This book provides an overview of computational analysis of genes and genomes, and of some most notable findings that come out of this work. Foundations of Comparative Genomics presents a historical perspective, beginning with early analysis of individual gene sequences, to present day comparison of gene repertoires encoded by completely sequenced genomes. The author discusses the underlying scientific principles of comparative genomics, argues that completion of many genome sequences started a new era in biology, and provides a personal view on several state-of-the-art issues, such as systems biology and whole-genome phylogenetic reconstructions. This book is an essential reference for researchers and students in computational biology, evolutionary biology, and genetics.
* Presents an historic overview of genome biology and its achievements
* Includes topics not covered in other books such as minimal and ancestral genomes
* Discusses the evolutionary resilience of protein-coding genes and frequent functional convergence at the molecular level
* Critically reviews horizontal gene transfer and other contentious issues
* Covers comparative virology as a somewhat overlooked foundation of modern genome science
This book provides an overview of computational analysis of genes and genomes, and of some most notable findings that come out of this work. Foundations of Comparative Genomics presents a historical perspective, beginning with early analysis of individual gene sequences, to present day comparison of gene repertoires encoded by completely sequenced genomes. The author discusses the underlying scientific principles of comparative genomics, argues that completion of many genome sequences started a new era in biology, and provides a personal view on several state-of-the-art issues, such as systems biology and whole-genome phylogenetic reconstructions. This book is an essential reference for researchers and students in computational biology, evolutionary biology, and genetics.
* Presents an historic overview of genome biology and its achievements
* Includes topics not covered in other books such as minimal and ancestral genomes
* Discusses the evolutionary resilience of protein-coding genes and frequent functional convergence at the molecular level
* Critically reviews horizontal gene transfer and other contentious issues
* Covers comparative virology as a somewhat overlooked foundation of modern genome science
Preface
1. The Beginning of Computational Genomics
2. Finding Sequence Similarities
3. Homology: Can We Get It Right?
4. Getting Ready for the Era of Comparative Genomics: The
Importance of Viruses
5. The First Fact of Comparative Genomics: Protein Sequences are
Remarkably Resilient in Evolution
6. The Second Fact of Comparative Genomics: Functional Convergence
at the Molecular Level
7. Prediction of Function and Reconstruction of Metabolism from
Genomic Data: Homology-Based Approaches
8. Prediction of Function and Reconstruction of Metabolism:
Post-Homology Approaches
9. Structural Genomics:What Does It Tell Us about Life?
10. How Many Protein Families are There?
11. Phylogenetic Inference and the Era of Complete Genomes
12. Two Stories about Evolution
13. Minimal and Ancestral Genomes
14. Comparative Genomics and Systems Biology
References
Index
Arcady R. Mushegian is Director of Bioinformatics at Stowers Institute for Medical Research in Kansas City and Professor of Microbiology at Kansas University Medical Center. He was born in Moscow, USSR, and graduated from Moscow State University.
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