Pub. Date:
Oxford University Press
Ancestral Sequence Reconstruction / Edition 1

Ancestral Sequence Reconstruction / Edition 1

by David A. LiberlesDavid A. Liberles


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Ancestral sequence reconstruction is a technique of growing importance in molecular biology and comparative genomics. As a powerful technique for both testing evolutionary and ecological hypotheses as well as uncovering the link between sequence and molecular phenotype, there are potential applications in a number of fields. Beginning with a historical overview of the field including apllications, the discussion then moves into potential applications in drug discovery and the pharmaceutical industry. A section on computational methodology provides a detailed discussion on available methods for reconstructing ancestral sequences, including advantages,disadvantages, and potential pitfalls. Purely computational applications, including whole proteome reconstruction are discussed. Another section provides a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory, while the last section describes scientific questions where experimental ancestral sequence reconstruction coupled to a computaional and experimental how-to guide, while simultaneously addressing some of the hot topics in the field.

Product Details

ISBN-13: 9780199299188
Publisher: Oxford University Press
Publication date: 07/26/2007
Series: Oxford Biosciences
Edition description: New Edition
Pages: 272
Product dimensions: 9.70(w) x 7.50(h) x 0.70(d)

About the Author

David A. Liberles is Assistant Professor at the Department of Molecular Biology, University of Wyoming

Table of Contents

1. The Early Days of Paleogenomics, Connecting Molecules to the Planet, Steven A. Benner
2. Ancestral Sequence Reconstruction as a Tool to Understand Natural History and Guide Synthetic Biology: Realizing and Extending the Vision of Zuckerkandl and Pauling, Eric A. Gaucher
3. Linking Sequence to Function in Drug Design with Ancestral Sequence Reconstruction, Janos T. Kodra, Marie Skovgaard, Dennis Madsen, and David A. Liberles
4. Probabilistic Models and Their Impact on the Accuracy of Reconstructed Ancestral Sequences, Tal Pupko, Adi Doron-Faigenboim, David A. Liberles, and Gina M. Cannarozzi
5. Probabilistic Ancestral Sequences Based on the Markovian Model of Evolution- Algorithms and Applications, Gina M. Cannarozzi, Adrian Schneider, and Gaston H. Gonnet
6. Estimating the History of Mutations on a Phylogeny, Jonathan P. Bollback, Paul P. Gardner, and Rasmus Nielsen
7. Coarse Projections of the Protein-Mutational Fitness Landscape, F. Nicholas Braun
8. Dealing with Uncertainty in Ancestral Sequence Reconstruction: Sampling from the Posterior Distribution, David D. Pollock and Belinda S. W. Chang
9. Evolutionary Properties of Sequences and Ancestral State Reconstruction, Lesley J. Collins and Peter J. Lockhart
10. Reconstructing the Ancestral Eukaryote- Lessons from the Past, Mary J. O'Connell and James O. McInerney
11. Using Ancestral Sequence Inference to Determine the Trend of Functional Divergence After Gene Duplication, Xun Gu, Ying Zheng, Yong Huang, and Dongping Xu
12. Reconstruction of Ancestral Proteomes, Toni Gabaldon and Martijn A. Huynen
13. Computational Reconstruction of Ancestral Genomic Regions from Evolutionarily Conserved Gene Clusters, Etienne G. J. Danchin, Eric A. Gaucher, and Pierre Pontarotti
14. Experimental Resurrection of Ancient Biomolecules: Gene Synthesis, Heterologous Protein Expression, and Functional Assays, Eric A. Gaucher
15. Dealing with Model Uncertainty in Reconstructing Ancestral Proteins in the Laboratory: Examples from Ancestral Visual Pigments and GFP-like Proteins, Belinda S. W. Chang, Mikhail V. Matz, Steven F. Field, Johannes M ller, and Ilke van Hazel
16. Unraveling the Evolution of Complexity by Resurrecting Ancient Genes, Joseph W. Thornton and Jamie T. Bridgham
17. A Thermophilic Last Universal Ancestor Inferred from its Estimated Amino Acid Composition, Dawn J. Brooks and Eric A. Gaucher
18. The Resurrection of Ribonucleases from Mammals. From Ecology to Medicine, Slim O. Sassi and Steven A. Benner
19. Evolution of Specificity and Diversity, Denis C. Shields, Kate Johnston, Iain M. Wallace, and Richard J. Edwards

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