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Comparative Genomics

International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009, Proceedings

  • Conference proceedings
  • © 2009

Overview

Editors:
  1. Francesca D. Ciccarelli

    1. European Institute of oncology, IFOM-IEO Campus,, Milan, Italy

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    You can also search for this editor in PubMed   Google Scholar

  2. István Miklós

    1. Rényi Institute, Hungarian Academy of Sciences, Budapest, Hungary

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    You can also search for this editor in PubMed   Google Scholar

Part of the book series: Lecture Notes in Computer Science (LNCS, volume 5817)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: RECOMB-CG 2009.

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Table of contents (19 papers)

  1. Front Matter

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  2. Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods

    • Eric Tannier
    Pages 1-12

  3. Natural Parameter Values for Generalized Gene Adjacency

    • Zhenyu Yang, David Sankoff
    Pages 13-23

  4. Parking Functions, Labeled Trees and DCJ Sorting Scenarios

    • Aïda Ouangraoua, Anne Bergeron
    Pages 24-35

  5. Counting All DCJ Sorting Scenarios

    • Marília D. V. Braga, Jens Stoye
    Pages 36-47

  6. Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction

    • Cedric Chauve, Utz-Uwe Haus, Tamon Stephen, Vivija P. You
    Pages 48-58

  7. Finding Nested Common Intervals Efficiently

    • Guillaume Blin, Jens Stoye
    Pages 59-69

  8. DCJ Median Problems on Linear Multichromosomal Genomes: Graph Representation and Fast Exact Solutions

    • Andrew Wei Xu
    Pages 70-83

  9. Rearrangement Models and Single-Cut Operations

    • Paul Medvedev, Jens Stoye
    Pages 84-97

  10. Aligning Two Genomic Sequences That Contain Duplications

    • Minmei Hou, Cathy Riemer, Piotr Berman, Ross C. Hardison, Webb Miller
    Pages 98-110

  11. Inferring the Recent Duplication History of a Gene Cluster

    • Giltae Song, Louxin Zhang, Tomáš Vinař, Webb Miller
    Pages 111-125

  12. Pseudo Boolean Programming for Partially Ordered Genomes

    • Sébastien Angibaud, Guillaume Fertin, Annelyse Thévenin, Stéphane Vialette
    Pages 126-137

  13. Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes Using Pseudo-Boolean Optimization

    • João Delgado, Inês Lynce, Vasco Manquinho
    Pages 138-149

  14. Reconstructing Histories of Complex Gene Clusters on a Phylogeny

    • Tomáš Vinař, Broňa Brejová, Giltae Song, Adam Siepel
    Pages 150-163

  15. Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples

    • Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin
    Pages 164-180

  16. Whole-Genome Analysis of Gene Conversion Events

    • Chih-Hao Hsu, Yu Zhang, Ross Hardison, Webb Miller
    Pages 181-192

  17. A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances

    • Zaky Adam, David Sankoff
    Pages 193-204

  18. Comparative Genomics and Extensive Recombinations in Phage Communities

    • Guylaine Poisson, Mahdi Belcaid, Anne Bergeron
    Pages 205-216

  19. Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana

    • Dale N. Richardson, Thomas Wiehe
    Pages 217-228

  20. Transcription Factor Binding Probabilities in Orthologous Promoters: An Alignment-Free Approach to the Inference of Functional Regulatory Targets

    • Xiao Liu, Neil D. Clarke
    Pages 229-240
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Other volumes

  1. Comparative Genomics

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About this book

As genome-sequencing costs continue their downward spiral, sequencing of closely related organisms has become increasingly a?ordable. The growing amount of genomic data available demands for the constant development of computational tools to be applied in comparative genomics. The RECOMB Workshop on C- parative Genomics (RECOMB-CG) is devoted to bringing together scientists working on all aspects of comparative genomics, from computer scientists, ma- ematicians and statisticians working on novel computational approaches for genome analysis and comparison, to biologists applying these computational tools to study the structure and the evolution of prokaryotic and eukaryotic genomes. This volume contains the 19 papers presented at the 7th Annual RECOMB-CG workshop held during September 27–29, 2009 at the Renyi Institute, in Budapest, Hungary. The papers published in these proceedings were selected for oral p- sentation from 31 submissions from scientists around the world. Each paper was reviewed by at least three members of the Program Committee in a stringent and thoughtful peer-review process.

Editors and Affiliations

  • European Institute of oncology, IFOM-IEO Campus,, Milan, Italy

    Francesca D. Ciccarelli

  • Rényi Institute, Hungarian Academy of Sciences, Budapest, Hungary

    István Miklós

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