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List of figures and tables
About the author
Chapter 1: Introduction
Chapter 2: Databases and software to make your research life easier
2.2 Primary databases
2.3 Secondary databases
2.4 Datasets to keep an eye out for
Chapter 3: How to program like a bioinformatician?
3.2 Setting up an environment
3.3 Writing Perl scripts
Chapter 4: Case study: C-It, knowledge database for screening evolutionarily conserved, tissue-enriched, uncharacterized genes
4.2 Concept of in silico screening
4.3 Case study: C-It
Chapter 5: Experimental validation: concepts and practice
5.2 Proposed experimental strategy
5.3 Step 1: validation of expression patterns
5.4 Step 2: phenotypic analysis
5.5 Step 3: molecular interactions
5.6 Other experiments
Chapter 6: Further application: adult stem cells and tissue regenerations
6.2 Cell types in heart and their lineages
6.3 Current status of cardiac stem cells
Chapter 7: Conclusion
In recent years, a number of academic and commercial software packages and databases have been developed for the analysis and screening of biological data; however, the usability of these data is compromised by so-called novel genes to which no biological function is assigned. Annotating new genes outlines an approach to the analysis of evolutionary-conserved, heart-enriched genes with unknown functions, offering a step-by-step description of the procedure from screening to validation. The book begins by offering an introduction to the databases and software available, before moving on to cover programming guidelines, including a specific case study on the use of C-It for in silico screening. The second half of the book offers a step-by-step guide to experimental validation concepts and procedures, as well as an overview of additional potential applications of this approach in the field of stem cells and tissue regeneration, before a concluding chapter summarises the concepts and theories presented.
- Focuses not only on screening but also on biological validations
- Provides details of databases and software (web interface) products for biologists with minimal computation skills
- Offers a step-by-step outline of the procedure involved
Academics and researchers in the field of bioinformatics and developmental biology; Geneticists and biologists
- No. of pages:
- © Woodhead Publishing 2012
- 6th August 2012
- Woodhead Publishing
- Hardcover ISBN:
- eBook ISBN:
Shizuka Uchida is a group leader in the Max-Planck Institute for Heart and Lung Research in Bad Nauheim, Germany. He is a trained bioinformatician and a developmental biologist with a specific focus on adult stem cell research, and has extensive experience in combining the power of computers and data mining methods with state-of-the-art experimental techniques.
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