Krawetz Bioinformatics for Systems Biology

2. Auflage 2009
ISBN: 978-1-59745-440-7
Verlag: Humana Press
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 639 Seiten

Bioinformatics for Systems Biology bridges and unifies many disciplines. It presents the life scientist, computational biologist, and mathematician with a common framework. Only by linking the groups together may the true life sciences revolution move forward.

Autoren/Hrsg.

Krawetz, Stephen

Inhaltsverzeichnis

1;Preface;4
2;Contents;6
3;Contributors;9
4;Life of a Cell and Its Analysis;12
4.1;Structure and Function of the Nucleus and Cell Organelles;13
4.2;Transcription and the Control of Gene Expression;42
4.3;RNA Processing and Translation;59
4.4;DNA Replication, Recombination, and Repair;75
4.5;Cell Signaling;96
4.6;Epigenetics of Spermiogenesis;112
4.7;Genomic Tools for Analyzing Transcriptional Regulatory Networks;125
5;Statistical Tools and Their Application;143
5.1;Probability and Hypothesis Testing;144
5.2;Stochastic Models for Biological Patterns;156
5.3;Population Genetics;168
5.4;Statistical Tools for Gene Expression Analysis and Systems Biology and Related Web Resources;186
6;Transcriptome Analysis;211
6.1;What Goes in is What Comes Out: How to Design and Implement a Successful Microarray Experiment;212
6.2;Tools and Approaches for an End-to-End Expression Array Analysis;229
6.3;Analysis of Alternative Splicing with Microarrays;268
7;Structural and Functional Sequence Analysis;281
7.1;An Introduction to Multiple Sequence Alignment — and the T- Coffee Shop. Beyond Just Aligning Sequences: How Good can you Make your Alignment, and so What?;282
7.2;A Spectrum of Phylogenetic-Based Approaches for Predicting Protein Functional Sites;313
7.3;The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection;336
7.4;In Silico Discovery of DNA Regulatory Sites and Modules;350
8;Literature Mining for Association and Meaning;364
8.1;Mining the Research Literature in Systems Biology;365
8.2;GoPubMed: Exploring PubMed with Ontological Background Knowledge;380
8.3;BiblioSphere — Hypothesis Generation in Regulatory Network Analysis;395
8.4;Biological Knowledge Extraction;407
9;Genomic Databases;428
9.1;Using KEGG in the Transition from Genomics to Chemical Genomics;429
9.2;Ensembl;445
9.3;Management of Spatially Organized Biological Data using EMAGE;460
9.4;Equality of the Sexes? Parent-of-Origin Effects on Transcription and de novo Mutations;476
10;Biological Networks;505
10.1;Methods for Structural Inference and Functional Module Identification in Intracellular Networks;506
10.2;Methods for Dynamical Inference in Intracellular Networks;529
10.3;ASIAN: Network Inference Web Server;550
11;Bridging the Gap;565
11.1;Bioinformatics for Metabolomics;566
11.2;Virtual Reality Meets Functional Genomics;585
11.3;Systems Biology of Personalized Medicine;598
12;Index;614