Volume 13 Supplement 19

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


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, Brazil

17-19 October 2012

  1. Proceedings

    On pairwise distances and median score of three genomes under DCJ

    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...

    Sergey Aganezov and Max A Alekseyev

    BMC Bioinformatics 2012 13(Suppl 19):S1

    Published on: 19 December 2012

  2. Proceedings

    Gene family assignment-free comparative genomics

    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...

    Daniel Doerr, Annelyse Thévenin and Jens Stoye

    BMC Bioinformatics 2012 13(Suppl 19):S3

    Published on: 19 December 2012

  3. Proceedings

    Medians seek the corners, and other conjectures

    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 ...

    Maryam Haghighi and David Sankoff

    BMC Bioinformatics 2012 13(Suppl 19):S5

    Published on: 19 December 2012

  4. Proceedings

    From event-labeled gene trees to species trees

    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...

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

    BMC Bioinformatics 2012 13(Suppl 19):S6

    Published on: 19 December 2012

  5. Proceedings

    Reconstructing genome mixtures from partial adjacencies

    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...

    Ahmad Mahmoody, Crystal L Kahn and Benjamin J Raphael

    BMC Bioinformatics 2012 13(Suppl 19):S9

    Published on: 19 December 2012

  6. Proceedings

    Compareads: comparing huge metagenomic experiments

    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...

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

    BMC Bioinformatics 2012 13(Suppl 19):S10

    Published on: 19 December 2012

  7. Proceedings

    Linearization of ancestral multichromosomal genomes

    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...

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

    BMC Bioinformatics 2012 13(Suppl 19):S11

    Published on: 19 December 2012

  8. Proceedings

    Restricted DCJ-indel model: sorting linear genomes with DCJ and indels

    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,...

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

    BMC Bioinformatics 2012 13(Suppl 19):S14

    Published on: 19 December 2012

  9. Proceedings

    Gene trees and species trees: irreconcilable differences

    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...

    Krister M Swenson and Nadia El-Mabrouk

    BMC Bioinformatics 2012 13(Suppl 19):S15

    Published on: 19 December 2012

  10. Proceedings

    A graph-theoretic approach for inparalog detection

    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...

    Olivier Tremblay-Savard and Krister M Swenson

    BMC Bioinformatics 2012 13(Suppl 19):S16

    Published on: 19 December 2012

  11. Proceedings

    ARG-based genome-wide analysis of cacao cultivars

    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...

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

    BMC Bioinformatics 2012 13(Suppl 19):S17

    Published on: 19 December 2012

  12. Proceedings

    TIGER: tiled iterative genome assembler

    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...

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

    BMC Bioinformatics 2012 13(Suppl 19):S18

    Published on: 19 December 2012