Toby Baril
@tobybarilbio.bsky.social
Postdoc Fellow @ Uni Neuchâtel 🇨🇭 | Transposable Elements + SV, Evolution across scales | #openscience | #FirstGen | 🇬🇧🇫🇷 | Ski | Bike | Climb | Join TEsky: https://bsky.app/profile/did:plc:mw4y54k2y45j5dqxrbelwvmu/feed/aaad7mmgzkfuu
tobybaril.github.io
tobybaril.github.io
Pinned
Toby Baril
@tobybarilbio.bsky.social
· Jan 5
GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline
Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey
github.com
☕Earl Grey v7.0.0 brewed fresh☕
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
Reposted by Toby Baril
#TEsky EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis doi.org/10.1186/s128...
EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis - BMC Genomics
BMC Genomics - Transposable elements (TEs) are major components of plant genomes, shaping genome architecture, gene regulation, and evolutionary innovation. While the Extensive de novo TE Annotator...
doi.org
January 30, 2026 at 3:10 PM
#TEsky EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis doi.org/10.1186/s128...
Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics
#TEworldwide #TEsky
www.sciencedirect.com/science/arti...
#TEworldwide #TEsky
www.sciencedirect.com/science/arti...
Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics
Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…
www.sciencedirect.com
January 22, 2026 at 10:23 AM
Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics
#TEworldwide #TEsky
www.sciencedirect.com/science/arti...
#TEworldwide #TEsky
www.sciencedirect.com/science/arti...
Reposted by Toby Baril
👏 Congratulations Toby for this Current Biology dispatch!
🎨 Happy to see my watercolours in it to illustrate this so-cool topic!
#illustration #sciart #scicomm #TE #fungi #watercolours #TEworldwide
🎨 Happy to see my watercolours in it to illustrate this so-cool topic!
#illustration #sciart #scicomm #TE #fungi #watercolours #TEworldwide
🍄Transposon traffic in the mycocosmos🍄
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide
January 20, 2026 at 10:44 AM
👏 Congratulations Toby for this Current Biology dispatch!
🎨 Happy to see my watercolours in it to illustrate this so-cool topic!
#illustration #sciart #scicomm #TE #fungi #watercolours #TEworldwide
🎨 Happy to see my watercolours in it to illustrate this so-cool topic!
#illustration #sciart #scicomm #TE #fungi #watercolours #TEworldwide
Reposted by Toby Baril
I'm recruiting 1-2 grad students through the AITHYRA-CeMM PhD program! Applications are due January 30th. This is a fully-funded PhD program, combining AI and biology to advance biological discovery. Please forward to anyone who may be interested! You can apply here: apply.cemm.at
Fullfabric :: AITHYRA-CeMM PhD
apply.cemm.at
January 8, 2026 at 10:48 AM
I'm recruiting 1-2 grad students through the AITHYRA-CeMM PhD program! Applications are due January 30th. This is a fully-funded PhD program, combining AI and biology to advance biological discovery. Please forward to anyone who may be interested! You can apply here: apply.cemm.at
🍄Transposon traffic in the mycocosmos🍄
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide
January 19, 2026 at 4:38 PM
🍄Transposon traffic in the mycocosmos🍄
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide
🔥🎉 🧠 SuperThrilled to share our paper (preprint) - Human erythropoietin (rhEPO) reshapes the adult hippocampal chromatin landscape, around transposons to promote neurogenesis. 🧵1/8
Massive kudos to #UmutCakir who drove multi-omics through dark roads of the genome.
www.biorxiv.org/content/10.1...
Massive kudos to #UmutCakir who drove multi-omics through dark roads of the genome.
www.biorxiv.org/content/10.1...
January 5, 2026 at 3:13 PM
#TEsky #TEworldwide #Transposons #Bioinformatics #Bioconda #GenomeAnnotation #TransposableElements #Genomics #ComparativeGenomics
☕Earl Grey v7.0.0 brewed fresh☕
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline
Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey
github.com
January 5, 2026 at 3:12 PM
☕Earl Grey v7.0.0 brewed fresh☕
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline
Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey
github.com
January 5, 2026 at 3:10 PM
☕Earl Grey v7.0.0 brewed fresh☕
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
Reposted by Toby Baril
Transposable elements can insert into genes, disrupting protein-coding potential. Researchers discover a mode of RNA processing, ‘SOS splicing’, that provides a quick fix @nature.com @harvardmed.bsky.social
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/d41...
www.nature.com/articles/s41...
December 10, 2025 at 7:03 PM
Transposable elements can insert into genes, disrupting protein-coding potential. Researchers discover a mode of RNA processing, ‘SOS splicing’, that provides a quick fix @nature.com @harvardmed.bsky.social
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/d41...
www.nature.com/articles/s41...
TEs aren’t just genomic parasites, they’re also engines of genomic novelty.
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications
In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...
www.nature.com
November 12, 2025 at 1:17 PM
TEs aren’t just genomic parasites, they’re also engines of genomic novelty.
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Reposted by Toby Baril
Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons
Background. Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual gene...
www.biorxiv.org
November 10, 2025 at 9:21 AM
Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
Reposted by Toby Baril
#TEsky A comparative analysis of transposable element diversity and evolution across 75 bee genomes doi.org/10.1186/s128...
A comparative analysis of transposable element diversity and evolution across 75 bee genomes - BMC Genomics
Transposable elements (TEs) are repetitive DNA sequences that can alter their position and abundance within genomes. While TEs are known to have various impacts on genome structure and function, our u...
doi.org
November 6, 2025 at 1:29 PM
#TEsky A comparative analysis of transposable element diversity and evolution across 75 bee genomes doi.org/10.1186/s128...
High-Quality Genome Assembly of Diplocarpon coronariae Unveils LTR Retrotransposon-Driven Structural Dynamics in Fungi Evolution
doi.org/10.1111/1755...
#TEworldwide #TEsky
doi.org/10.1111/1755...
#TEworldwide #TEsky
High‐Quality Genome Assembly of Diplocarpon coronariae Unveils LTR Retrotransposon‐Driven Structural Dynamics in Fungi Evolution
Long terminal repeat retrotransposons (LTR-RTs) are recognised as a significant evolutionary force capable of shaping the structure and function of the genomes in eukaryotes, including animals, plant...
doi.org
November 6, 2025 at 8:27 AM
High-Quality Genome Assembly of Diplocarpon coronariae Unveils LTR Retrotransposon-Driven Structural Dynamics in Fungi Evolution
doi.org/10.1111/1755...
#TEworldwide #TEsky
doi.org/10.1111/1755...
#TEworldwide #TEsky
Had an absolute blast presenting my “Last Minute Breakthrough talk” at #EMBOmobilegenome today! 🔥 What an incredible crowd, the energy in the room was unreal. Huge thanks to the organizers for selecting me and to everyone who came, asked questions, and made it such a fun session! 🙌
November 6, 2025 at 8:26 AM
Reposted by Toby Baril
#TEsky Evolution of Mutator transposons in the genomes of worms doi.org/10.1016/j.ge...
Redirecting
doi.org
November 5, 2025 at 3:10 PM
#TEsky Evolution of Mutator transposons in the genomes of worms doi.org/10.1016/j.ge...
Reposted by Toby Baril
☕ Coffee break time at #EMBOMobileGenome!
Inspiring talks, lively discussions, and plenty of caffeine to keep the ideas flowing. The sun’s out, the conversations are buzzing, and tonight we’ll keep the networking going with rooftop lounge drinks 🍂🍁
Looking forward to an exciting week ahead! 🧬
Inspiring talks, lively discussions, and plenty of caffeine to keep the ideas flowing. The sun’s out, the conversations are buzzing, and tonight we’ll keep the networking going with rooftop lounge drinks 🍂🍁
Looking forward to an exciting week ahead! 🧬
November 4, 2025 at 4:32 PM
☕ Coffee break time at #EMBOMobileGenome!
Inspiring talks, lively discussions, and plenty of caffeine to keep the ideas flowing. The sun’s out, the conversations are buzzing, and tonight we’ll keep the networking going with rooftop lounge drinks 🍂🍁
Looking forward to an exciting week ahead! 🧬
Inspiring talks, lively discussions, and plenty of caffeine to keep the ideas flowing. The sun’s out, the conversations are buzzing, and tonight we’ll keep the networking going with rooftop lounge drinks 🍂🍁
Looking forward to an exciting week ahead! 🧬
At @embo.org #EMBOMobileGenome and want to connect with other TE researchers and follow the latest goings on?
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
November 5, 2025 at 5:14 AM
At @embo.org #EMBOMobileGenome and want to connect with other TE researchers and follow the latest goings on?
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
great to be at the #EMBOMobileGenome meeting in Heidelberg with a wonderful bunch of colleagues, speakers and attendees.
this meeting is a good reflection of the excitement and collegiality in the transposon field.
kindly sponsored by @embo.org
this meeting is a good reflection of the excitement and collegiality in the transposon field.
kindly sponsored by @embo.org
Welcome to Day 1 of 'The mobile genome: genetic and physiological impacts of transposable elements'! 🧬
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
November 4, 2025 at 8:42 PM
Time to kick off #EMBOMobileGenome for 2025! A great selection of speakers and posters on the agenda!
#TEWorldwide #TESky
#TEWorldwide #TESky
November 4, 2025 at 12:32 PM
Time to kick off #EMBOMobileGenome for 2025! A great selection of speakers and posters on the agenda!
#TEWorldwide #TESky
#TEWorldwide #TESky
Reposted by Toby Baril
Transposable elements (TEs) do more than regulate genes; they help shape and preserve 3D genome structure across species.
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Co-opted transposons help perpetuate conserved higher-order chromosomal structures
Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include binding sites for architectural proteins, such as CTCF, RAD21, and SMC3, that are involved in ...
pmc.ncbi.nlm.nih.gov
October 29, 2025 at 7:31 PM
Transposable elements (TEs) do more than regulate genes; they help shape and preserve 3D genome structure across species.
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Reposted by Toby Baril
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
October 29, 2025 at 4:32 PM
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
October 29, 2025 at 9:02 AM
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
Come and join our team! A 2-year postdoc position is available in our "Genome Evolution" department at Univ Paris Saclay. We want to play with phylogenetic models accounting for horizontal transfers of transposable elements. Application& details on the official portal: emploi.cnrs.fr/Offres/CDD/U...
October 10, 2025 at 6:54 PM
Reposted by Toby Baril
"(...) an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the hoxc12a 3' UTR. This insertion decreased hoxc12a expression & (...) also affected neighboring hox genes, resulting in variations in fin size and the presence or absence of dorsal fins."
The phenotypic variation of widefins medaka is due to the insertion of a giant transposon containing a viral genome within hoxca cluster
Abstract. Phenotypic variation in species arises from genetic differences and environmental influences on gene expression. Differences in epigenetic modifi
academic.oup.com
October 9, 2025 at 8:30 AM
"(...) an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the hoxc12a 3' UTR. This insertion decreased hoxc12a expression & (...) also affected neighboring hox genes, resulting in variations in fin size and the presence or absence of dorsal fins."