Genome Informatics Vol. 21 (2008)

Presented at the 19th International Conference on Genome Informatics
December 1-3, 2008, Gold Coast, Queensland, Australia

Published as: J. Arthur, S.-K. Ng
"Genome Informatics Vol. 21"
Imperial College Press, London

Preface by Jonathan Arthur, See-Kiong Ng, and Mark Ragan

Acknowlegments

Program Committee

  • Papers
  • Keynote Addresses

    • Papers

    An Approach to Transcriptome Analysis of Non-Model Organisms Using Short-Read Sequences
    Lesley J. Collins, Patric J. Biggs, Claudia Voelckel, Simon Joly
    Genome Informatics 21: 3-14 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Factoring Local Sequence Composition in Motif Significance Analysis
    Patric Ng, Uri Keich
    Genome Informatics 21: 15-26 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A New Model of Multi-Marker Correlation for Genome-Wide Tag SNP Selection
    Wei-Bung Wang, Tao Jiang
    Genome Informatics 21: 27-41 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Phenotype Profiling of Single Gene Deletion Mutants of E. coli Using Biolog Techonology
    Yukako Tohsato, Hirotada Mori
    Genome Informatics 21: 42-52 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Improved Algorithms for Enumerating Tree-Like Chemical Graphs with Given Path Frequency
    Yusuke Ishida, Liang Zhao, Hitoshi Nagamochi, Tatsuya Akutsu
    Genome Informatics 21: 53-64 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    BSAlign: A Rapid Graph-Based Algorithm for Detecting Ligand-Binding Sites in Protein Structures
    Zeyar Aung, Joo Chuan Tong
    Genome Informatics 21: 65-76 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Protein Complex Prediction Based on Mutually Exclusive Interactions in Protein Interaction Network
    Suk Hoon Jung, Woo-Hyuk Jang, Hee-Yyun Hur, Bora Hyun, Dong-Soo Han
    Genome Informatics 21: 77-88 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    On the Reconstruction of the Mus musculus Genome-Scale Metabolic Network Model
    Lake-Ee Quek, Lars K. Nielsen
    Genome Informatics 21: 89-100 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

    Predicting Differences in Gene Regulatory Systems by State Space Models
    Rui Yamaguchi, Seiya Imoto, Mai Yamauchi, Masao Nagasaki, Ryo Yoshida, Teppei Shimamura, Yosuek Hatanaka, Kazuko Ueno, Tomoyuki Higuchi, Noriko Gotoh, Satoru Miyano
    Genome Informatics 21: 101-113 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Exploratory Simulation of Cell Ageing Using Hierarchical Models
    Marija Cvijovic, Hayssam Soueidan, David James Sherman, Edda Klipp, Macha Nikolski
    Genome Informatics 21: 114-125 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Inferring Differential Leukocyte Activity from Antibody Microarrays Using a Latent Variable Model
    Joshua W.K. Ho, Rajeev Koundinya, Tibério S. Caetano, Cristobal G. dos Remedios, Michael A. Charleston
    Genome Informatics 21: 126-137 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Assessing and Predicting Protein Interactions Using Both Local and Global Network Topological Metrics
    Guimei Liu, Jinyan Li, Limsoon Wong
    Genome Informatics 21: 138-149 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Modelling the Evolution of Protein Coding Sequences Sampled from Measurably Evolving Populations
    Mattew Goode, Stéphane Guindon, Allen Rodrigo
    Genome Informatics 21: 150-164 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    A Phylogenomic Approach for Studying Plastid Endosymbiosis
    Ahmed Moustafa, Cheong Xin Chan, Megan Danforth, David Zear, Hiba Ahmed, Nagnath Jadhav, Trevor Savage, Debashish Bhattacharya
    Genome Informatics 21: 165-176 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Cis-Regulatory Element Based Gene Finding: An Application in Arabidopsis thaliana
    Yong Li, Yanming Zhu, Yang Liu, Yongjun Shu, Fanjiang Meng, Yanmin Lu, Bei Liu, Xi Bai, Diangjin Guo
    Genome Informatics 21: 177-187 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Using Simple Rules on Presence and Positioning of Motifs for Promoter Structure Modeling and Tissue-Specific Expression Prediction
    Alexis Vandenbon, Kenta Nakai
    Genome Informatics 21: 188-199 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Improving Gene Expression Cancer Molecular Pattern Discovery Using Nonnegative Principal Component Analysis
    Xiaoxu Han
    Genome Informatics 21: 200-211 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Simulation Analysis for the Efffect of Light-Dark Cycle on the Entrainment in Circadian Rhythm
    Natumi Mitou, Yuto Ikegami, Hiroshi Matsuno, Satoru Miyano, Shin-ichi T. Inouye
    Genome Informatics 21: 212-223 (2008)
    [Abstract]   [Full-text HTML]   [Full-text PDF]

    Keynote Addresses

    Sequencing the Transcriptome in toto
    Sean M. Grimmond
    Genome Informatics 21: 227-228 (2008)
    [Full-text HTML]   [Full-text PDF]

    Modern Homology Search
    Ming Li
    Genome Informatics 21: 229 (2008)
    [Full-text HTML]   [Full-text PDF]

    Modeling Human Genome-Wide Combinatorial Regulatory Networks Initiated by Transcription Factors and microRNAs Using Forward and Reverse Engineering
    Yi-Xue Li
    Genome Informatics 21: 230 (2008)
    [Full-text HTML]   [Full-text PDF]

    Reconstructing the Circuits of Disease: From Molecular States to Physiological States
    Eric E. Schadt
    Genome Informatics 21: 231 (2008)
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    The Emerging Generalizations of Prokaryotic Genomics
    Eugene V. Koonin
    Genome Informatics 21: 232 (2008)
    [Full-text HTML]   [Full-text PDF]

    A New Understanding of the Human Genome
    John Mattick
    Genome Informatics 21: 233-234 (2008)
    [Full-text HTML]   [Full-text PDF]