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Volume 13 Supplement 19

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

Proceedings

Edited by Mathieu Banchette, Marilia D V Braga and Marie-France Sagot

This supplement has not been supported by sponsorship or other external funding.

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

Niteroi, Brazil17-19 October 2012

  1. In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evo...

    Authors: Sergey Aganezov Jr and Max A Alekseyev

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S1

    Content type: Proceedings

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  3. The comparison of relative gene orders between two genomes offers deep insights into functional correlations of genes and the evolutionary relationships between the corresponding organisms. Methods for gene or...

    Authors: Daniel Doerr, Annelyse Thévenin and Jens Stoye

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S3

    Content type: Proceedings

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  5. Median construction is at the heart of several approaches to gene-order phylogeny. It has been observed that the solution to a median problem is generally not unique, and that alternate solutions may be quite ...

    Authors: Maryam Haghighi and David Sankoff

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S5

    Content type: Proceedings

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  6. Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is k...

    Authors: Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T Huber, Vincent Moulton and Peter F Stadler

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S6

    Content type: Proceedings

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  8. It has recently been shown that fractionation, the random loss of excess gene copies after a whole genome duplication event, is a major cause of gene order disruption. When estimating evolutionary distances be...

    Authors: Katharina Jahn, Chunfang Zheng, Jakub Kováč and David Sankoff

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S8

    Content type: Proceedings

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  9. Many cancer genome sequencing efforts are underway with the goal of identifying the somatic mutations that drive cancer progression. A major difficulty in these studies is that tumors are typically heterogeneo...

    Authors: Ahmad Mahmoody, Crystal L Kahn and Benjamin J Raphael

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S9

    Content type: Proceedings

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  10. Nowadays, metagenomic sample analyses are mainly achieved by comparing them with a priori knowledge stored in data banks. While powerful, such approaches do not allow to exploit unknown and/or "unculturable" spec...

    Authors: Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier and Pierre Peterlongo

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S10

    Content type: Proceedings

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  11. Recovering the structure of ancestral genomes can be formalized in terms of properties of binary matrices such as the Consecutive-Ones Property (C1P). The Linearization Problem asks to extract, from a given binar...

    Authors: Ján Maňuch, Murray Patterson, Roland Wittler, Cedric Chauve and Eric Tannier

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S11

    Content type: Proceedings

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  14. The double-cut-and-join (DCJ) is a model that is able to efficiently sort a genome into another, generalizing the typical mutations (inversions, fusions, fissions, translocations) to which genomes are subject,...

    Authors: Poly H da Silva, Raphael Machado, Simone Dantas and Marília DV Braga

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S14

    Content type: Proceedings

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  15. Reconciliation is the classical method for inferring a duplication and loss history from a set of extant genes. It is based upon the notion of embedding the gene tree into the species tree, the incongruence be...

    Authors: Krister M Swenson and Nadia El-Mabrouk

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S15

    Content type: Proceedings

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  16. Understanding the history of a gene family that evolves through duplication, speciation, and loss is a fundamental problem in comparative genomics. Features such as function, position, and structural similarit...

    Authors: Olivier Tremblay-Savard and Krister M Swenson

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S16

    Content type: Proceedings

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  17. Ancestral recombinations graph (ARG) is a topological structure that captures the relationship between the extant genomic sequences in terms of genetic events including recombinations. IRiS is a system that es...

    Authors: Filippo Utro, Omar Eduardo Cornejo, Donald Livingstone, Juan Carlos Motamayor and Laxmi Parida

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S17

    Content type: Proceedings

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  18. With the cost reduction of the next-generation sequencing (NGS) technologies, genomics has provided us with an unprecedented opportunity to understand fundamental questions in biology and elucidate human disea...

    Authors: Xiao-Long Wu, Yun Heo, Izzat El Hajj, Wen-Mei Hwu, Deming Chen and Jian Ma

    Citation: BMC Bioinformatics 2012 13(Suppl 19):S18

    Content type: Proceedings

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