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Bioinformatics A Swiss Perspective 1st Edition by Ron D Appel, Ernest Feytmans ISBN 9812838775 9789812838773

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Bioinformatics A Swiss Perspective 1st Edition Ron D. Appel Digital Instant Download

Author(s): Ron D. Appel, Ernest Feytmans, Ron D Appel
ISBN(s): 9789812838773, 9812838775
Edition: 1
File Details: PDF, 12.94 MB
Year: 2009
Language: english
SKU: EB-1373088 Category: Tags: ,

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ISBN 10: 9812838775 
ISBN 13: 9789812838773
Author: Ron D Appel, Ernest Feytmans

Biological research and recent technological advances have resulted in an enormous increase in research data that require large storage capacities, powerful computing resources, and accurate data analysis algorithms. Bioinformatics is the field that provides these resources to life science researchers.The Swiss Institute of Bioinformatics (SIB), which has celebrated its 10th anniversary in 2008, is an institution of national importance, recognized worldwide for its state-of-the-art work. Organized as a federation of bioinformatics research groups from Swiss universities and research institutes, the SIB provides services to the life science community that are highly appreciated worldwide, and coordinates research and education in bioinformatics nationwide. The SIB plays a central role in life science research both in Switzerland and abroad by developing extensive and high-quality bioinformatics resources that are essential for all life scientists. Knowledge developed by SIB members in areas such as genomics, proteomics, and systems biology is directly transformed by academia and industry into innovative solutions to improve global health. Such an astounding concentration of talent in a given field is unusual and unique in Switzerland.This book provides an insight into some of the key areas of activity in bioinformatics in Switzerland. With contributions from SIB members, it covers both research work and major infrastructure efforts in genome and gene expression analysis, investigations on proteins and proteomes, evolutionary bioinformatics, and modeling of biological systems.

Bioinformatics A Swiss Perspective 1st Table of contents:

SECTION I: GENES AND GENOMES

Chapter 1: Methods for Discovery and Characterization of DNA Sequence Motifs – Philipp Bucher

  1. Introduction

  2. Motif Discovery in a Nutshell

  3. Overview of the Methods

  4. Bottlenecks and Limitations

  5. Locally Overrepresented Sequence Motifs

  6. Conclusions and Perspectives

Chapter 2: Comparative Genome Analysis – Robert M. Waterhouse, Evgenia V. Kriventseva, Evgeny M. Zdobnov

  1. Introduction

  2. Gene Annotation

  3. Protein Families

  4. Orthologs and Paralogs

  5. Genome Architecture

  6. RNA Genes and Conserved Noncoding Sequences

  7. Perspectives

Chapter 3: From Modules to Models: Advanced Analysis Methods for Large-Scale Data – Sven Bergmann

  1. Introduction

  2. Modular Algorithms

  3. Module Analysis

  4. Outlook

Chapter 4: Integrated Analysis of Gene Expression Profiling Studies — Examples in Breast Cancer

  1. Introduction

  2. Combining Information

  3. Individual Patient Data (IPD)

  4. SwissBrod

  5. Spectrum of Possible Analyses

  6. Data Integration Methodology

  7. Breast Cancer Examples

  8. Conclusion

Chapter 5: Computational Biology of Small Regulatory RNAs – Mihaela Zavolan and Lukasz Jaskiewicz

  1. Introduction

  2. Identification of Small Regulatory RNAs

  3. Classes of Small Regulatory RNAs

  4. Biogenesis of Small Regulatory RNAs

  5. Function of Small Regulatory RNAs

  6. MicroRNA Gene Prediction

  7. MicroRNA Target Prediction

  8. Conclusions

SECTION II: PROTEINS AND PROTEOMES

Chapter 6: UniProtKB/Swiss-Prot Manual and Automated Annotation of Complete Proteomes

  1. Introduction

  2. Annotation Pipeline

  3. Conclusion

Chapter 7: Analytical Bioinformatics for Proteomics – Patricia M. Palagi and Frédérique Lisacek

  1. Introduction

  2. Proteome Imaging

  3. Protein Identification and Characterization

  4. Proteomics Knowledge Integration and Databases

  5. Conclusion

Chapter 8: Protein–Protein Interaction Networks: Assembly and Analysis – Christian von Mering

  1. Introduction

  2. Experimental Protein Interaction Data

  3. Networks That Include Indirect Associations

  4. Clustering, Modules, and Motifs

  5. Interpreting Network Topology

  6. Online Resources

Chapter 9: Protein Structure Modeling and Docking at the Swiss Institute of Bioinformatics – Torsten Schwede

  1. Introduction

  2. Protein Structure Prediction with SWISS-MODEL

  3. Large-Scale Protein Structure Prediction

  4. Protein Model Quality

  5. Applications of Protein Models

  6. Protein Model Portal

  7. Future Outlook

Chapter 10: Molecular Modeling of Proteins: From Simulations to Drug Design Applications – Vincent Zoete

  1. Introduction

  2. Molecular Force Fields

  3. Molecular Dynamics Simulations

  4. Free Energy Calculations

  5. Examples of Applications

SECTION III: PHYLOGENETICS AND EVOLUTIONARY BIOINFORMATICS

Chapter 11: An Introduction to Phylogenetics and Its Molecular Aspects

  1. Introduction

  2. Homology and Homoplasy

  3. Molecular Phylogenetics

  4. Tree Reconstitution

  5. Uses of Phylogenetics in Molecular Biology

  6. Phylogenetics Resources

Chapter 12: Phylogenetic Tree Building Methods – Manuel Gil and Gaston H. Gonnet

  1. Introduction

  2. Types of Tree Building Methods

  3. Tree Building with an Objective Function

  4. Least Squares Tree Construction

  5. Outlook

Chapter 13: Bioinformatics for Evolutionary Developmental Biology – Marc Robinson-Rechavi

  1. Introduction

  2. The Easy Part: The Evolution of Gene Sequences

  3. Developing Bioinformatic Tools for Evo-Devo

  4. Conclusion

SECTION IV: MODELING OF BIOLOGICAL SYSTEMS

Chapter 14: Spatiotemporal Modeling and Simulation in Biology – Ivo F. Sbalzarini

  1. Introduction

  2. Properties of Biological Systems

  3. Spatiotemporal Modeling Techniques

  4. Spatiotemporal Simulation Methods

  5. Introduction to Continuum Particle Methods

  6. Efficient Algorithms for Particle Methods

  7. Particle Methods for the Simulation of Diffusion Processes

  8. Reaction-Diffusion Processes

  9. Conclusions

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Tags: Ron D Appel, Ernest Feytmans, Bioinformatics