Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks
A Baud, M Wan, D Nouaud… - Peer Community …, 2022 - peercommunityjournal.org
Transposable elements (TEs) are mobile, repetitive DNA sequences that make the largest
contribution to genome bulk. They thus contribute to the so-called “dark matter of the genome”, …
contribution to genome bulk. They thus contribute to the so-called “dark matter of the genome”, …
[HTML][HTML] CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which
correspond to partial and sometimes entire viral genomes that have been captured in the …
correspond to partial and sometimes entire viral genomes that have been captured in the …
Traces of past transposable element presence in Brassicaceae genome dark matter
A Baud, M Wan, D Nouaud, D Anxolabéhère… - BioRxiv, 2019 - biorxiv.org
1 Abstract Transposable elements (TEs) are mobile, repetitive DNA sequences that have
been found in every branch of life. In many organisms TEs are the primary contributors to the …
been found in every branch of life. In many organisms TEs are the primary contributors to the …
REPET novelties: a versatile and modular package
J Confais, M Wan, S Saidi… - CNET 2023: 24th National …, 2023 - hal.science
The detection and annotation of transposable elements (TEs) are now considered
mandatory to any genome sequencing project. To this aim, the REPET package integrates …
mandatory to any genome sequencing project. To this aim, the REPET package integrates …
Transposable elements, from their annotation to their integration into knowledge graphs
J Confais, M Wan, S Saidi, N Francillonne… - … Artificielle et Text …, 2022 - hal.science
Transposable elements (TEs) are major players of structure and evolution of eukaryote
genomes. Thanks to their ability to move around and to replicate within genomes, they are …
genomes. Thanks to their ability to move around and to replicate within genomes, they are …
REPET evolutions: faster and easier
J Confais, M Wan, H Quesneville - 23rd National Congress on …, 2022 - hal.science
Transposable elements (TEs) are major players of structure and evolution of eukaryote
genomes. Thanks to their ability to move around and to replicate within genomes, they are …
genomes. Thanks to their ability to move around and to replicate within genomes, they are …
RepetDB: a unified resource for transposable element references
M Wan, N Francillonne, R Flores, F Alfama… - Journées Ouvertes en …, 2022 - hal.science
Transposable elements (TEs) are major players in the structure and evolution of eukaryote
genomes. Thanks to their ability to move around and replicate within genomes, they are …
genomes. Thanks to their ability to move around and replicate within genomes, they are …
REPET evolutions: faster and easier
WAN Mariène, J Confais, H Quesneville - Jobim 2022, 2022 - hal.science
Transposable elements (TEs) are major players of structure and evolution of eukaryote
genomes. Thanks to their ability to move around and to replicate within genomes, they are …
genomes. Thanks to their ability to move around and to replicate within genomes, they are …
REPET v3. 0
V Jamilloux, F Alfama-Depauw, J Confais, M Wan… - 2019 - hal.science
The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and
analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) …
analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) …
[CITATION][C] Parallel computations
…, E Ortie, E Penneçot, H Quesneville, M Wan - urgi.versailles.inra.fr
In this aim, we developed a specific Python module managing these tasks: launching the
jobs in parallel, tracking the errors and re-launching each job in error up to two times. Errors …
jobs in parallel, tracking the errors and re-launching each job in error up to two times. Errors …