Cecile Lorrain
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ccilelorrain.bsky.social
Cecile Lorrain
@ccilelorrain.bsky.social
200 followers 270 following 9 posts
SNSF Ambizione Fellow | Junior PI in Plant Pathology @ ETH Zürich | Specializing in fungal genome architecture & TE-driven evolution
lorrainlab.owlstown.net
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Reposted by Cecile Lorrain
nature.com
Nature research paper: Specificity, length and luck drive gene rankings in association studies

go.nature.com/47Fsqax
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
go.nature.com
November 10, 2025 at 11:36 AM
Reposted by Cecile Lorrain
natplants.nature.com
New OA Article: "Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana" rdcu.be/ePaOY

GWAS identifies CDCA7 as a regulator of DNA methylation in Arabidopsis thaliana . CDCA7 binds the chromatin remodeller DDM1 and modulates the control of CG methylation.
November 10, 2025 at 1:23 PM
Reposted by Cecile Lorrain
elife.bsky.social
Lifestyles shape genome size and gene content in fungal pathogens.
buff.ly/tec1Tds
Genomic traits associated with pathogenicity.
November 2, 2025 at 11:01 AM
Reposted by Cecile Lorrain
pascal-frey.bsky.social
Packed room for Emma Corre's PhD defense on transposable elements in rust fungi genomes.
Congratulations Dr @emma--c.bsky.social 👏👏👏

And what a lovely tribute to Barbara McClintock who discovered transposable elements in 🌽!!!
October 31, 2025 at 11:28 PM
Reposted by Cecile Lorrain
signor-molevol.bsky.social
My awesome grad student Shashank and I wrote this paper trying to look at broader patterns of HT in TEs. HT is happening everywhere! DNA transposons jump further than other classes! www.biorxiv.org/content/10.1...
Recent horizontal transfer of transposable elements in Drosophila
Transposable elements (TEs) are genetic elements also known as "jumping genes" that increase their copy numbers within a host through various mechanisms of transposition. TEs can also move between spe...
www.biorxiv.org
October 31, 2025 at 3:58 PM
Reposted by Cecile Lorrain
jgahan.bsky.social
Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!
Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates
Nature Communications - Here, the authors investigate chromatin-based gene regulation in the closest relative of animal, choanoflagellates. They uncover a putative dual role for the histone...
rdcu.be
October 29, 2025 at 1:40 PM
Reposted by Cecile Lorrain
epigenometech.bsky.social
Epigenetics Update - RNA m6A regulates the transcription and heterochromatin state of retrotransposons in Arabidopsis go.nature.com/47jvfiF

Guifang Jia (Peking University) in Nat Plants
#Epigenetics #Plants #Chromatin

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Empower your research with high-res epigenetic insight at epigenometech.com
October 28, 2025 at 1:01 PM
Reposted by Cecile Lorrain
tobybarilbio.bsky.social
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...
October 29, 2025 at 9:02 AM
Reposted by Cecile Lorrain
michaelhabig.bsky.social
Want to understand how entire fungal chromosomes can be horizontally transferred?
Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available.
fungal-evolutionary-genetics.de/open-positio...
Open Positions
ERC-funded project on the mechanism of horizontal transfer of entire fungal chromosomes PhD PostDoc
fungal-evolutionary-genetics.de
October 13, 2025 at 9:39 AM
Reposted by Cecile Lorrain
lkremer1.bsky.social
Thrilled to share our most recent paper describing the antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular mycobacteria in macrophages and zebrafish. Outstanding work headed by Yara Tasrini, John Jairo Aguilera Correa, Miguel Gisbert and others.
rdcu.be/eAcN4
August 11, 2025 at 11:22 AM
Reposted by Cecile Lorrain
waltzingpiglet.bsky.social
Hominoid-specific retrotransposons fuel regulatory novelty in early brain development , by @retrogenomics.bsky.social.

➡️ www.cell.com/cell-genomic...
October 10, 2025 at 12:57 PM
Reposted by Cecile Lorrain
bartdeplancke.bsky.social
🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics
This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.
www.nature.com
October 6, 2025 at 6:57 AM
Reposted by Cecile Lorrain
chloegirard.bsky.social
🚨 First pre-print from my team !!

TL;DR: presence of polymorphism (sequence differences between the homologous chromosomes) can *increase* the local rate of recombination in Arabidopsis thaliana, turning cold regions of the genome hot (purple v. grey) !
The recombination frequency (cM/Mb) along chromosome 4 of A. thaliana (female meiosis). In full hybrids (grey), where polymorphism is distributed all along chromosomes, most crossovers occur in the regions surrounding the Centromere (Cen), and very few at chromosome ends (Tel: telomeres). In lines where polymorphism is restricted to chromosome ends (purple), the local recombination rate increases drastically, at the expense of the non-polymorphic regions (yellow).
October 1, 2025 at 8:31 AM
Reposted by Cecile Lorrain
genomebiolevol.bsky.social
Weng et al. examined 431 genomes of butterflies and related lineages, revealing that horizontal transfer of digestion and detoxification genes facilitated the evolution of herbivory, enabling butterflies to co-evolve with angiosperm hosts.

🔗 doi.org/10.1093/gbe/evaf156

#genome #evolution #HGTsky
GBE | Gene Family Evolution Suggests Correlated Dietary Adaptations in Butterflies and Moths
September 30, 2025 at 9:17 AM
Reposted by Cecile Lorrain
tatsuyanobori.bsky.social
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance www.nature.com/articles/s41...
Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance - Nature Methods
This work presents scEpi2-seq, a method for simultaneous single-cell profiling of DNA methylation and histone modifications, enabling direct investigation of the interplay between these two epigenomic marks.
www.nature.com
September 25, 2025 at 10:49 AM
Reposted by Cecile Lorrain
lalouxlab.bsky.social
📝New preprint! #MicroSky

🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy.

🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation.

www.biorxiv.org/content/10.1...
Dynamics and interplay of gene expression and chromosome organization across a predatory lifecycle
The obligate predatory bacterium Bdellovibrio bacteriovorus alternates between a motile attack phase and a growth phase inside another bacterium, during which it undergoes multiple rounds of DNA repli...
www.biorxiv.org
September 25, 2025 at 7:12 AM
Reposted by Cecile Lorrain
stephenturner.us
Apple is entering the protein folding arena.
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...
September 25, 2025 at 9:02 AM
Reposted by Cecile Lorrain
jiangzhaoqian.bsky.social
Thrilled to share that our TEtrimmer paper has just been published in Nature Communications! A big thank you to all collaborators — the article is now online ;)

www.nature.com/articles/s41...
TEtrimmer: a tool to automate the manual curation of transposable elements - Nature Communications
Transposons are repetitive DNA sequences that are hard to identify and map accurately. TEtrimmer automates key manual steps, enabling faster and more reliable annotation of transposable elements in any genome.
www.nature.com
September 25, 2025 at 12:32 PM
Reposted by Cecile Lorrain
arnausebe.bsky.social
Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...
September 24, 2025 at 3:12 PM
Reposted by Cecile Lorrain
bossdorf.bsky.social
Job Alert! We're hiring a BIOINFORMATICIAN / NGS SPECIALIST to support our new Molecular Biodiversity Lab in the @terra-cluster.org at @unituebingen.bsky.social. Like the idea to use your skills for understanding biodiversity? To work on diverse questions in a wonderful place? Apply!
Please repost!
September 24, 2025 at 8:46 AM
Reposted by Cecile Lorrain
arnaudlerouzic.bsky.social
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...
Object: Postdoc Position Building a phylogenetic model for horizontal transfers of transposable elements A postdoctoral position (24 months) is available to work at EGCE (Gif-sur-Yvette, France, CNRS / Université Paris-Saclay) from January 2026. Transposable elements (TEs) are repetitive DNA sequences capable of promoting their own mobility. They are widespread across the tree of life and often represent a substantial fraction of eukaryotic genomes. Beyond their ability to invade genomes, TEs are frequently reported to undergo horizontal transfer, enabling their colonization of new hosts. However, understanding and predicting how horizontal transfers shape the distribution of TEs among species is far from straightforward. In particular, estimates of transfer rates based on documented cases are both biased and approximate, since transfers occurring close to speciation events are virtually undetectable. This project aims to develop explicit phylogenetic models of TE evolution that incorporate horizontal transfers, and to use these models to obtain statistical estimates of key evolutionary dynamics of TE families across species (e.g., horizontal transfer and extinction rates). The postdoctoral project will focus on exploring the impact of horizontal transfers on the distribution of TE presence/absence among related species, using statistical and/or computational approaches. Context The position will be part of a 4-year collaborative project funded by the French National Agency (ANR). The research consortium gathers two departments (from Paris-Saclay university and from Université Lyon 1), and involves 7 Pls and 5 postdocs and PhD students devoted to distinct workpackages of the project. The postdoc will be based at EGCE, which is part of the Institute for Ecology and Evolution (IDEEV). The institute offers an exciting and active scientific life, it is located on the new research campus of Paris-Saclay, 35 km south of Paris. Relevant references Gilbert C et al. 2018. Horizontal acquisition of transposable elements and viral sequences: patterns and consequences. Cur. Opin. Genet. Dev. 49:15-24. Le Rouzic A et al. 2013. Reconstructing the Evolutionary History of Transposable Elements. Genome Biol. Evol. 5:77-86. Wallau GL et al. 2016. VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila. Mol Biol Evol 33:1094-1109. Profile We are looking for a motivated early career theoretical biologist, with a PhD in theoretical evolutionary biology. Skills in statistics, programming, bio-informatics, and phylogenetic models will be appreciated. Application Formal applications (CV and cover letter) have to be deposited on the CNRS job portal https://emploi.cnrs.fr/Offres/CDD/UMR9191-ARNLER-006/Default.aspx?lang=EN.
September 24, 2025 at 12:26 PM
Reposted by Cecile Lorrain
dmacguig.bsky.social
Check out our new preprint! We compare sequence versus synteny approaches for resolving a challenging #phylogenetic problem. In this case, synteny is far more informative! Also includes the first chromosome-level #genome for the enigmatic #fish family Gyrinocheilidae. doi.org/10.1101/2025...
September 22, 2025 at 1:22 PM
Reposted by Cecile Lorrain
natplants.nature.com
New OA Article: "A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution" rdcu.be/eHce3

Chromatin accessibility in rice & related grasses: how regulatory DNA elements evolve across cell types & species; identifying potential silencers.
September 19, 2025 at 8:51 AM
Reposted by Cecile Lorrain
pierrebaduel.bsky.social
Happy to share the results of a long-haul post-doc project, now online @science.org, aiming at understanding the rules of transgeneration epigenetic inheritance over TEs in plants and its extent and impact in nature. More below!
doi.org/10.1126/scie...
Transposable elements are vectors of recurrent transgenerational epigenetic inheritance
DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...
doi.org
September 18, 2025 at 6:35 PM
Reposted by Cecile Lorrain
juliusbrennecke.bsky.social
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.

But how does piRNA-guided target interaction translate into silencing?

PhD student Júlia Portell Montserrat has an intriguing answer

www.cell.com/molecular-ce...
September 17, 2025 at 10:39 AM