Genome Informatics 2008: Genome Informatics Series Volume 21: Proceedings of the 19th International Conference

Genome Informatics 2008: Genome Informatics Series Volume 21: Proceedings of the 19th International Conference

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Product Details

ISBN-13: 9781848163317
Publisher: Imperial College Press
Publication date: 11/06/2008
Pages: 252
Product dimensions: 6.60(w) x 9.80(h) x 0.70(d)

Table of Contents

Preface ix

Acknowledgments xi

Committees xiii

Part A Full Papers 1

An Approach to Transcriptome Analysis of Non-Model Organisms Using Short-Read Sequences L. J. Collins P. J. Biggs C. Voelckel S. Joly 3

Factoring Local Sequence Composition in Motif Significance Analysis P. Ng U. Keich 15

A New Model of Multi-Marker Correlation for Genome-Wide Tag SNP Selection W.-B Wang T. Jiang 27

Phenotype Profiling of Single Gene Deletion Mutants of E. coli Using Biolog Technology Y. Tohsato H. Mori 42

Improved Algorithms for Enumerating Tree-Like Chemical Graphs with Given Path Frequency Y. Ishida L. Zhao H. Nagamochi T. Akutsu 53

BSAlign: A Rapid Graph-Based Algorithm for Detecting Ligand-Binding Sites in Protein Structures Z. Aung J. C. Tong 65

Protein Complex Prediction Based on Mutually Exclusive Interactions in Protein Interaction Network S. H. Jung W.-H. Jang H.-Y. Hur B. Hyun D.-S. Han 77

On the Reconstruction of the Mus musculus Genome-Scale Metabolic Network Model L.-E. Quek L. Nielsen 89

Predicting Differences in Gene Regulatory Systems by State Space Models R. Yamauchi S. Imoto M. Yamauchi M. Nagasaki R. Yoshida T. Shimamura Y. Hatanaka K. Ueno T. Higuchi N. Gotoh S. Miyano 101

Exploratory Simulation of Cell Ageing Using Hierarchical Models M. Cvijovic H. Soueidan D. J. Sherman E. Klipp M. Nikolski 114

Inferring Differential Leukocyte Activity from Antibody Microarrays Using a Latent Variable Model J. W. K. Ho R. Koundinya T. S. Caetano C. G. dos Remedios M. A. Charleston 126

Assessing and Predicting Protein Interactions Using Both Local and Global Network Topological Metrics G. Liu J. Li L. Wong 138

Modelling the Evolution of Protein Coding SequencesSampled from Measurably Evolving Populations M. Goode S. Guindon A. Rodrigo 150

A Phylogenomic Approach for Studying Plastid Endosymbiosis A. Moustafa C. X. Chan M. Danforth D. Zear H. Ahmed N. Jadhav T. Savage D. Bhattacharya 165

Cis-Regulatory Element Based Gene Finding: An Application in Arabidopsis thaliana Y. Li. Y. Zhu Y. Liu Y. Shu F. Meng Y. Lu B. Liu X. Bai D. Guo 177

Using Simple Rules on Presence and Positioning of Motifs for Promoter Structure Modeling and Tissue-Specific Expression Prediction A. Vandenbon K. Nakai 188

Improving Gene Expression Cancer Molecular Pattern Discovery Using Nonnegative Principal Component Analysis X. Han 200

Simulation Analysis for the Effect of Light-Dark Cycle on the Entrainment in Circadian Rhythm N. Mitou Y. Ikegami H. Matsuno S. Miyano S.-I. T. Inouye 212

Part B Keynote Addresses 225

Sequencing the Transcriptome in toto S. M. Grimmond 227

Modern Homology Search M. Li 229

Modeling Human Genome-Wide Combinatorial Regulatory Networks Initiated by Transcription Factors and microRNAs Using Forward and Reverse Engineering Y.-X. Li 230

Reconstructing the Circuits of Disease: From Molecular States to Physiological States E. E. Schadt 231

The Emerging Generalizations of Prokaryotic Genomics E. V. Koonin 232

A New Understanding of the Human Genome J. Mattick 233

Author Index 235

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