Volume 13 Supplement 19
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
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S1
The computational prediction of Transcription Factor Binding Sites (TFBS) remains a challenge due to their short length and low information content. Comparative genomics approaches that simultaneously consider...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S2
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S3
The "small phylogeny" problem consists in inferring ancestral genomes associated with each internal node of a phylogenetic tree of a set of extant species. Existing methods can be grouped into two main categor...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S4
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 ...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S5
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S6
Mancheron, Uricaru and Rivals (Nucleic Acids Res. 39:e101, 2011) recently introduced a new approach in the context of multiple genome comparison that allows to detect regions of strong overlaps in a set of pairwi...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S7
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S8
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S9
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S10
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S11
Maximum likelihood has been widely used for over three decades to infer phylogenetic trees from molecular data. When reticulate evolutionary events occur, several genomic regions may have conflicting evolution...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S12
Computing the edit distance between two genomes under certain operations is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic resea...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S13
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,...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S14
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S15
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S16
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S17
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...
Citation: BMC Bioinformatics 2012 13(Suppl 19):S18
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