Serves as an ideal reference for young and experienced researchers alike
Features practical, step-by-step guidance to methodologies being used in the field
Includes key implementation advice from the experts
Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight. Volume 2 begins with phylogenomics and continues with in-depth coverage of natural selection, recombination, and genomic innovation. The remaining chapters treat topics of more recent interest, including population genomics, -omics studies, and computational issues related to the handling of large-scale genomic data. Written in the highly successful Methods in Molecular Biology™ series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses.
Comprehensive and cutting-edge,
Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.
Part I: Phylogenomics
1. Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Non-Coalescent Genes
Christian Anderson, Liang Liu, Dennis Pearl, and Scott V. Edwards
2. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord
Gergely J Szöllosi and Vincent Daubin
3. Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life
Pere Puigbò, Yuri I. Wolf, and Eugene V. Koonin
4. Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns
Eric Bapteste, Frederic Bouchard, and Richard M. Burian
Part II: Natural Selection, Recombination, and Innovation in Genomic Sequences
5. Selection on the Protein Coding Genome
Carolin Kosiol and Maria Anisimova
6. Methods to Detect Selection on Non-Coding DNA
Ying Zhen and Peter Andolfatto
7. The Origin and Evolution of New Genes
Margarida Cardoso-Moreira and Manyuan Long
8. Evolution of Protein Domain Architectures
Kristoffer Forslund and Erik L.L. Sonnhammer
9. Estimating Recombination Rates from Genetic Variation in Humans
Adam Auton and Gil McVean
10. Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
Sergei L. Kosakovsky Pond, Ben Murrell, and Art F.Y. Poon
Part III: Population Genomics
11. Association Mapping and Disease: Evolutionary Perspectives
Søren Besenbacher, Thomas Mailund, and Mikkel H. Schierup
12. Ancestral Population Genomics
Julien Y. Dutheil and Asger Hobolth
13. Non-Redundant Representation of Ancestral Recombinations Graphs
Laxmi Parida
Part IV: The "-omics"
14. Using Genomic Tools to Study Regulatory Evolution
Yoav Gilad
15. Characterization and Evolutionary Analysis of Protein-Protein Interaction Networks
Gabriel Musso, Andrew Emili, and Zhaolei Zhang
16. Statistical Methods in Metabolomics
Alexander Korman, Amy Oh, Alexander Raskind, and David Banks
17. Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN
Daniel H. Huson and Suparna Mitra
18. Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases
Lars Feuerbach, Konstantin Halachev, Yassen Assenov, Fabian Müller, Christoph Bock, and Thomas Lengauer
19. Genetical Genomics for Evolutionary Studies
Pjotr Prins, Geert Smant, and Ritsert C. Jansen
Part V: Handling Genomic Data: Resources and Computation
20. Genomics Data Resources: Frameworks and Standards
Mark D. Wilkinson
21. Sharing Programming Resources Between Bio* Projects through Remote Procedure Call and Native Call Stack Strategies
Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter Willis, Christopher Fields, and Toshiaki Katayama
22. Scalable Computing for Evolutionary Genomics
Pjotr Prins, Dominique Belhachemi, Steffen Möller, and Geert Smant
This highly practical volume, with its step-by-step techniques, brings together recent developments in the statistical methodology of evolutionary genomics and the challenges that followed as a result of rapidly improving sequencing technologies.
Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight. Volume 2 begins with phylogenomics and continues with in-depth coverage of natural selection, recombination, and genomic innovation. The remaining chapters treat topics of more recent interest, including population genomics, -omics studies, and computational issues related to the handling of large-scale genomic data. Written in the highly successful Methods in Molecular Biology(TM) series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses.
Comprehensive and cutting-edge,
Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.
Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Non-Coalescent Genes.- Modeling Gene Family Evolution and Reconciling Phylogenetic Discord.- Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life.- Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns.- Selection on the Protein Coding Genome.- Methods to Detect Selection on Non-Coding DNA.- The Origin and Evolution of New Genes.- Evolution of Protein Domain Architectures.- Estimating Recombination Rates from Genetic Variation in Humans.- Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces.- Association Mapping and Disease: Evolutionary Perspectives.- Ancestral Population Genomics.- Non-Redundant Representation of Ancestral Recombinations Graphs.- Using Genomic Tools to Study Regulatory Evolution.- Characterization and Evolutionary Analysis of Protein-Protein Interaction Networks.- Statistical Methods in Metabolomics.- Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN.- Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases.- Genetical Genomics for Evolutionary Studies.- Genomics Data Resources: Frameworks and Standards.- Sharing Programming Resources Between Bio* Projects through Remote Procedure Call and Native Call Stack Strategies.- Scalable Computing for Evolutionary Genomics.
Inhaltsverzeichnis
Part I: Phylogenomics
1.
Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Non-Coalescent Genes
Christian Anderson, Liang Liu, Dennis Pearl, and Scott V. Edwards
2. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord
Gergely J Szöllosi and Vincent Daubin
3.
Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life
Pere Puigbò, Yuri I. Wolf, and Eugene V. Koonin
4.
Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns
Eric Bapteste, Frederic Bouchard, and Richard M. Burian
Part II:
Natural Selection, Recombination, and Innovation in Genomic Sequences
5.
Selection on the Protein Coding Genome
Carolin Kosiol and Maria Anisimova
6.
Methods to Detect Selection on Non-Coding DNA
Ying Zhen and Peter Andolfatto
7.
The Origin and Evolution of New Genes
Margarida Cardoso-Moreira and Manyuan Long
8.
Evolution of Protein Domain Architectures
Kristoffer Forslund and Erik L.L. Sonnhammer
9.
Estimating Recombination Rates from Genetic Variation in Humans
Adam Auton and Gil McVean
10.
Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
Sergei L. Kosakovsky Pond, Ben Murrell, and Art F.Y. Poon
Part III: Population Genomics
11.
Association Mapping and Disease: Evolutionary Perspectives
Søren Besenbacher, Thomas Mailund, and Mikkel H. Schierup
12.
Ancestral Population Genomics
Julien Y. Dutheil and Asger Hobolth
13. Non-Redundant Representation of Ancestral Recombinations Graphs
Laxmi Parida
Part IV: The "-omics"
14. Using Genomic Tools to Study Regulatory Evolution
Yoav Gilad
15. Characterization and Evolutionary Analysis of Protein-Protein Interaction Networks
Gabriel Musso, Andrew Emili, and Zhaolei Zhang
16. Statistical Methods in Metabolomics
Alexander Korman, Amy Oh, Alexander Raskind, and David Banks
17. Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN
Daniel H. Huson and Suparna Mitra
18.
Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases
Lars Feuerbach, Konstantin Halachev, Yassen Assenov, Fabian Müller, Christoph Bock, and Thomas Lengauer
19.
Genetical Genomics for Evolutionary Studies
Pjotr Prins, Geert Smant, and Ritsert C. Jansen
Part V:
Handling Genomic D
ata
: Resources and C
omputation
20. Genomics Data Resources: Frameworks and Standards
Mark D. Wilkinson
21.
Sharing Programming Resources Between Bio* Projects through Remote Procedure Call and Native Call Stack Strategies
Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter Willis, Christopher Fields, and Toshiaki Katayama
22.
Scalable Computing for Evolutionary Genomics
Pjotr Prins, Dominique Belhachemi, Steffen Möller, and Geert Smant
Klappentext
Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight. Volume 2 begins with phylogenomics and continues with in-depth coverage of natural selection, recombination, and genomic innovation. The remaining chapters treat topics of more recent interest, including population genomics, -omics studies, and computational issues related to the handling of large-scale genomic data. Written in the highly successful Methods in Molecular Biology¿ series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses.n Comprehensive and cutting-edge, Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.
Serves as an ideal reference for young and experienced researchers alike
rn
Features practical, step-by-step guidance to methodologies being used in the field
rn
Includes key implementation advice from the experts
rn
