Genome Informatics 2009

Intro -- CONTENTS -- Preface -- Acknowledgments -- Committees -- Part A Full Papers -- Predicting Protein-Protein Relationships from Literature Using Latent Topics T. Aso €j K. Eguchi -- 1. Introduction -- 2. LDA and Estimation Algorithms -- 2.1. Generative Process of LDA -- 2.2. Collapsed Gibbs Sampling Inference -- 2.3. Collapsed Variational Bayesian Inference -- 3. Protein-Protein Relationship Prediction based on LDA -- 4. Data and Entity Representation -- 4.1. GENIA Collection -- 4.2. TREC Collection and GENIA Tagger -- 5. Experiments -- 5.1. Log-Likelihood -- 5.2. Entity-Link Prediction -- 5.2.1. Experimental Settings -- 5.2.2. Task-based Evaluation -- 5.2.3 . Protein-Protein Relationship Network -- 6. Conclusions -- Acknowledgments -- References -- Evaluation of DNA Intramolecular Interactions for Nucleosome Positioning in Yeast M. Fernandez, S. Fujii, H. Kono €j A. Sarai -- 1. Introduction -- 2. Method and Results -- 2.1. Intramolecular Interaction Energy Calculation -- 2.2. Oscillation Pattern of Dinucleotides Along the Nucleosome Structure -- 2.3. Intramolecular Energy Profile of Yeast Genome -- 3. Discussions -- References -- Quality Control and Reproducibility in DNA Microarray Experiments A. Fujita, J. R. Sato, F. H. L. da Silva, M. C. Galviio, M. C. Sogayar €j S. Miyano -- 1. Introduction -- 2. Materials and Methods -- 2.1. Dahlberg's Error (D.E.) -- 2.2. Support Vector Regression (SVR) -- 2.3. Modeling DNA Microarray Data -- 2.4. DNA Microarray -- 2.4 .1. Cell Lysis and RNA Extraction -- 2.4.2. Labeling and Purification of Targets -- 2.4.3. Hybridization and Washing of the DNA Arrays -- 3. Results and Discussions -- Acknowledgments -- References -- Comparative Analysis of Topological Patterns in Different Mammalian Networks B. Goemann, A. P. Potapov, M. Ante €j E. Wingender -- 1. Introduction -- 2 Methods.