Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
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.
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 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 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 Bagci, 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
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.
Open Access This book is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made. The images or other third party material in this book are included in the book's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the book's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
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.
Introduction to Genome Biology and Diversity.- Probability, Statistics, and Computational Science.- A Not-So-Long Introduction to Computational Molecular Evolution.- Whole-Genome Alignment.- Inferring Orthology and Paralogy.- Transposable Elements and Their Identification.- Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model.- Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life.- The Methodology Behind Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.- Bayesian Molecular Clock Dating Using Genome-Scale Datasets.- Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species.- Selection Acting on Genomes.- Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship between Model and Data.- Evolution of Viral Genomes: Interplay between Selection, Recombination, and Other Forces.- Evolution of Protein Domain Architectures.- New Insights on the Evolution of GenomeContent: Population Dynamics of Transposable Elements in Flies and Humans.- Association Mapping and Disease: Evolutionary Perspectives.- Ancestral Population Genomics.- Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN.- Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials.- Systems Genetics for Evolutionary Studies.- Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases.- Semantic Integration and Enrichment of Heterogeneous Biological Databases.- High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE.- Scalable Workflows and Reproducible Data Analysis for Genomics.- Sharing Programming Resources between Bio* Projects.
Inhaltsverzeichnis
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 Makäowski, Valer Gotea, Amit Pande, and Izabela Makäowska
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 Bäc¿, 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
Klappentext
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.
n
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.
Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
