Overview

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.

Full Product Details

Author:   Maria Anisimova
Publisher:   Humana Press Inc.
Imprint:   Humana Press Inc.
Edition:   2nd ed. 2019
Volume:   1910
Weight:   1.682kg
ISBN:  

9781493990733

ISBN 10:   149399073
Pages:   780
Publication Date:   06 July 2019
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Active
Availability:   Manufactured on demand  
We will order this item for you from a manufactured on demand supplier.

Table of Contents

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 Stephane 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 Makalowski, Valer Gotea, Amit Pande, and Izabela Makalowska 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 Puigbo, 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, Raphael Meheust, 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 Glemin, Clementine M. Francois, 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 Gonzalez Part V: Population Genomics and Omics in Light of Disease and Evolution 17. Association Mapping and Disease: Evolutionary Perspectives Soren Besenbacher, Thomas Mailund, Bjarni J. Vilhjalmsson, 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 Bagci, Sina Beier, Anna Gorska, 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 Muller, 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 Moeller, 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

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