BIOINFORMATICS<br> A Swiss Perspective

BIOINFORMATICS
A Swiss Perspective

CONTENTS


FRONT MATTER	i
SECTION I GENES AND GENOMES
Methods for Discovery and Characterization of DNA Sequence Motifs Philipp Bucher	3
Comparative Genome Analysis Robert M. Waterhouse, Evgenia V. Kriventseva and Evgeny M. Zdobnov	33
From Modules to Models: Advanced Analysis Methods for Large-Scale Data Sven Bergmann	59
Integrated Analysis of Gene Expression Profiling Studies — Examples in Breast Cancer Pratyaksha Wirapati, Darlene R. Goldstein and Mauro Delorenzi	85
Computational Biology of Small Regulatory RNAs Mihaela Zavolan and Lukasz Jaskiewicz	115
SECTION II PROTEINS AND PROTEOMES
UniProtKB/Swiss-Prot Manual and Automated Annotation of Complete Proteomes: The Dictyostelium discoideum Case Study Amos Bairoch and Lydie Lane	149
Analytical Bioinformatics for Proteomics Patricia M. Palagi and Frédérique Lisacek	169
Protein–Protein Interaction Networks: Assembly and Analysis Christian von Mering	197
Protein Structure Modeling and Docking at the Swiss Institute of Bioinformatics Torsten Schwede and Manuel C. Peitsch	219
Molecular Modeling of Proteins: From Simulations to Drug Design Applications Vincent Zoete, Michel Cuendet, Ute F. Röhrig, Aurélien Grosdidier and Olivier Michielin	247
SECTION III PHYLOGENETICS AND EVOLUTIONARY BIOINFORMATICS
An Introduction to Phylogenetics and Its Molecular Aspects Gabriel Jîvasattha Bittar and Bernhard Pascal Sonderegger	285
Phylogenetic Tree Building Methods Manuel Gil and Gaston H. Gonnet	329
Bioinformatics for Evolutionary Developmental Biology Marc Robinson-Rechavi	355
SECTION IV MODELING OF BIOLOGICAL SYSTEMS
Spatiotemporal Modeling and Simulation in Biology Ivo F. Sbalzarini	381
BACK MATTER	433
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