Knowledge–Based Bioinformatics: From Analysis to Interpretation

In order to deal with issues that arise from the current increase of biological data in genomic and proteomic research and present it effectively to a wider audience, broader coverage of recent developments in the field of knowledge–based systems and their applications is required. Most current texts are either outdated or do not include all the aspects in knowledge and data–driven representation, integration, analysis, and interpretation. This collection aims to address this issue by providing comprehensive coverage of knowledge driven approaches to bioinformatics.

Spis treści:
A Preface to Knowledge–Based BioinformaticsPART I: FUNDAMENTALSSection 1: Knowledge–Driven ApproachesChapter 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 Egaña Aranguren, Robert Stevens, Jesualdo Tomás Fernández 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
Section 2: Data–Analysis Approaches
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
PART II: APPLICATIONSSection 3: Gene and Protein InformationChapter 8 Fundamentals of Gene Ontology Functional Annotation
Varsha K. Khodi yar, Emily C. Dimmer, Rachael P. Huntley and Ruth C.Lovering
Chapter 9 Methods for Improving Genome Annotation
Jonathan Mudge, Jennifer HarrowChapter 10 Sequences from all Prokaryotic, Eukaryotic and Viral Genomes CurrentlyAvailable could be Clustered According to Phylotype on a Large–scale Self–Organizing Map Constructed with High–Performance Supercomputers.
Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura
Section 4: Biomolecular Relationships and Meta RelationshipsChapter 11 Molecular Network Analysis and Applications
Minlu Zhang, Jingyuan Deng, Chunsheng V. Fang, Xiao Zhang and Long J. LuChapter 12 Reactome and Integrative Pathway Knowledge bases
Robin A. Haw, Marc Gillespie,Michael A. Caudy
Chapter 13 Methods and Challenges of Identifying Bio–Molecular Relationships andNetworks Associated with Complex Diseases/Phenotypes and theirApplication to Drug Treatments.
Mie Rizig
Index