Michelle Vincendeau

Happy to share our new preprint! 📊

We benchmarked methods for locus-level transposable element quantification in short-read scRNA-seq, using both real datasets and simulations with read-level ground truth.

Huge thanks to @catavallejos.bsky.social and @antonio-scialdone.bsky.social!

#TEsky

The role of KRAB zinc-finger proteins in expanding the domestication potential of transposable elements - Nature Genetics This Perspective explores the co-evolution of transposable elements and KRAB zinc-finger proteins in relation to their integration into human gene regulatory networks, highlighting their potential eff...

Find our latest Perspective article in Nature Genetics on "The role of KRAB zinc-finger proteins in expanding the domestication potential of transposable elements" at www.nature.com/articles/s41..., with implications for the future of research on the cause of human disease.

Concurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis LINE-1 (L1) retrotransposition generates somatic genomic variation in human cancer, but short-read sequencing has limited our understanding of its structural consequences and dynamics. Using long-read...

Today in
@science.org:
We are pleased to present our last work entitled:
"Concurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis"
by Zumalave et al.
www.science.org/doi/10.1126/...

Ancient co-option of LTR retrotransposons as yeast centromeres - Nature Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with retrotransposon-rich centromeres and that long-terminal-repeat retrotransposons are the genetic substrate.

Nature research paper: Ancient co-option of LTR retrotransposons as yeast centromeres

go.nature.com/4c3kP9A

Transposable element regulation as a therapeutic target for #Aging

activating Suv39h1
inhibiting KDM4A
inhibiting TET

CRISPRi/a to program TEs in the genome

#OpenBiol 2026
royalsocietypublishing.org/rsob/article...

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism Abstract. Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal spec

Dauphin et al. assembled a telomere-to-telomere reference genome for an ectomycorrhizal fungus with a large, repeat-rich genome, showing its genome expansion was driven by a few lineage-specific TE families in recent history.

🔗 doi.org/10.1093/gbe/evag017

#genome #evolution #TEsky

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs Nature Structural & Molecular Biology - METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining...

🚨 Happy to see that my PhD work is finally published!

We present METALoci, a tool that integrates #3Dgenome and #Epigenetics to identify regulatory hubs.

Applied to #sexdetermination we uncover:
✔️ Non-coding regulatory region controlling Fgf9
✔️ Meis genes as key players

👉 rdcu.be/e5sm2

Fellowship application dealdine for students from low income countries 🌐will be in 1️⃣ week.
Dont miss out on this opportunity ! Hands on Summer School.
Cut&Run, Cut@Tag, ChIP, ATACseq and analyse your own data ! ➡️Unique opportunity ! 15 exiting days ➕ Daily high profile lectures.
👉 bit.ly/4oGDR8f

Events for February 2026 06-07 July 2026 | Munich, GermanyDNA Replication and Its Impact on Genome and Chromatin MaintenanceWe are RepliFate, a European Training Doctoral Network dedicated to understanding how DNA replication...

We go live!!!

Join us Munich July5-7th to hear exciting research on #Replication by leaders in the field

AND !! registration is FREE 🥳 (but mandatory) - we hope to see many in Munich 🍺 @helmholtzmunich.bsky.social

@replifate.bsky.social @epicrossborders.bsky.social

replifate.eu/event/meetin...

Loss of SETDB1-mediated H3K9me3 in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons Abstract. Heterochromatin is characterized by an inaccessibility to the transcriptional machinery and is associated with the histone mark H3K9me3. However,

New paper from my lab out in NAR. We found that young L1 elements are controlled by SETDB1 and H3K9me3 in human neural progenitor cells via a mechanism independent of HUSH and TRIM28/KZNFs.

academic.oup.com/nar/article/...

Können alte Virusreste Alzheimer auslösen? YouTube video by Alzheimer Forschung Initiative

Dr. Vincendeau @m-vincendeau.bsky.social von @helmholtzmunich.bsky.social untersucht in ihrem AFI-Projekt, welche Virusreste im Erbgut mit Alzheimer in Zusammenhang stehen könnten und welche Mechanismen dadurch ausgelöst werden.

▶️ Mehr Infos zum Projekt gibt es im Video

Together with colleague and friend Carl Herrmann @uniheidelberg.bsky.social, we are looking for a motivated postdoc with experience in organoid culture and data analysis (#bioinformatics), for a project in the @hlsalliance.bsky.social Joint Postdoc call.

www.health-life-sciences.de/opportunitie...

Scraps of viral DNA in biobank samples reveal secrets of Epstein–Barr virus Viral DNA that is usually dismissed when sequencing the human genome could help to uncover useful information about complex diseases.

Viral DNA that is usually dismissed when sequencing the human genome could help to uncover useful information about complex diseases

go.nature.com/4qMy6rD

Aging drives a program of DNA methylation decay in plant organs Plants display a wide range of life spans and aging rates. Although dynamic changes to DNA methylation are a hallmark of aging in mammals, it is unclear whether similar molecular signatures reflect ra...

Out in @science.org this week: A decline in epigenetic silencing of TEs in older plant organs but not in the shoot meristem. TCX5 and TCX6 help regulate DNA methylation in this context.
www.science.org/doi/10.1126/...

#plantscience

The IGNITION PhD Programme is now open! We’re offering 13 fully funded PhD positions across 10 institutions in 8 EU countries to study immune mediated neurodegeneration.

If you're passionate about research, innovation & international collaboration, this is for you.

ignition-consortium.eu/home/

New preprint from the lab! We dig into the regulatory roles of TEs in the mouse placenta, with some surprising findings. Led by the awesome @smamante.bsky.social. Particular kudos to him for navigating the many twists and turns of the project.

Thanks and yes new initiatives are in the cooking to keep the #TEsky up above :).

Können alte Virusreste eine Alzheimer-Erkrankung auslösen? <h3>Was wird erforscht?</h3> <p>Alzheimer ist die häufigste Form der Demenz und betrifft weltweit mehrere Millionen Menschen. Wie die Krankheit entsteht, ist bislang nicht vollständig geklärt. Neueste...

Thanks to @afi-ev.bsky.social for funding our project @helmholtzmunich.bsky.social ! Excited to delve into new aspects of Alzheimers research!

www.alzheimer-forschung.de/forschung/fo...

Endogenous retroviruses synthesize heterologous chimeric RNAs to reinforce human early embryo development Zygotic genome activation (ZGA) failure leads to developmental arrest and poses a clinical challenge to women’s fertility. We observed that human embryos arresting at the eight-cell ZGA stage exhibite...

New findings in Science offer insight into why some embryos fail to develop past zygotic genome activation, pointing to an unexpected root of human infertility.

Learn more: https://scim.ag/46cc4WI

Pre-assembly of biomolecular condensate seeds drives RSV replication Nature - Viral ribonucleoprotein–viral protein networks form pre-replication centres that nucleate viral factories and drive respiratory syncytial virus replication.

Now out in Nature! We visualize infection of the RNA virus RSV in real-time with single-vRNP resolution to understand how RSV establishes viral factories, biomolecular condensates that act as sites of viral replication. A huge collaborative effort led by Dhanushika Ratnayake!

rdcu.be/e1bBW

The way to accelerate science is to SLOW it down.

Fewer papers please! We’re drowning in meaningless text.

One GREAT paper per lab per decade is more than enough.

q.e.d 👇

We're hosting Postdoc Night Science on February 11. If you're a postdoc in NYC, please join us!

Emerging advances in prokaryotic transposition: TnPedia as a promising tool TnPedia provides a curated framework for understanding prokaryotic transposable elements (TEs), including general and historical information and basic concepts, while integrating mechanistic insights,...

Emerging advances in prokaryotic transposition: TnPedia as a promising tool www.cell.com/trends/micro... #jcampubs

Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...

🔬 Call to create junior research groups at the Institut Pasteur

Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies

📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD

Apply now 📝 research.pasteur.fr/en/call/crea...

#JobOpportunity #Research

🦠 Closing our session is @manusingh.bsky.social discussing the "Long Shadow of Viral Infections".
He's showing how HIV & EBV can reactivate persistent, ancient Endogenous Retroviral proteins. A powerful reminder that our genome's history still dictates our health today!🧬

Prof. Fiona Doetsch has been awarded the 2026 Louis-Jeantet Prize for Medicine!
Her discoveries reveal how neural stem cells support lifelong brain plasticity and repair. 🧠
Read more: www.biozentrum.unibas.ch/news/detail/...

Iterative engineering of a compact Cas9 ortholog for in vivo gene editing via single AAV delivery The development of compact and efficient CRISPR-Cas systems is crucial for biomedical and therapeutic genome editing, particularly in vivo applications based on viral delivery. Here, we performed a co...

Novel compact CRISPR systems unlock easier delivery and more applications... epigenome editing anyone 👀

Very happy to be involved in work to rationally engineer enhanced Cme2 - an ultra-high fidelity & compact Cas, delivered in vivo in a single AAV (with gRNA)

www.biorxiv.org/content/10.6...

There's still time to apply to be a 2026 @dev-journal.bsky.social Pathway to Independence fellow

For those about to apply for their first independent academic position, the programme offers

- mentoring
- leadership training
- profile rising
- networking

journals.biologists.com/dev/pages/pi...

TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons, crypTEs, in iPSC derived neurons and ALS/FTD patient tissues TDP-43 is an RNA and DNA binding protein that plays major roles in regulating RNA processing. In particular, TDP-43 dysfunction leads to the accumulation of cryptic splice isoforms that result from im...

📣Excited to announce a new pre-print from the lab 📣

Led by my student @storiesofisobel.bsky.social in collab with Hemali Phatnani @nygenome.org
We discovered a novel class of TDP-43 dependent cryptic gene-TE spliced transcripts: crypTEs

#TEsky #RNAsky #ALS
doi.org/10.64898/2026.01.09.698641

International Genome Dynamics course in Institut Curie-Paris (April 8-15), experimental and computational methods in multiomics,with a #TE centered session.
Free registration, until Jan 15th
Don’t miss it!
👉https://training.institut-curie.org/courses/Genome-Dynamics-2026
@institutcurie.bsky.social