Krawetz, Stephen

Bioinformatics for Systems Biology

Krawetz, Stephen - Bioinformatics for Systems Biology, ebook


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ISBN: 9781597454407
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Table of contents

Part I. Life of a Cell and Its Analysis

1. Structure and Function of the Nucleus and Cell Organelles
Jon Holy, Ed Perkins

2. Transcription and the Control of Gene Expression
Nadine Wiper-Bergeron, Ilona S. Skerjanc

3. RNA Processing and Translation
Christina Karamboulas, Nadine Wiper-Bergeron, Ilona S. Skerjanc

4. DNA Replication, Recombination, and Repair
Linda B. Bloom

5. Cell Signaling
Daniel A. Rappolee, D. Randall Armant

6. Epigenetics of Spermiogenesis
Sophie Rousseaux, Myriam Ferro

7. Genomic Tools for Analyzing Transcriptional Regulatory Networks
John J. Wyrick

Part II. Statistical Tools and Their Application

8. Probability and Hypothesis Testing
Michael L. Kruger

9. Stochastic Models for Biological Patterns
Gautam B. Singh

10. Population Genetics
Jill S. Barnholtz-Sloan, Hemant K. Tiwari

11. Statistical Tools for Gene Expression Analysis and Systems Biology and Related Web Resources
Chiara Romualdi, Gerolamo Lanfranchi

Part III. Transcriptome Analysis

12. What Goes in is What Comes Out: How to Design and Implement a Successful Microarray Experiment
Jeffrey A. Loeb, Thomas L. Beaumont

13. Tools and Approaches for an End-to-End Expression Array Analysis
Adrian E. Platts, Stephen A. Krawetz

14. Analysis of Alternative Splicing with Microarrays
Jingyi Hui, Shivendra Kishore, Amit Khanna, Stefan Stamm

Part IV. Structural and Functional Sequence Analysis

15. 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?
Steven M. Thompson

16. A Spectrum of Phylogenetic-Based Approaches for Predicting Protein Functional Sites
Dukka Bahadur K. C., Dennis R. Livesay

17. The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection
Thomas Werner

In Silico Discovery of DNA Regulatory Sites and Modules
Panayiotis V. Benos

Part V. Literature Mining for Association and Meaning

19. Mining the Research Literature in Systems Biology
Keir T. Reavie

20. GoPubMed: Exploring PubMed with Ontological Background Knowledge
Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Liliana Barrio-Alvers, Bill Andreopoulos, Andreas Doms, Jörg Hakenberg, Jan Mönnich, Conrad Plake, Andreas Reischuck, Loïc Royer, Thomas Wächter, Matthias Zschunke, Michael Schroeder

21. BiblioSphere — Hypothesis Generation in Regulatory Network Analysis
Anton Epple, Matthias Scherf

22. Biological Knowledge Extraction
Florian Leitner, Robert Hoffmann, Alfonso Valencia

Part VI. Genomic Databases

23. Using KEGG in the Transition from Genomics to Chemical Genomics
Kiyoko F. Aoki-Kinoshita, Minoru Kanehisa

24. Ensembl
Anne Parker, Fiona Cunningham

25. Management of Spatially Organized Biological Data using EMAGE
Jeffrey H. Christiansen, Duncan R. Davidson, Richard A Baldock

26. Equality of the Sexes? Parent-of-Origin Effects on Transcription and de novo Mutations
Rivka L. Glaser, Ian M. Morison

Part VII. Biological Networks

27. Methods for Structural Inference and Functional Module Identification in Intracellular Networks
Maria Manioudaki, Eleftheria Tzamali, Martin Reczko, Panayiota Poirazi

28. Methods for Dynamical Inference in Intracellular Networks
Eleftheria Tzamali, Panayiota Poirazi, Martin Reczko

29. ASIAN: Network Inference Web Server
Sachiyo Aburatani, Shigeru Saito, Katsuhisa Horimoto

Part VIII. Bridging the Gap

30. Bioinformatics for Metabolomics
David S. Wishart

31. Virtual Reality Meets Functional Genomics
Andrei L. Turinsky, Christoph W. Sensen

32. Systems Biology of Personalized Medicine
Craig Paul Webb, David Michael Cherba

Keywords: SCIENCE / Life Sciences / Biology / General SCI008000

Publication year
Natural Sciences

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