This item is in: Biomedicine > Bioinformatics, computing and life sciences

Annotating new genes: From in silico screening to experimental validation

S Uchida, Max-Planck-Institute, Germany

Woodhead Publishing Series in Biomedicine No. 15

 - 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
 - includes a case-study of C-It for use in in silico screening

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.

ISBN 1 907568 68 9
ISBN-13: 978 1 907568 68 8
August 2012
196 pages  234 x 156mm  hardback  
£99.00 / US$170.00 / €120.00

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About the author

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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Contents

Introduction

Databases and software to make your research life easier
 - Introduction
 - Primary databases
 - Secondary databases
 - Datasets to keep an eye out for
 - Conclusion

How to program like a bioinformatician?
 - Introduction
 - Setting up an environment
 - Writing Perl scripts
 - Conclusion

Case study: C-It, knowledge database for screening evolutionarily conserved, tissue-enriched, uncharacterized genes
 - Introduction
 - Concept of in silico screening
 - Case study: C-It
 - Conclusion

Experimental validation: concepts and practice
 - Introduction
 - Proposed experimental strategy
 - Step 1: validation of expression patterns
 - Step 2: phenotypic analysis
 - Step 3: molecular interactions
 - Other experiments
 - Conclusion

Further application: adult stem cells and tissue regenerations
 - Introduction
 - Cell types in heart and their lineages
 - Current status of cardiac stem cells
 - Conclusion

Conclusion