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Bernard Moret

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Related publications (57)

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How many bootstrap replicates are necessary?

Bernard Moret, Alexandros Stamatakis

Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reco ...

2010

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance

Bernard Moret, Mingfu Shao

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 ...

Mary Ann Liebert, Inc2016

A fast and exact algorithm for the exemplar breakpoint distance

Bernard Moret, Mingfu Shao

Springer2015

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

Bernard Moret, Yu Lin, Vaibhav Rajan

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, ...

Oxford University Press2012

On the DCJ Median Problem

Bernard Moret, Mingfu Shao

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 ...

Springer-Verlag Berlin2014

Refining transcriptional regulatory networks using network evolutionary models and gene histories

Bernard Moret, Xiuwei Zhang

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 ...

2010

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

Bernard Moret, Alisa Yurovsky

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 ...

IEEE Press2010

Maximum independent sets of commuting and noninterfering inversions

Bernard Moret, Krister Swenson

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 ...

2009

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

Bernard Moret, Yu Lin

Springer-Verlag2010

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

Bernard Moret, Philipp Bucher, Nishanth Ulhas Nair

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 ...

Public Library of Science2012

Bootstrapping phylogenies inferred from rearrangement data

Bernard Moret, Yu Lin, Vaibhav Rajan

Springer Verlag2011

Sorting genomes with rearrangements and segmental duplications through trajectory graphs

Bernard Moret, Yu Lin, Mingfu Shao

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. ...

Biomed Central Ltd2013

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

Bernard Moret, Philipp Bucher, Nishanth Ulhas Nair

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 ...

Oxford University Press2014

Inferring transcript phylogenies

Bernard Moret, Yann Christinat

Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals-some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite m ...

IEEE Press2011

Heuristics for the inversion median problem

Bernard Moret, Yu Lin, Krister Swenson, Vaibhav Rajan

2010

Phylogenetic reconstruction from complete gene orders of whole genomes

Bernard Moret, Krister Swenson

Imperial College Press2008

Comparing genomes with rearrangements and segmental duplications

Bernard Moret, Mingfu Shao

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 ...

Oxford University Press2015

Using phylogenetic relationships to improve the inference of transcriptional regulatory networks

Bernard Moret, Xiuwei Zhang

IEEE Computer Society2008

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

Bernard Moret, Xiuwei Zhang

Springer2008

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

Bernard Moret, Yu Lin

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 ...

Mary Ann Liebert2011