Cecile Lorrain

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

Hominoid-specific retrotransposons fuel regulatory novelty in early brain development , by @retrogenomics.bsky.social.

➡️ www.cell.com/cell-genomic...

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.

🧵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

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).

🚨 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) !

GBE | Gene Family Evolution Suggests Correlated Dietary Adaptations in Butterflies and Moths

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

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.

Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance www.nature.com/articles/s41...

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...

📝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...

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...

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.

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...

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...

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!

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.

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...

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...

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.

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...

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...

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...

Active learning enables discovery of transcriptional activators across fungal evolutionary space https://www.biorxiv.org/content/10.1101/2025.09.12.675635v1

Reawakening retrotransposons: immune modulation in normal and malignant hematopoiesis Retrotransposons are mobile repetitive elements that constitute around 43% of the human genome. Normally silenced through epigenetic mechanisms, retrotransposons can become reactivated in response to ...

Our new review is out in Trends in Cancer. We had fund writing this :) We discuss the roles of retrotransposons in immune modulation in normal and malignant
hematopoiesis. www.cell.com/trends/cance...

Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods https://www.biorxiv.org/content/10.1101/2025.08.29.672809v1

Multi-scale and multi-context interpretable mapping of cell states across heterogeneous spatial samples - Nature Communications The alignment of heterogeneous spatial samples has become a growing challenge. Here, authors present a multi-scale, multi-context, and interpretable mapping strategy to map cells across space, time, a...

Vesalius 2.0 is in ‪‪@natcomms.nature.com‬ !

We show how using spatial context improves cell-to-cell mapping across heterogenous spatial samples.

Thanks to the reviewers, editors, and collaborators for making this possible.

GitHub: github.com/WonLab-CS/Ve...
Paper: www.nature.com/articles/s41...

Elementary 3D organization of active and silenced E. coli genome - Nature An ultra-high-resolution chromatin organization map of E. coli, using Micro-C, reveals intricate chromatin structures involved in the silencing of horizontally transferred genes and those associated with active operons.

Nature research paper: Elementary 3D organization of active and silenced E. coli genome

go.nature.com/4n1DTY7

Plant-associated fungi co-opt ancient antimicrobials for host manipulation Evolutionary histories of effector proteins secreted by fungal pathogens to mediate plant colonization remain largely elusive. While most functionally characterized effectors modulate plant immunity, ...

📣 NEW PREPRINT 📝

We identified evolutionary origins of many fungal effectors!
We show that fungi secrete lots of antimicrobial proteins, and that some of them were repurposed by plant pathogens for host immune suppression.
www.biorxiv.org/content/10.1...

cc @teamthomma.bsky.social

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals - Genome Biology Background Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypometh...

Paper led by @movillome.bsky.social on unbiased detection of (somatic) #TE insertions in #Arabidopsis with @pacbio.bsky.social long reads out after peer review. Thanks to academic editor Leandro Quadrana for shepherding it through the review process.
#plantscience
link.springer.com/article/10.1...?

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp

Dissecting the enhancer gene regulatory network in early Drosophila spermatogenesis - Nature Communications Single-cell multi-omics in Drosophila testis reveals enhancer-driven gene regulatory networks and shows how Wnt signaling and key transcription factors orchestrate stem cell maintenance and lineage pr...

I am so happy to announce that our Drosophila testis multiome paper is now published in Nature Communications !!! I am very happy and proud of all who contributed, in particular Patrick and Pallavi who did an amazing job! www.nature.com/articles/s41...

We are looking for a student to continue our work on chromatin evolution:
www.nature.com/articles/s41...
www.biorxiv.org/content/10.1...

The project with @seanamontgomery.bsky.social will focus on chromatin state readers across eukaryotes.

More info: recruitment.crg.eu/content/jobs...

1/2 Somatic TE transposition in plants is getting traction again (70 years after McClintock's discovery of "controlling elements")! A very large collection of somatic TE insertions in A. thaliana described by Ambreen et al.(www.biorxiv.org/content/10.1...).

Conservation of chromatin states and their association with transcription factors in land plants The complexity of varied modifications of chromatin composition is integrated in archetypal combinations called chromatin states that predict the local potential for transcription. The degree of conse...

New Pre-print! A long-standing question for transcription factor biology is how their chromatin context dependency works in plants. In this collaboration with Fred Berger lab, we present some new ideas not only in Arabidopsis but also in Marchantia. www.biorxiv.org/content/10.1...

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene programme in bat wing development - Nature Ecology & Evolution Single-cell comparison of developing bat and mouse limbs reveals conservation of cell populations and gene expression patterns, and suggests repurposing of genes involved in proximal limb development ...

How bats developed their wings? 🦇

Turns out they reutilize existing gene programs 🔧

Find out more in our paper @natecoevo.nature.com in collaboration with @fany-real.bsky.social and @stemundi.bsky.social labs

www.nature.com/articles/s41...