Front Matter -- Fundamentals. Knowledge-Based Bioinformatics / Eric Karl Neumann -- Knowledge-Driven Approaches to Genome-Scale Analysis / Hannah Tipney, Lawrence Hunter -- Technologies and Best Practices for Building Bio-Ontologies / Mikel Eĝna Aranguren, Robert Stevens, Erick Antezana, Jesualdo Tom̀s Ferǹndez-Breis, Martin Kuiper, Vladimir Mironov -- Design, Implementation and Updating of Knowledge Bases / Sarah Hunter, Rolf Apweiler, Maria Jesus Martin -- Classical Statistical Learning in Bioinformatics / Mark Reimers -- Bayesian Methods in Genomics and Proteomics Studies / Ning Sun, Hongyu Zhao -- Automatic Text Analysis for Bioinformatics Knowledge Discovery / Dietrich Rebholz-Schuhmann, Jung-jae Kim -- Applications. Fundamentals of Gene Ontology Functional Annotation / Varsha K Khodiyar, Emily C Dimmer, Rachael P Huntley, Ruth C Lovering -- Methods for Improving Genome Annotation / Jonathan Mudge, Jennifer Harrow -- Sequences from Prokaryotic, Eukaryotic, and Viral Genomes Available Clustered According to Phylotype on a Self-Organizing Map / Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura -- Molecular Network Analysis and Applications / Minlu Zhang, Jingyuan Deng, Chunsheng V Fang, Xiao Zhang, Long Jason Lu -- Biological Pathway Analysis: An Overview of Reactome and Other Integrative Pathway Knowledge Bases / Robin A Haw, Marc E Gillespie, Michael A Caudy -- Methods and Challenges of Identifying Biomolecular Relationships and Networks Associated with Complex Diseases/Phenotypes, and Their Application to Drug Treatments / Mie Rizig -- Trends and conclusion -- Index.

(Publisher-supplied data) Chapter 1 Knowledge Based Bioinformatics Eric Karl Neumann Chapter 2 Knowledge-Driven Approaches to Genome-Scale Analysis Hannah Tipney and Lawrence Hunter Chapter 3 Technologies and Best Practices for Building Bio-Ontologies Mikel Egaa Aranguren, Robert Stevens, Jesualdo Tom s Fern ndez Breis, Erick Antezana, Vladimir Mironov and Martin Kuiper Chapter 4 Design, Implementation and Updating of Knowledge Bases Sarah Hunter, Rolf Apweiler and Maria Jesus Martin Chapter 5 Classical Statistical Learning in Bioinformatics Mark Reimers Chapter 6 Bayesian Methods in Genomics and Proteomics Studies Ning Sun and Hongyu Zhao Chapter 7 Automatic Text Analysis for Bioinformatics Knowledge Discovery Dietrich Rebholz-Schuhmann, Jung-jae Kim Chapter 8 Fundamentals of Gene Ontology Functional Annotation Varsha K. Khodiyar, Emily C. Dimmer, Rachael P. Huntley and Ruth C. Lovering Chapter 9 Methods for Improving Genome Annotation Jonathan Mudge, Jennifer Harrow Chapter 10 Sequences from all Prokaryotic, Eukaryotic and Viral Genomes Currently Available could be Clustered According to Phylotype on a Large-scale Self-Organizing Map Constructed with High-Performance Supercomputers. Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura Chapter 11 Molecular Network Analysis and Applications Minlu Zhang, Jingyuan Deng, Chunsheng V. Fang, Xiao Zhang and Long J. Lu Chapter 12 Reactome and Integrative Pathway Knowledge bases Robin A. Haw, Marc Gillespie, ÿ Michael A. Caudy Chapter 13 Methods and Challenges of Identifying Bio-Molecular Relationships and Networks Associated with Complex Diseases/Phenotypes and their Application to Drug Treatments. Mie Rizig.