GENOME INFORMATICS 2007

This volume contains papers presented at the 18th International Conference on Genome Informatics (GIW 2007) held at the Biopolis, Singapore from December 3 to 5, 2007. The GIW Series provides an international forum for the presentation and discussion of original research papers on all aspects of bioinformatics, computational biology and systems biology. Its scope includes biological sequence analysis, protein folding prediction, gene regulatory network, clustering algorithms, comparative genomics, and text mining. Boasting a history of 18 years, GIW is likely the longest-running international bioinformatics conference.
A total of 16 papers were selected for presentation at GIW 2007 and inclusion in this book. The notable authors include Ming Li (University of Waterloo, Canada), Minoru Kanehisa (Kyoto University, Japan), Vladimir Kuznetsov (Genome Institute of Singapore), Tao Jiang (UC Riverside, USA), Christos Ouzounis (European Bioinformatics Institute, UK), and Satoru Miyano (University of Tokyo, Japan). In addition, this book contains abstracts from the five invited speakers: Frank Eisenhaber (Bioinformatics Institute, Singapore), Sir David Lane (Institute of Molecular and Cell Biology, Singapore), Hanah Margalit (The Hebrew University of Jerusalem, Israel), Lawrence Stanton (Genome Institute of Singapore), and Michael Zhang (Cold Spring Harbor Laboratory, USA).

Detection of Monosaccharide Types from Coordinates (M Arita & T Tokimatsu); Mining Super-secondary Structure Motifs from 3D Protein Structures: A Sequence Order Independent Approach (Z Aung & J Li); FragQA: Predicting Local Fragment Quality of a Sequence-Structure Alignment (X Gao et al.); Predicting B Cell Epitope Residues with Network Topology-based Amino Acid Indices (J Huang); Comparative Pairwise Domain Combinations for Screening the Clade-Specific Domain Architectures in Metazoan Genomes (S Kawashima et al.); A Conservative Parametric Approach to Motif Significance Analysis (U Keich & P Ng); Recognition of Polyadenylation Sites from Arabidopsis Genomic Sequences (C H Koh & L Wong); Computational Analysis and Modeling of Genome-Scale Avidity Distribution of Transcription Factor Binding Sites in ChIP-PET Experiments (V Kuznetsov et al.); Linear-Time Reconstruction of Zero-Recombinant Mendelian Inheritance on Pedigrees Without Mating Loops (L Liu & T Jiang); Computed Protonation Properties: Unique Capabilities for Protein Functional Site Prediction (L F Murga et al.); An Accurate and Efficient Algorithm for Peptide and PTM Identification by Tandem Mass Spectrometry (K Ning et al.); The Comparative Genomics of Protein Interactions (J M Peregrin-Alvarez & C Ouzounis); Weighted Lasso in Graphical Gaussian Modeling for Large Gene Network Estimation Based on Microarray Data (T Shimamura et al.); GO-based Tissue-Specific Functions of Mouse Using Countable Gene Expression Profiles (Y Takenaka et al.); Functional Centrality: Detecting Lethality of Proteins in Protein Interaction Networks (K L Tew et al.); The in silico Prediction of Promoters in Bacterial Genomes (M Towsey et al.); Discovering Biomolecular Mechanisms with Protein Sequence Studies (F Eisenhaber); The p53 Pathway (D Lane); Regulation of Gene Expression by Small Non-coding RNAs (H Margalit); Mapping the Transcriptional Network in Stem Cells Regulated by REST (L W Stanton); Computational Dissection of Mammalian Regulation Networks (M Zhang).