Volume 14 Supplement 15

Proceedings of the Eleventh Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Proceedings

Edited by Macha Nikolski and Yves Van de Peer

Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. Articles have undergone the journal's standard peer review process for supplements. The Supplement Editors declare that they have no competing interests.

Eleventh Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics. Go to conference site.

Lyon, France

17-19 October 2013

  1. Proceedings

    The dynamics of alternative pathways to compensatory substitution

    The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have rece...

    Chris A Nasrallah

    BMC Bioinformatics 2013 14(Suppl 15):S2

    Published on: 15 October 2013

  2. Proceedings

    On the inversion-indel distance

    The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be computed thanks to a pioneering approach of Hannenhalli an...

    Eyla Willing, Simone Zaccaria, Marília DV Braga and Jens Stoye

    BMC Bioinformatics 2013 14(Suppl 15):S3

    Published on: 15 October 2013

  3. Proceedings

    Lateral gene transfer, rearrangement, reconciliation

    Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via ...

    Murray Patterson, Gergely Szöllősi, Vincent Daubin and Eric Tannier

    BMC Bioinformatics 2013 14(Suppl 15):S4

    Published on: 15 October 2013

  4. Proceedings

    Gene tree correction guided by orthology

    Reconciled gene trees yield orthology and paralogy relationships between genes. This information may however contradict other information on orthology and paralogy provided by other footprints of evolution, su...

    Manuel Lafond, Magali Semeria, Krister M Swenson, Eric Tannier and Nadia El-Mabrouk

    BMC Bioinformatics 2013 14(Suppl 15):S5

    Published on: 15 October 2013

  5. Proceedings

    Practical aliquoting of flowering plant genomes

    We pose the problem of dissecting an ancient polyploid genome into its constituent subgenomes despite fragmentation and noise caused by genome rearrangements and fractionation of multi-copy genes. We formulate...

    Chunfang Zheng and David Sankoff

    BMC Bioinformatics 2013 14(Suppl 15):S8

    Published on: 15 October 2013

  6. Proceedings

    Genome-wide probabilistic reconciliation analysis across vertebrates

    Gene duplication is considered to be a major driving force in evolution that enables the genome of a species to acquire new functions. A reconciliation - a mapping of gene tree vertices to the edges or vertice...

    Owais Mahmudi, Joel Sjöstrand, Bengt Sennblad and Jens Lagergren

    BMC Bioinformatics 2013 14(Suppl 15):S10

    Published on: 15 October 2013

  7. Proceedings

    In silico experimental evolution: a tool to test evolutionary scenarios

    Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic re...

    Bérénice Batut, David P Parsons, Stephan Fischer, Guillaume Beslon and Carole Knibbe

    BMC Bioinformatics 2013 14(Suppl 15):S11

    Published on: 15 October 2013

  8. Proceedings

    Haploid to diploid alignment for variation calling assessment

    Variation calling is the process of detecting differences between donor and consensus DNA via high-throughput sequencing read mapping. When evaluating the performance of different variation calling methods, a ...

    Veli Mäkinen and Jani Rahkola

    BMC Bioinformatics 2013 14(Suppl 15):S13

    Published on: 15 October 2013

  9. Proceedings

    Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat

    Using Next Generation Sequencing, SNP discovery is relatively easy on diploid species and still hampered in polyploid species by the confusion due to homeology. We develop HomeoSplitter; a fast and effective s...

    Vincent Ranwez, Yan Holtz, Gautier Sarah, Morgane Ardisson, Sylvain Santoni, Sylvain Glémin, Muriel Tavaud-Pirra and Jacques David

    BMC Bioinformatics 2013 14(Suppl 15):S15

    Published on: 15 October 2013

  10. Proceedings

    Finishing bacterial genome assemblies with Mix

    Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available...

    Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand-Pugnet, Florence Tardy, Christine Citti, Virginie Dupuy and Macha Nikolski

    BMC Bioinformatics 2013 14(Suppl 15):S16

    Published on: 15 October 2013

  11. Proceedings

    Reconstructing the modular recombination history of Staphylococcus aureus phages

    Viruses that infect bacteria, called phages, are well-known for their extreme mosaicism, in which an individual genome shares many different parts with many others. The mechanisms for creating these mosaics are l...

    Krister M Swenson, Paul Guertin, Hugo Deschênes and Anne Bergeron

    BMC Bioinformatics 2013 14(Suppl 15):S17

    Published on: 15 October 2013

  12. Proceedings

    Mapping proteins in the presence of paralogs using units of coevolution

    We study the problem of mapping proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protei...

    Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth and Gunnar W Klau

    BMC Bioinformatics 2013 14(Suppl 15):S18

    Published on: 15 October 2013

  13. Proceedings

    The dynamics of functional classes of plant genes in rediploidized ancient polyploids

    To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids fixed as whole genome duplicates, including patterns of re...

    Eric CH Chen, Carlos Fernando Buen Abad Najar, Chunfang Zheng, Alex Brandts, Eric Lyons, Haibao Tang, Lorenzo Carretero-Paulet, Victor A Albert and David Sankoff

    BMC Bioinformatics 2013 14(Suppl 15):S19

    Published on: 15 October 2013

  14. Proceedings

    Statistics for approximate gene clusters

    Genes occurring co-localized in multiple genomes can be strong indicators for either functional constraints on the genome organization or remnant ancestral gene order. The computational detection of these patt...

    Katharina Jahn, Sascha Winter, Jens Stoye and Sebastian Böcker

    BMC Bioinformatics 2013 14(Suppl 15):S14

    Published on: 13 December 2013