Publications de Bernard Moret | EPFL Graph Search

Inferring transcript phylogenies

BioMed Central2012

Bootstrapping phylogenies inferred from rearrangement data

Background: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have be ...

BioMed Central2012

Refining Regulatory Networks through Phylogenetic Transfer of Information

Bernard Moret, Xiuwei Zhang

The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while computational methods to infer these networks provide only modest accuracy. The latter can be attributed partly to the limit ...

2012

A Metric for Phylogenetic Trees Based on Matching

Bernard Moret, Vaibhav Rajan, Yu Lin

Comparing two or more phylogenetic trees is a fundamental task in computational biology. The simplest outcome of such a comparison is a pairwise measure of similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so f ...

2012

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

Bernard Moret, Vaibhav Rajan, Yu Lin

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

A transcript perspective on evolution

Yann Christinat, Bernard Moret

Springer Verlag2012

Inferring transcript phylogenies

Yann Christinat, Bernard Moret

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

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

Phylogenetic Analysis of Whole Genomes

Bernard Moret

Springer-Verlag2011

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

Bernard Moret, Alisa Yurovsky

BioMed Central2011

Bootstrapping phylogenies inferred from rearrangement data

Bernard Moret, Vaibhav Rajan, Yu Lin

Springer Verlag2011

GASTS: Parsimony scoring under rearrangements

Bernard Moret, Wei Xu

Springer Verlag2011

ProPhyC: a probabilistic phylogenetic model for refining regulatory networks

Bernard Moret, Xiuwei Zhang

The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while computational methods to infer these networks provide only modest accuracy. The latter can be attributed in part to the limi ...

Springer Verlag2011

A metric for phylogenetic trees based on matching

Bernard Moret, Vaibhav Rajan, Yu Lin

Comparing two or more phylogenetic trees is a fundamental task in computational biology. The simplest outcome of such a comparison is a pairwise measure of similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so t ...

Springer Verlag2011

Uncovering hidden phylogenetic consensus in large datasets

Bernard Moret, Alexandros Stamatakis, Krister Swenson

Institute of Electrical and Electronics Engineers2011

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Vaibhav Rajan, Yu Lin

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...

2011

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Vaibhav Rajan, Yu Lin

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...

Springer2010

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

Bernard Moret, Yu Lin

Springer-Verlag2010

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

Sorting signed permutations by inversions in O(nlogn) time

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin

The study of genomic inversions (or reversals) has been a mainstay of computational genomics for nearly 20 years. After the initial breakthrough of Hannenhalli and Pevzner, who gave the first polynomial-time algorithm for sorting signed permutations by inv ...

2010