The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing,...
-
March 2016 (v1)Journal articleUploaded on: February 28, 2023
-
November 2012 (v1)Journal article
International audience
Uploaded on: February 28, 2023 -
December 2016 (v1)Journal article
Based on their small size and genomic properties, ultrasmall prokaryotic groups like the Candidate Phyla Radiation have been proposed as possible symbionts dependent on other bacteria or archaea. In this study, we use a bipartite graph analysis to examine patterns of sequence similarity between draft and complete genomes from ultrasmall...
Uploaded on: February 28, 2023 -
2010 (v1)Journal article
International audience
Uploaded on: February 28, 2023 -
2018 (v1)Journal article
Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification, and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major...
Uploaded on: December 4, 2022 -
July 6, 2019 (v1)Book section
In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and...
Uploaded on: December 4, 2022 -
November 16, 2018 (v1)Journal article
In this work, we used comparative transcriptomics to identify regulatory outliers (ROs) in the human pathogen Candida glabrata. ROs are genes that have very different expression patterns compared to their orthologs in other species. From comparative transcriptome analyses of the response of eight yeast species to toxic doses of selenite, a...
Uploaded on: December 4, 2022