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E-raamat: Evolutionary Genomics: Statistical and Computational Methods, Volume 1

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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 1 includes a helpful introductory section of bioinformatician primers followed by detailed chapters detailing genomic data assembly, alignment, and homology inference as well as insights into genome evolution from statistical analyses.  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.
Preface v
Contributors xiii
PART I INTRODUCTION: BIOINFORMATICIAN'S PRIMERS
1 Introduction to Genome Biology: Features, Processes, and Structures
3(48)
Aidan Budd
2 Diversity of Genome Organisation
51(26)
Aidan Budd
3 Probability, Statistics, and Computational Science
77(34)
Niko Beerenwinkel
Juliane Siebourg
4 The Essentials of Computational Molecular Evolution
111(44)
Stephane Aris-Brosou
Nicolas Rodrigue
PART II GENOMIC DATA ASSEMBLY, ALIGNMENT, AND HOMOLOGY INFERENCE
5 Next-Generation Sequencing Technologies and Fragment Assembly Algorithms
155(20)
Heewook Lee
Haixu Tang
6 Gene Prediction
175(28)
Tyler Alioto
7 Alignment Methods: Strategies, Challenges, Benchmarking, and Comparative Overview
203(34)
Ari Loytynoja
8 Whole-Genome Alignment
237(22)
Colin N. Dewey
9 Inferring Orthology and Paralogy
259(22)
Adrian M. Altenhoff
Christophe Dessimoz
10 Detecting Laterally Transferred Genes
281(30)
Rajeev K. Azad
Jeffrey G. Lawrence
PART III GENOME EVOLUTION: INSIGHTS FROM STATISTICAL ANALYSES
11 Genome Evolution in Outcrossing Versus Selfing Versus Asexual Species
311(26)
Sylvain Glemin
Nicolas Galtier
12 Transposable Elements and Their Identification
337(24)
Wojciech Makalowski
Amit Pande
Valer Gotea
Izabela Makalowska
13 Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans
361(24)
Josefa Gonzalez
Dmitri A. Petrov
14 Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications
385(12)
Shigehiro Kuraku
Axel Meyer
15 Analysis of Gene Order Evolution Beyond Single-Copy Genes
397(34)
Nadia El-Mabrouk
David Sankoff
16 Discovering Patterns in Gene Order
431(26)
Laxmi Parida
Niina Haiminen
Index 457