Evolutionary Genomics: Statistical and Computational Methods

ISBN-13: 9781493990733 / Angielski / Twarda / 2019 / 780 str.

Maria Anisimova

Spis treści

Part I: Introduction: Bioinformatician’s Primers

 

1. Introduction to Genome Biology and Diversity

            Noor Youssef, Aidan Budd, and Joseph P. Bielawski

 

2. Probability, Statistics, and Computational Science

            Niko Beerenwinkel and Juliane Siebourg

 

3. A Not-So-Long Introduction to Computational Molecular Evolution

            Stéphane Aris-Brosou and Nicolas Rodrigue

 

Part II: Genomic Alignment and Homology Inference

 

4. Whole-Genome Alignment

            Colin Dewey

 

5. Inferring Orthology and Paralogy

            Adrian M. Altenhoff, Natasha M. Glover, and Christophe Dessimoz

 

6. Transposable Elements and Their Identification

            Wojciech Makałowski, Valer Gotea, Amit Pande, and Izabela Makałowska

 

Part III: Phylogenomics and Genome Evolution

 

7. Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model

            Liang Liu, Christian Anderson, Dennis Pearl, and Scott V. Edwards

 

8. Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life

            Pere Puigbò, Yuri I. Wolf, and Eugene V. Koonin

 

9. The Methodology Behind Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution

            Andrew K. Watson, Romain Lannes, Jananan S. Pathmanathan, Raphaël Méheust, Slim Karkar, Philippe Colson, Eduardo Corel, Philippe Lopez, and Eric Bapteste

 

10. Bayesian Molecular Clock Dating Using Genome-Scale Datasets

            Mario dos Reis and Ziheng Yang

 

11. Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species

            Sylvain Glémin, Clémentine M. François, and Nicolas Galtier

 

Part IV: Natural Selection and Innovation in Genomic Sequences

 

12. Selection Acting on Genomes

            Carolin Kosiol and Maria Anisimova

 

13. Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship between Model and Data

            Christopher T. Jones, Edward Susko, and Joseph P. Bielawski

 

14. Evolution of Viral Genomes: Interplay between Selection, Recombination, and Other Forces

            Stephanie J. Spielman, Steven Weaver, Stephen D. Shank, Brittany Rife Magalis, Michael Li, and Sergei L. Kosakovsky Pond

 

15. Evolution of Protein Domain Architectures

            Sofia K. Forslund, Mateusz Kaduk, and Erik L.L. Sonnhammer

 

16. New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

            Lain Guio and Josefa González

 

Part V: Population Genomics and Omics in Light of Disease and Evolution

 

17. Association Mapping and Disease: Evolutionary Perspectives

            Søren Besenbacher, Thomas Mailund, Bjarni J. Vilhjálmsson, and Mikkel H. Schierup

 

18. Ancestral Population Genomics

            Julien Y. Dutheil and Asger Hobolth

 

19. Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN

            Caner Bağcı, Sina Beier, Anna Górska, and Daniel H. Huson

 

20. Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials

            Suparna Mitra

 

21. Systems Genetics for Evolutionary Studies

            Pjotr Prins, Geert Smant, Danny Arends, Megan K. Mulligan, Rob W. Williams, and Ritsert C. Jansen

 

22. Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases

            Lars Feuerbach, Fabian Müller, Peter Ebert, Thomas Lengauer, Christoph Bock, Yassen Assenov

 

Part VI: Handling Genomic Data: Resources and Computation

 

23. Semantic Integration and Enrichment of Heterogeneous Biological Databases

            Ana Claudia Sima, Kurt Stockinger, Tarcisio Mendes de Farias, and Manuel Gil

 

24. High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE

            Guy Baele, Daniel L. Ayres, Andrew Rambaut, Marc A. Suchard, and Philippe Lemey

 

25. Scalable Workflows and Reproducible Data Analysis for Genomics

            Francesco Strozzi, Roel Janssen, Ricardo Wurmus, Michael R. Crusoe, George Githinji, Paolo Di Tommaso, Dominique Belhachemi, Steffen Möller, Geert Smant, Joep de Ligt, and Pjotr Prins

 

26. Sharing Programming Resources between Bio* Projects

            Raoul J.P. Bonnal, Andrew Yates, Naohisa Goto, Laurent Gautier, Scooter Willis, Christopher Fields, Toshiaki Katayama, and Pjotr Prins

Blurb

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. 

Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward.