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Models and Algorithms for Genome Evolution

  • Book
  • © 2013

Overview

Editors:
  1. Cedric Chauve

    1. Department of Mathematics, Simon Fraser University, Burnaby, Canada

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    You can also search for this editor in PubMed   Google Scholar

  2. Nadia El-Mabrouk

    1. Computer Science and Operations Research, University of Montreal, Montreal, Canada

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    You can also search for this editor in PubMed   Google Scholar

  3. Eric Tannier

    1. Biometry and Evolutionary Biology, INRIA Rhône-Alpes, University of Lyon, Villeurbanne, France

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    You can also search for this editor in PubMed   Google Scholar

  • Discusses the latest developments in computational tools for complex biological datasets
  • Contains contributions from an international and interdisciplinary selection of experts
  • Provides a tribute to David Sankoff's 50 years of contributions to this field
  • Includes supplementary material: sn.pub/extras

Part of the book series: Computational Biology (COBO, volume 19)

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About this book

This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.

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Table of contents (14 chapters)

  1. Front Matter

    Pages I-XII
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  2. Emergence of Standard Algorithms

    1. Front Matter

      Pages 1-1
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    2. What’s Behind Blast

      • Gene Myers
      Pages 3-15

    3. Forty Years of Model-Based Phylogeography

      • David Bryant, Jamie Kydd
      Pages 17-28

    4. How to Infer Ancestral Genome Features by Parsimony: Dynamic Programming over an Evolutionary Tree

      • Miklós Csűrös
      Pages 29-45

    5. Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

      • Cedric Chauve, Nadia El-Mabrouk, Laurent Guéguen, Magali Semeria, Eric Tannier
      Pages 47-62

    6. The Genesis of the DCJ Formula

      • Anne Bergeron, Jens Stoye
      Pages 63-81

  3. New Lights on Current Paradigms

    1. Front Matter

      Pages 83-83
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    2. Large-Scale Multiple Sequence Alignment and Phylogeny Estimation

      • Tandy Warnow
      Pages 85-146

    3. Rearrangements in Phylogenetic Inference: Compare, Model, or Encode?

      • Bernard M. E. Moret, Yu Lin, Jijun Tang
      Pages 147-171

    4. Status of Research on Insertion and Deletion Variations in the Human Population

      • Liqing Zhang, Mingming Liu, Layne T. Watson
      Pages 173-181

    5. A Retrospective on Genomic Preprocessing for Comparative Genomics

      • Binhai Zhu
      Pages 183-206

    6. The Emperor Has No Caps! A Comparison of DCJ and Algebraic Distances

      • Joao Meidanis, Sophia Yancopoulos
      Pages 207-243

  4. Promising Directions

    1. Front Matter

      Pages 245-245
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    2. Fractionation, Rearrangement, Consolidation, Reconstruction

      • David Sankoff, Chunfang Zheng
      Pages 247-260

    3. Error Detection and Correction of Gene Trees

      • Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk
      Pages 261-285

    4. The Potential of Family-Free Genome Comparison

      • Marília D. V. Braga, Cedric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin et al.
      Pages 287-307

    5. Genetic History of Populations: Limits to Inference

      • Daniel E. Platt, Filippo Utro, Marc Pybus, Laxmi Parida
      Pages 309-323

  5. Back Matter

    Pages 325-328
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Editors and Affiliations

  • Department of Mathematics, Simon Fraser University, Burnaby, Canada

    Cedric Chauve

  • Computer Science and Operations Research, University of Montreal, Montreal, Canada

    Nadia El-Mabrouk

  • Biometry and Evolutionary Biology, INRIA Rhône-Alpes, University of Lyon, Villeurbanne, France

    Eric Tannier

About the editors

Dr. Cedric Chauve is an associate professor at the Department of Mathematics of Simon Fraser University, Canada.

Dr. Nadia El-Mabrouk is a full professor at the Computer Science Department of the University of Montreal, Canada.

Dr. Eric Tannier is a researcher at the Bioinformatics and Evolutionary Genomics Group of Inria Grenoble – Rhône-Alpes, France.

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