Clément Goubert
@clementgoubert.bsky.social
🤘🧬 Transposable
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Elements 🧬🤘
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Assistant Research Professor @wheelerlab.org
University of Arizona
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Elements 🧬🤘
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Assistant Research Professor @wheelerlab.org
University of Arizona
Pinned
https://www.nature.com/articles/s41467-024-53294-2
t.co
🎉 Our #GraffiTE paper is out!!! t.co/TmoSL3WQ1P If you are interested in #Transposon insertion polymorphism, this is for you!
Yummy! www.cell.com/current-biol...
Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation
Using a unique longitudinal sampling approach, Louw et al. demonstrate how a cheese-associated
Penicillium population has adapted in an artisan cheese production facility in Vermont,
USA. Adaptation i...
www.cell.com
September 15, 2025 at 7:35 PM
Yummy! www.cell.com/current-biol...
Rapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defence journals.plos.org/plosgenetics...
Rapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defence
Author summary Transposable elements (TEs) are short, self-replicating DNA sequences found in nearly all genomes. While they can be harmful to their hosts, many organisms have evolved defence systems,...
journals.plos.org
August 28, 2025 at 4:01 PM
Rapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defence journals.plos.org/plosgenetics...
A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes -- by the excellent @valentinapeona.bsky.social link.springer.com/protocol/10....
A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes
Transposable elements (TEs) can play a huge role in shaping the structure and evolution of genes and genomes, but it can be difficult, especially in non-model organisms, to confidently characterize th...
link.springer.com
August 26, 2025 at 4:12 PM
A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes -- by the excellent @valentinapeona.bsky.social link.springer.com/protocol/10....
Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties
Transposable elements are genetic parasites whose mobilization throughout the genome is a major source of deleterious mutations. However, some TE insertions are beneficial because they improve host fi...
www.biorxiv.org
July 25, 2025 at 4:55 PM
Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
How the complex issue of delineating #Transposons families plays out in the interpretation of epigenetic experiments. Congrats Xun Chen and @guilbourque.bsky.social for leading this work, and thank you for having me on this! www.science.org/doi/10.1126/... #TEsky
A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage
A phylogenetic approach reveals cryptic LTR subfamilies and functional insights at nucleotide resolution in primates.
www.science.org
July 23, 2025 at 5:22 PM
How the complex issue of delineating #Transposons families plays out in the interpretation of epigenetic experiments. Congrats Xun Chen and @guilbourque.bsky.social for leading this work, and thank you for having me on this! www.science.org/doi/10.1126/... #TEsky
Challenging the TE burst hypothesis in the adaptive radiation of Galápagos Asteraceae trees (Scalesia) with @naturalselection.bsky.social and team!
mobilednajournal.biomedcentral.com/articles/10....
mobilednajournal.biomedcentral.com/articles/10....
No evidence of transposable element bursts in the Galápagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts - Mobile DNA
Transposable elements (TEs) have been hypothesized to play a pivotal role in driving diversification by facilitating the emergence of novel phenotypes and the accumulation of divergence between specie...
mobilednajournal.biomedcentral.com
June 2, 2025 at 3:29 PM
Challenging the TE burst hypothesis in the adaptive radiation of Galápagos Asteraceae trees (Scalesia) with @naturalselection.bsky.social and team!
mobilednajournal.biomedcentral.com/articles/10....
mobilednajournal.biomedcentral.com/articles/10....
Waho this is impressive: github.com/zeqianli/tgv
GitHub - zeqianli/tgv: Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion.
Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion. - zeqianli/tgv
github.com
May 27, 2025 at 10:30 PM
Waho this is impressive: github.com/zeqianli/tgv
Reposted by Clément Goubert
New genomic & genetic insights into Mendel’s pea genes, including previously uncharacterised alleles
159 years after Mendel published his work, this is a real delight (especially for a geneticist)
🧪
@nature.com
www.nature.com/articles/s41...
159 years after Mendel published his work, this is a real delight (especially for a geneticist)
🧪
@nature.com
www.nature.com/articles/s41...
Genomic and genetic insights into Mendel’s pea genes - Nature
Characterization of the genetic architecture underlying the 7 pairs of contrasting traits studied by Mendel and the over 70 additional agronomic traits in pea (Pisum sativum) reveals their m...
www.nature.com
April 24, 2025 at 5:38 AM
New genomic & genetic insights into Mendel’s pea genes, including previously uncharacterised alleles
159 years after Mendel published his work, this is a real delight (especially for a geneticist)
🧪
@nature.com
www.nature.com/articles/s41...
159 years after Mendel published his work, this is a real delight (especially for a geneticist)
🧪
@nature.com
www.nature.com/articles/s41...
Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin www.biorxiv.org/content/10.1...
www.biorxiv.org
April 29, 2025 at 3:57 PM
Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin www.biorxiv.org/content/10.1...
Reposted by Clément Goubert
🧬🖥️
Thanks to Evangelos Karatzas at @ebi.embl.org, our _nail_ software for fast and sensitive protein sequence search
is now available as an @nf-co.re module (nf-co.re/modules/nail...)
(crates.io/crates/nail, github.com/TravisWheele...)
Thanks Evangelos!
Thanks to Evangelos Karatzas at @ebi.embl.org, our _nail_ software for fast and sensitive protein sequence search
is now available as an @nf-co.re module (nf-co.re/modules/nail...)
(crates.io/crates/nail, github.com/TravisWheele...)
Thanks Evangelos!
April 22, 2025 at 10:29 PM
🧬🖥️
Thanks to Evangelos Karatzas at @ebi.embl.org, our _nail_ software for fast and sensitive protein sequence search
is now available as an @nf-co.re module (nf-co.re/modules/nail...)
(crates.io/crates/nail, github.com/TravisWheele...)
Thanks Evangelos!
Thanks to Evangelos Karatzas at @ebi.embl.org, our _nail_ software for fast and sensitive protein sequence search
is now available as an @nf-co.re module (nf-co.re/modules/nail...)
(crates.io/crates/nail, github.com/TravisWheele...)
Thanks Evangelos!
Reposted by Clément Goubert
The writing’s been on the wall for a while, and in case anyone was unaware: YOUR GENOMIC DATA IS THE MOST VALUABLE ASSET THEY HAVE LEFT.
Delete your data. Make sure you opt-out of any opt-outable options.
Tell your friends and family - you know that technophobe cousin missed the memo. 🧪
Delete your data. Make sure you opt-out of any opt-outable options.
Tell your friends and family - you know that technophobe cousin missed the memo. 🧪
Column | Delete your DNA from 23andMe right now
The genetic information company declared bankruptcy on Sunday, and California’s attorney general has issued a privacy “consumer alert.”
www.washingtonpost.com
March 24, 2025 at 7:36 PM
The writing’s been on the wall for a while, and in case anyone was unaware: YOUR GENOMIC DATA IS THE MOST VALUABLE ASSET THEY HAVE LEFT.
Delete your data. Make sure you opt-out of any opt-outable options.
Tell your friends and family - you know that technophobe cousin missed the memo. 🧪
Delete your data. Make sure you opt-out of any opt-outable options.
Tell your friends and family - you know that technophobe cousin missed the memo. 🧪
Polymorphic transposable elements contribute to variation in recombination landscapes (drosohila 🪰) www.pnas.org/doi/full/10.... #TEsky
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
March 24, 2025 at 9:01 PM
Polymorphic transposable elements contribute to variation in recombination landscapes (drosohila 🪰) www.pnas.org/doi/full/10.... #TEsky
Rapid emergence of hyperparasitic elements may stop P-element invasions in the absence of a piRNA-based host defence www.biorxiv.org/content/10.1...
Rapid emergence of hyperparasitic elements may stop P-element invasions in the absence of a piRNA-based host defence
Transposable element (TE) invasions pose risks to both the TE and the host. All copies of a TE may be lost via genetic drift, or host populations may suffer fitness declines, potentially leading to ex...
www.biorxiv.org
March 19, 2025 at 7:35 PM
Rapid emergence of hyperparasitic elements may stop P-element invasions in the absence of a piRNA-based host defence www.biorxiv.org/content/10.1...
#Transposons are just the best!
Cool study! Plant defense usually means looking 'not-diseased,' making these genes invisible until lost. But here, the authors found that a 254bp transposon in bHLH35 boosts anthocyanins, visually camouflaging the plant from herbivores. A defense you can see!
Multi-omics analysis reveals that a 254-bp transposon induces defensive camouflage in an alpine plant and reduces herbivory by caterpillars of a specialist butterfly. Protective effects of this camouflage are reflected in the long-term dynamics of co-evolving plant and butterfly populations.
March 12, 2025 at 9:15 PM
#Transposons are just the best!
Reposted by Clément Goubert
Here, we demonstrate that Starships, a newly discovered group of cargo-mobilizing transposable elements, are active vectors of horizontally transferred DNA among eukaryotic species.
March 12, 2025 at 9:21 AM
Here, we demonstrate that Starships, a newly discovered group of cargo-mobilizing transposable elements, are active vectors of horizontally transferred DNA among eukaryotic species.
DFAM (database of transposable elements) 3.9 is out! A lot of cool new stuff and a special update for Drosophila melanogaster... 1/2 #Transposon #DFAM
Today we released Dfam 3.9 with many new community submissions and the result of a thorough curation and update of the Drosophila Melanogaster library. www.dfam.org (release notes: www.dfam.org/releases/Dfa...)
Dfam
Open database of transposable elements and repetitive DNA families
www.dfam.org
March 10, 2025 at 9:20 PM
DFAM (database of transposable elements) 3.9 is out! A lot of cool new stuff and a special update for Drosophila melanogaster... 1/2 #Transposon #DFAM
Cool stuff from the Trono lab, as usual! Zinc-finger proteins with a co-opted capsid domain
anchor nucleosomes over transposon sequences www.biorxiv.org/content/10.1...
anchor nucleosomes over transposon sequences www.biorxiv.org/content/10.1...
www.biorxiv.org
March 7, 2025 at 7:33 PM
Cool stuff from the Trono lab, as usual! Zinc-finger proteins with a co-opted capsid domain
anchor nucleosomes over transposon sequences www.biorxiv.org/content/10.1...
anchor nucleosomes over transposon sequences www.biorxiv.org/content/10.1...
Reposted by Clément Goubert
LOCATE: using Long-read to Characterize All Transposable Elements
doi.org/10.1101/2025...
Mapping-based Genome Size Estimation
doi.org/10.1101/607390
#Genomics #Bioinformatics #OpenScience
doi.org/10.1101/2025...
Mapping-based Genome Size Estimation
doi.org/10.1101/607390
#Genomics #Bioinformatics #OpenScience
LOCATE: using Long-read to Characterize All Transposable Elements
Transposons constitute ~45% of the human genome, driving gene evolution and contributing to disease, but their repetitive nature complicates the identification of new insertions. We present LOCATE (Lo...
doi.org
March 3, 2025 at 5:58 AM
LOCATE: using Long-read to Characterize All Transposable Elements
doi.org/10.1101/2025...
Mapping-based Genome Size Estimation
doi.org/10.1101/607390
#Genomics #Bioinformatics #OpenScience
doi.org/10.1101/2025...
Mapping-based Genome Size Estimation
doi.org/10.1101/607390
#Genomics #Bioinformatics #OpenScience
Reposted by Clément Goubert
Do you want to annotate your #pangenome graph and its embedded genome ? Then GrAnnoT is for you !
🖥️🧬 🧪
In the present paper, our PhD student Nina Marthe developed a Python tool, a user friendly one, that allows to
1/5
www.biorxiv.org/content/10.1...
🖥️🧬 🧪
In the present paper, our PhD student Nina Marthe developed a Python tool, a user friendly one, that allows to
1/5
www.biorxiv.org/content/10.1...
www.biorxiv.org
March 3, 2025 at 9:51 AM
Do you want to annotate your #pangenome graph and its embedded genome ? Then GrAnnoT is for you !
🖥️🧬 🧪
In the present paper, our PhD student Nina Marthe developed a Python tool, a user friendly one, that allows to
1/5
www.biorxiv.org/content/10.1...
🖥️🧬 🧪
In the present paper, our PhD student Nina Marthe developed a Python tool, a user friendly one, that allows to
1/5
www.biorxiv.org/content/10.1...
RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells - Nature Genetics
The N6-methyladenosine reader YTHDC2 recruits TET1 to remove 5-methylcytosine from LTR7/HERV-H loci in human embryonic stem cells. The YTHDC2/LTR7 pathway inhibits neural fate commitment.
www.nature.com
February 24, 2025 at 5:22 PM
RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Very promising approach to characterize the mobilome in pangenomes from ! I wonder how this compares/complements to Pantera (@piosierra.bsky.social) and GraffiTE www.biorxiv.org/content/10.1... #TESky #SV #Pangenomes
Pannagram: unbiased pangenome alignment and the Mobilome calling
Pannagram is a toolkit for unbiased pangenome alignment and Mobilome detection based on full-genome assemblies. It consists of two components: a command-line interface for performing the multiple geno...
www.biorxiv.org
February 18, 2025 at 5:52 PM
Very promising approach to characterize the mobilome in pangenomes from ! I wonder how this compares/complements to Pantera (@piosierra.bsky.social) and GraffiTE www.biorxiv.org/content/10.1... #TESky #SV #Pangenomes
Highly recommend!
We are recruiting a Bioinformatics PostDoctoral Research to join our team @ibb-botanic.bsky.social @csic.es. Reach out if you have questions! #transposons #Drosophila
bioinformaticsbarcelona.eu/job/bioinfor...
bioinformaticsbarcelona.eu/job/bioinfor...
Bioinformatics Postdoctoral Researcher - Bioinformatics Barcelona
bioinformaticsbarcelona.eu
January 27, 2025 at 4:52 PM
Highly recommend!