Publications de Bernard Moret | EPFL Graph Search

Chattez avec Graph Search

Posez n’importe quelle question sur les cours, conférences, exercices, recherches, actualités, etc. de l’EPFL ou essayez les exemples de questions ci-dessous.

AVERTISSEMENT : Le chatbot Graph n'est pas programmé pour fournir des réponses explicites ou catégoriques à vos questions. Il transforme plutôt vos questions en demandes API qui sont distribuées aux différents services informatiques officiellement administrés par l'EPFL. Son but est uniquement de collecter et de recommander des références pertinentes à des contenus que vous pouvez explorer pour vous aider à répondre à vos questions.

A fundamental problem in comparative genomics is to compute the distance between two genomes. For two genomes without duplicate genes, we can easily compute a variety of distance measures in linear time, but the problem is NP-hard under most models when ge ...

TIBA is a tool to reconstruct phylogenetic trees from rearrangement data that consist of ordered lists of synteny blocks (or genes), where each synteny block is shared with all of its homologues in the input genomes. The evolution of these synteny blocks, ...

As many whole genomes are sequenced, comparative genomics is moving from pairwise comparisons to multiway comparisons framed within a phylogenetic tree. A central problem in this process is the inference of data for internal nodes of the tree from data giv ...

Background: Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present evolutionary approaches to improve the inference of regulatory networks for ...

Background: Reassortments are events in the evolution of the genome of influenza (flu), whereby segments of the genome are exchanged between different strains. As reassortments have been implicated in major human pandemics of the last century, their identi ...

Background: Given three signed permutations, an inversion median is a fourth permutation that minimizes the sum of the pairwise inversion distances between it and the three others. This problem is NP-hard as well as hard to approximate. Yet median-based ap ...

The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit diff ...

We study the problem of sorting genomes under an evolutionary model that includes genomic rearrangements and segmental duplications. We propose an iterative algorithm to improve any initial evolutionary trajectory between two genomes in terms of parsimony. ...

Motivation: We have witnessed an enormous increase in ChIP-Seq data for histone modifications in the past few years. Discovering significant patterns in these data is an important problem for understanding biological mechanisms. Results: We propose probabi ...

Motivation: Large-scale evolutionary events such as genomic rearrange. ments and segmental duplications form an important part of the evolution of genomes and are widely studied from both biological and computational perspectives. A basic computational pro ...

Genomic rearrangements have been studied since the beginnings of modern genetics and models for such rearrangements have been the subject of many papers over the last 10 years. However, none of the extant models can predict the evolution of genomic organiz ...

Background: Reconstructing complete ancestral genomes (at least in terms of their gene inventory and arrangement) is attracting much interest due to the rapidly increasing availability of whole genome sequences. While modest successes have been reported fo ...

Bernard Moret

Chattez avec Graph Search

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

On the DCJ Median Problem

Refining transcriptional regulatory networks using network evolutionary models and gene histories

FluReF, an automated flu virus reassortment finder based on phylogenetic trees

Maximum independent sets of commuting and noninterfering inversions

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes

ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries

Sorting genomes with rearrangements and segmental duplications through trajectory graphs

Probabilistic partitioning methods to find significant patterns in ChIP-Seq data

Heuristics for the inversion median problem

Phylogenetic reconstruction from complete gene orders of whole genomes

Comparing genomes with rearrangements and segmental duplications

Using phylogenetic relationships to improve the inference of transcriptional regulatory networks

Boosting the performance of inference algorithms for transcriptional regulatory networks using a phylogenetic approach

A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes

Estimating true evolutionary distances under rearrangements, duplications, and losses

Phylogenetic Analysis of Cell Types Using Histone Modifications

An exact algorithm to compute the DCJ distance for genomes with duplicate genes

Inversion-based genomic signatures