Microarray DataFull-text access may be available. Sign in or learn about subscription options.pp. 48-51
by Peter Tino, Hongya Zhao, Hong Yan
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Multiclass Gene Selection on Microarray Data Using l1-norm Least Square RegressionFull-text access may be available. Sign in or learn about subscription options.pp. 52-55
by Xiyi Hang
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Framework for Knowledge-Based Integrative Analysis of Microarray DataFull-text access may be available. Sign in or learn about subscription options.pp. 56-59
by Jiantao Shi, Kankan Wang, Ji zhang
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Genome Evolution in Malaria Parasites: I. Core Genome ComponentsFull-text access may be available. Sign in or learn about subscription options.pp. 63-69
by Hong Cai, Yufeng Wang, Jianying Gu
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Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing UnitsFull-text access may be available. Sign in or learn about subscription options.pp. 70-76
by Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, Zhihong Yu
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Genomic Comparison of Bacterial Species Based on Metabolic CharacteristicsFull-text access may be available. Sign in or learn about subscription options.pp. 77-83
by Gaurav Jain, Haozhu Wang, Li Liao, E. Fidelma Boyd
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The Core and Pan-Genome of the VibrionaceaeFull-text access may be available. Sign in or learn about subscription options.pp. 84-90
by Timothy G. Lilburn, Hong Cai, Jianying Gu
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An Improved Algorithm for the Location of Heaviest Segments in Genomic SequencesFull-text access may be available. Sign in or learn about subscription options.pp. 91-97
by Nikola Stojanovic
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GeneIndex: An Open Source Parallel Program for Enumerating and Locating Words in a GenomeFull-text access may be available. Sign in or learn about subscription options.pp. 98-102
by Huian Li, David Hart, Matthias Mueller, Ulf Markwardt, Craig Stewart
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Proteogenomic Mapping for Structural Annotation of Prokaryote GenomesFull-text access may be available. Sign in or learn about subscription options.pp. 103-106
by Nan Wang, Shane Burgess, Mark Lawrence, Susan Bridges
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A Classification System for Predicting RNA Hairpin LoopsFull-text access may be available. Sign in or learn about subscription options.pp. 109-115
by Monther Aldwairi, Rehab Duwairi, Wafa'a Alqarqaz
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Mapping miRNA Regulation to Functional Gene SetsFull-text access may be available. Sign in or learn about subscription options.pp. 122-125
by Yidong Chen, Harry Hung-I Chen, Yufei Huang
Layout and Post-Processing of Transcriptional ModulesFull-text access may be available. Sign in or learn about subscription options.pp. 116-121
by Hong Sun, Tim Van den Bulcke, Bart De Moor, Karen Lemmens, Kristof Engelen, Kathleen Marchal
A Primer Design Algorithm for Global Analysis of CpG MethylationFull-text access may be available. Sign in or learn about subscription options.pp. 126-130
by Hehuang Xie, Min Wang, Yuichi Tange, Maria de F. Bonaldo, Marcelo B. Soares
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Accurate Prediction of Alternatively Spliced Cassette Exons Using Evolutionary Conservation Information and Logitlinear ModelFull-text access may be available. Sign in or learn about subscription options.pp. 131-134
by Chuang Ma, Fangyuan Deng, Hui Liu, Yanhong Zhou
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A Neural Network Based on Rough Set (RSNN) for Prediction of Solitary Pulmonary NodulesFull-text access may be available. Sign in or learn about subscription options.pp. 135-138
by Hui Liu, Wei Kong, Tian-Shuang Qiu, Guo-Li Li
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Variation in the Predicted Biosynthetic Capabilities of Seven VibrionaceaeFull-text access may be available. Sign in or learn about subscription options.pp. 139-142
by Jennifer Neary, Yufeng Wang, Timothy G. Lilburn
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Molecular Cloning and Expression of Ppdc-ldhL Fusion Gene in Zymomonas Mobilis ATCC 10988Full-text access may be available. Sign in or learn about subscription options.pp. 143-146
by Nian-Fa Gao, Yong Wang, Qiang Gao, Bin-Zhe Wang, Jian Zhang, Bo-Ya Liu
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Clustering of SNPs by a Structural EM AlgorithmFull-text access may be available. Sign in or learn about subscription options.pp. 147-150
by Yulong Zhang, Liang Ji
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A Parallel Algorithm for Three-Profile Alignment MethodFull-text access may be available. Sign in or learn about subscription options.pp. 153-159
by Che-Lun Hung, Chun-Yuan Lin, Yeh-Ching Chung, Chuan Yi Tang
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Mapping Transcription Factors from a Model to a Non-model OrganismFull-text access may be available. Sign in or learn about subscription options.pp. 160-166
by Rachita Sharma, Patricia Evans, Virendra Bhavsar
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On the Design of RNA Sequences for Realizing Extended ShapesFull-text access may be available. Sign in or learn about subscription options.pp. 167-173
by Marc Hellmuth, Daniel Merkle, Martin Middendorf
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Practical and Efficient Algorithms for Degenerate and Weighted Sequences Derived from High Throughput Sequencing TechnologiesFull-text access may be available. Sign in or learn about subscription options.pp. 174-180
by Pavlos Antoniou, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis
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An Adaptive Suffix Tree Based Algorithm for Repeats Recognition in a DNA SequenceFull-text access may be available. Sign in or learn about subscription options.pp. 181-184
by Hongwei Huo, Xiaowu Wang, Vojislav Stojkovic
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A Bayesian Approach for Identifying miRNA Targets by Combining Sequence Prediction and Expression ProfilingFull-text access may be available. Sign in or learn about subscription options.pp. 185-189
by Hui Liu, Lin Zhang, Shou-Jiang Gao, Yufei Huang
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Next Generation Sequence Analysis Using Genetic Algorithms on Multi-core TechnologyFull-text access may be available. Sign in or learn about subscription options.pp. 190-191
by Kaiqi Xiong, Sang C. Suh, Jack Y. Yang, Mary Qu Yang, Hamid Arabnia
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Structural Domain Based Multiple Instance Learning for Predicting Gram-Positive Bacterial Protein Subcellular LocalizationFull-text access may be available. Sign in or learn about subscription options.pp. 195-200
by S.Y. Mei, Wang Fei
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Biological Features for Sequence-Based Prediction of Protein Stability Changes upon Amino Acid SubstitutionsFull-text access may be available. Sign in or learn about subscription options.pp. 201-206
by Shaolei Teng, Anand K. Srivastava, Liangjiang Wang
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GO Semantic Similarity Based Analysis for Huaman Protein InteractionsFull-text access may be available. Sign in or learn about subscription options.pp. 207-210
by Gang Chen, Jianxin Wang, Min Li
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GO Semantic Similarity-Based False Positive Reduction of Protein-Protein InteractionsFull-text access may be available. Sign in or learn about subscription options.pp. 211-214
by Jianxing Wang, Lijian Dai, Min Li
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Using Mutual Information and Models of Evolution for Improved Pattern PetectionFull-text access may be available. Sign in or learn about subscription options.pp. 215-221
by Stephan Kitchovitch, Ian Leung, Yuedong Song, Pietro Liò
Using Mutual Information and Models of Evolution for Improved Pattern DetectionFull-text access may be available. Sign in or learn about subscription options.pp. 215-221
by Stephan Kitchovitch, Ian Leung, Yuedong Song, Pietro Lio
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Network Approaches for Shotgun Proteomics Data AnalysisFull-text access may be available. Sign in or learn about subscription options.pp. 222
by Bing Zhang, Jing Li, David L. Tabb, Byung-Hoon Park
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SVM-Based Approach for Predicting DNA-Binding Residues in Proteins from Amino Acid SequencesFull-text access may be available. Sign in or learn about subscription options.pp. 225-229
by Xin Ma, Jian-Sheng Wu, Hong-De Liu, Xi-Nan Yang, Jian-Ming Xie, Xiao Sun
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Putative Cell Cycle Related Genes in Plasmodium FalciparumFull-text access may be available. Sign in or learn about subscription options.pp. 230-236
by Hong Cai, Maribel Sanchez, Yufeng Wang, Jianying Gu
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Identifying New Methylated Arginines via Granular Decision Fusion with SVM ModelingFull-text access may be available. Sign in or learn about subscription options.pp. 237-241
by Zejin Jason Ding, Yan-Qing Zhang, Nan Xie, Yujun George Zheng
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A Comparative Study of Ensemble Learning Approaches in the Classification of Breast Cancer MetastasisFull-text access may be available. Sign in or learn about subscription options.pp. 242-245
by Wangshu Zhang, Feng Zeng, Xuebing Wu, Xuegong Zhang, Rui Jiang
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New Descriptors of Evolutionary Information for Accurate Prediction of DNA and RNA-Binding Residues in Protein SequencesFull-text access may be available. Sign in or learn about subscription options.pp. 246-250
by Liangjiang Wang, Caiyan Huang
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Improving Prediction of the Contact Numbers of Residues in Proteins from Primary SequencesFull-text access may be available. Sign in or learn about subscription options.pp. 251-254
by Qiwen Dong, Shuigeng Zhou, Jihong Guan
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Protein Remote Homology Detection Using Order ProfilesFull-text access may be available. Sign in or learn about subscription options.pp. 255-260
by Bin Liu, Lei Lin, Xiaolong Wang, Xuan Wang
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Semi-supervised Learning of Text Classification on Bacterial Protein-Protein Interaction DocumentsFull-text access may be available. Sign in or learn about subscription options.pp. 263-270
by Guixian Xu, Zhendong Niu, Peter Uetz, Xu Gao, Xuping Qin, Hongfang Liu
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ANN Based Protein Function Prediction Using Integrated Protein-Protein Interaction DataFull-text access may be available. Sign in or learn about subscription options.pp. 271-277
by Lei Shi, Young-Rae Cho, Aidong Zhang
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3D-interologs: A Protein-Protein Interacting Evolution Database across Multiple SpeciesFull-text access may be available. Sign in or learn about subscription options.pp. 278-285
by Jinn-Moon Yang, Yung-Chiang Chen, Yu-Shu Lo
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Assessing the Most Effective Depth for PPI AnalysisFull-text access may be available. Sign in or learn about subscription options.pp. 286-292
by Jaine K Blayney, Huiru Zheng, Haiying Wang, Francisco Azuaje
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Discovery of Motif Pairs from Protein-Protein Interaction NetworksFull-text access may be available. Sign in or learn about subscription options.pp. 293-296
by Hong Zhang, Yun Xu, Yuzhong Zhao
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A Systems Biology Approach to Identify Affected Regulatory and Signaling Circuits in Protein Interaction NetworksFull-text access may be available. Sign in or learn about subscription options.pp. 297-300
by Ting Gong, Jianhua Xuan, Rebecca B. Reggins, Robert Clarke
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Automaton Models of Computational Genetic Regulatory Networks with Combinatorial Gene-Protein Logical InteractionsFull-text access may be available. Sign in or learn about subscription options.pp. 301-307
by Peter C.Y. Chen, Yulin Weng
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Towards a Comprehensive HBV-Human Interaction MapFull-text access may be available. Sign in or learn about subscription options.pp. 311-314
by Fei Li, Yuxing Peng, Wenjian Xu, Guangchuang Yu, Peng LI, Xiaochen Bo, Shengqi Wang
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Prediction of Peptides Binding to MHC Class I Alleles by Partial Periodic Pattern MiningFull-text access may be available. Sign in or learn about subscription options.pp. 315-318
by Cem Meydan, Hasan Otu, Ugur Sezerman
MRI Based Fat Segmentation at 7T with Confidence ImageFull-text access may be available. Sign in or learn about subscription options.pp. 319-322
by Yang Tang, Susan Lee, Marvin D. Nelson Jr, Rex A. Moats
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An Artificial Immune System for Temporal Anomaly Detection Using Cell Activation Thresholds and Clonal Size Regulation with HomeostasisFull-text access may be available. Sign in or learn about subscription options.pp. 323-326
by Mário J. Antunes, Manuel E. Correia
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Global Stochastic Contact Modeling of Infectious DiseasesFull-text access may be available. Sign in or learn about subscription options.pp. 327-330
by Armin R. Mikler, Angel Bravo-Salgado, Courtney D. Corley
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Optimal Overlay of Ligands with Flexible Bonds Using Differential EvolutionFull-text access may be available. Sign in or learn about subscription options.pp. 331-334
by Thomas Greve Kristensen, Christian Nørgaard Storm Pedersen
Analyzing Response Feasibility for BioemergenciesFull-text access may be available. Sign in or learn about subscription options.pp. 337-343
by Tamara Schneider, Armin R. Mikler, Marty O'Neill II
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Estimation of Heart Rate Variability Changes during Different Visual Stimulations Using Non-invasive Continuous ECG Monitoring SystemFull-text access may be available. Sign in or learn about subscription options.pp. 344-347
by Wanqing Wu, Jungtae Lee, Haifeng Chen
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A Study on Prognosis of Brain Tumors Using Fuzzy Logic and Genetic Algorithm Based TechniquesFull-text access may be available. Sign in or learn about subscription options.pp. 348-351
by Arpita Das, Mahua Bhattacharya
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Feature Extraction and Classification of EEG Signals Using Wavelet Transform, SVM and Artificial Neural Networks for Brain Computer InterfacesFull-text access may be available. Sign in or learn about subscription options.pp. 352-355
by Mohammad Reza Nazari Kousarrizi, AbdolReza Asadi Ghanbari, Mohammad Teshnehlab, Mahdi Aliyari Shorehdeli, Ali Gharaviri
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A Novel Method of De-noising and Classifying on Mental EEG of Imaging Left-Right Hands MovementFull-text access may be available. Sign in or learn about subscription options.pp. 356-359
by Shaochun Wu, Duhong Song, Mingdong Li, Lingyu Xu
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A Computational Framework to Study Public Health EpidemiologyFull-text access may be available. Sign in or learn about subscription options.pp. 360-363
by Courtney D. Corley, Armin R. Mikler
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Exploring Systems Biology Approaches to Traditional Chinese Medicine Cancer ResearchFull-text access may be available. Sign in or learn about subscription options.pp. 367-370
by Dan Xi, Jeffrey D. White
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Genomic Imaging: A Modern Environment for TCM ResearchFull-text access may be available. Sign in or learn about subscription options.pp. 371-376
by Su-Shing Chen, Qingfeng Song, Yu-Ping Wang
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YinYang Bipolar Relativity - A Unifying Theory of Nature, Agents and Life ScienceFull-text access may be available. Sign in or learn about subscription options.pp. 377-383
by Wen-Ran Zhang
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Concordance of Diagnosis Based on Zangfu-Organs Syndrome Differentiation by Clinicians of Traditional Chinese MedicineFull-text access may be available. Sign in or learn about subscription options.pp. 384-387
by Liu Guo-Ping, Wang Yi-Qin, Zhao Nai-Qing, Xu Zhao-Xiao, Li Fu-Feng, Dong Ying, Qian Peng
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A TCM Platform for Maters' Experience SharingFull-text access may be available. Sign in or learn about subscription options.pp. 388-391
by Mingyu You, Lei Ge, Guo-Zheng Li, Liaoyu Xu, Suying Huang
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Facial Complexion Acquisition and Recognition System for Clinical Diagnosis in Traditional Chinese MedicineFull-text access may be available. Sign in or learn about subscription options.pp. 392-396
by Li Fufeng, Di Dan, Li Xiaoqiang, Wang Yiqin, Qian Peng, Zheng Xiaoyan, Liu Guoping
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TCM in Innate Immunity: A YinYang-N-Element Hypothesis of the Innate Immunological SystemFull-text access may be available. Sign in or learn about subscription options.pp. 397-401
by Stefan Jaeger, Su-Shing Chen, Wen-Ran Zhang
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In-Silico Effects of Mg2+ Diffusion Rates on Stochastic Event Based Simulation of the PhoPQ SystemFull-text access may be available. Sign in or learn about subscription options.pp. 405-411
by Preetam Ghosh, Kalyan Basu, Sajal K. Das, Chaoyang Zhang
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Global Network Features of Cancer Genes in the Human InteractomeFull-text access may be available. Sign in or learn about subscription options.pp. 412-416
by Jingchun Sun, Peilin Jia, Zhongming Zhao
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A Granular Hierarchical Approach to Biophysical and Biochemical Evaluations of Transgenic ModificationsFull-text access may be available. Sign in or learn about subscription options.pp. 417-421
by Moshe A. Gadish, David K. Chiu, Cecil W. Forsberg, Serguei P. Golovan
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Integrative Computational Identifications of the Signaling Pathway Network Related to TNF-alpha Stimulus in Vascular Endothelial CellsFull-text access may be available. Sign in or learn about subscription options.pp. 422-427
by Jin Gu, Shao Li, Yang Chen, Yanda Li
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Using Frequent Co-expression Network to Identify Gene Clusters for Breast Cancer PrognosisFull-text access may be available. Sign in or learn about subscription options.pp. 428-434
by Jie Zhang, Kun Huang, Yang Xiang, Ruoming Jin
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A Numerical Study of Pulsatile Flow Through a Hollow Fiber Cartridge: Growth Factor-Receptor Binding and Dissociation AnalysisFull-text access may be available. Sign in or learn about subscription options.pp. 435-441
by Changjiang Zhang, Wensheng Shen, Bing Zhao, Michael Fannon, Kimberly Forsten-Williams, Jun Zhang
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Pathway and Network Analysis of Schizophrenia Candidate Genes under Meta-Analysis Linkage PeaksFull-text access may be available. Sign in or learn about subscription options.pp. 442-447
by Peilin Jia, Jingchun Sun, Leng Han, Zhongming Zhao
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Enhancing Automatic Biological Pathway Generation with GO-Based Gene SimilarityFull-text access may be available. Sign in or learn about subscription options.pp. 448-453
by Antonio Sanfilippo, Bob Baddeley, Nat Beagley, Rick Riensche, Banu Gopalan
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Estimation of Kinetic Rates of MAP Kinase Activation from Experimental DataFull-text access may be available. Sign in or learn about subscription options.pp. 457-462
by Tianhai Tian
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Connecting Biological Themes Using a Single Human Network of Gene AssociationsFull-text access may be available. Sign in or learn about subscription options.pp. 463-471
by Hai Fang, Ji Zhang, Kan-Kan Wang
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Statistical Analysis of Discrete Dynamical System Models for Biological NetworksFull-text access may be available. Sign in or learn about subscription options.pp. 472-478
by Zhengyu Ouyang, Mingzhou Song
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Parameterized Complexity of Finding Elementary Modes in Metabolic NetworksFull-text access may be available. Sign in or learn about subscription options.pp. 479-482
by Hong Liu, Haodi Feng, Daming Zhu
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Two Dimensional Modeling and Fractal Characterization of Tumor Vascular NetworkFull-text access may be available. Sign in or learn about subscription options.pp. 483-486
by Radu Dobrescu, Loretta Ichim
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Gene Regulatory Network Inference Using Predictive Minimum Description Length Principle and Conditional Mutual InformationFull-text access may be available. Sign in or learn about subscription options.pp. 487-490
by Vijender Chaitankar, Chaoyang Zhang, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng
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Dynamic Propagation Properties of Virus-Host Protein Interaction NetworkFull-text access may be available. Sign in or learn about subscription options.pp. 491-493
by Fei Li, Wenjian Xu, Peng LI, Xiaochen Bo, Yuxing Peng
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Systematically Identifying Genes and Pathways in Multiple Cancer Types Using HGD & PSO-SVMFull-text access may be available. Sign in or learn about subscription options.pp. 494-497
by Mahesh Visvanathan, Adagarla Bhargav Srinivas, Gerald Lushington, Sitta Sittapalam
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