It was a pleasure to collaborate on this project. Special thanks to @campobes.bsky.social @arburga.bsky.social for the opportunity ☺️

Tools and tactics for studying alternative splicing Nature Reviews Genetics, Published online: 17 April 2026; doi:10.1038/s41576-026-00952-4In this Review, Sousa-Luís and Carmo-Fonseca discuss the various tools available to detect and quantify alternative splicing, functionally test splice isoforms and investigate the link between genetic variation, splicing and disease.

New online! Tools and tactics for studying alternative splicing

This is pretty cool

Our last manuscript is out! 🚨

We identify double stranded RNAs in embryonic stem cells - full of transposons, especially young LINEs and LTRs 🧐

🧬Happy Friday Reading🧬

FYI: New online! How classical genetics uncovered key determinants of TE silencing

Curiosity, cell clearance, and improv: A chat with Julia Batki In this interview, Julia Batki, FMI’s newest group leader, reflects on the early curiosity that drew her to science, why FMI is the right home for her lab, how studying cell clearance could help us un...

In this interview, @juliabatki.bsky.social, FMI’s newest group leader, reflects on the early curiosity that drew her to science, why FMI is the right home for her lab, how studying cell clearance could help us understand disease, and her love of improv.
www.fmi.ch/news-events/...

Interesting study suggesting a sequence signature reflecting DNMT1 activity explain losses of DNA methylation with cell division, aging and cancer: www.biorxiv.org/content/10.6...
#epigenetics

Actually, what is a gain-of-function mutation? Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien

academic.oup.com/genetics/adv...

Also thanks to Lyndall & @psarkies.bsky.social, @ahocher.bsky.social, and members of the lab for their comments and Francis Barr @oxfordbiochemistry.bsky.social for encouraging me to write down my thoughts.

ICYMI: New online! How classical genetics uncovered key determinants of TE silencing

Oh bless 💀

No grant gripe here, but studied ageing in flies and definitely had the experience of being asked of its relevance to mouse/human model 😂

Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis piRNAs are an important genome regulatory mechanism conserved across metazoans. In the nematode C. elegans, piRNA biogenesis evolved several differences from other metazoans. Beltran et al. study the ...

Happy pi (RNA) day everyone! And what better way to enjoy than to revisit the unusual features of nematode piRNAs: www.cell.com/developmenta...

Ever wondered how a eukaryotic transcription factor finds its specific DNA motif in the vast genome? In this preprint, we directly measured the dynamics of this search process in living cells, revealing a cooperative mechanism mediated by disordered regions. 1/10 doi.org/10.64898/202...

Fun project to have worked on with very talented colleagues. Thanks for the shoutout @genomebiolevol.bsky.social ☺️

Gene regulatory networks: from correlative models to causal explanations Nature Reviews Genetics - In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without...

New Perspective form Rory Maizels & me: "Gene regulatory networks: from correlative models to causal explanations"

Gene regulatory networks are supposed to give us mechanistic explanations of development, so why are we drowning in 'hairballs' of statistical correlations?

rdcu.be/e7zx7

Flyer for symposium: https://ctrlepiedit.sciencesconf.org/

Very excited to announce the FIRST symposium on epigenome editing! These tools are becoming widely used in mol bio, ag & therapy. It's time to bring leaders together to discuss this rapidly growing and exciting field. And why not in Paris! Please register & share! (1/2) ctrlepiedit.sciencesconf.org

I’m thrilled to share that my PhD work has been just published in Cell. After a long and bumpy ride, we uncovered the core function of nuclear speckles -splicing of GC-levelled exons- and traced the evolution of this gene architecture and condensates themselves to amniotes.

Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila Identification of ZAD-ZnF genes as key regulators of genome organization during Drosophila embryogenesis.

Diving into evolutionary biology! What is the origin of the most abundant class of insect transcription factors, ZAD-ZnFs? We suggest that they evolved from ancestral insulator-binding proteins that control 3D genome topology.

www.science.org/doi/10.1126/...

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life Giant DNA viruses encode a cap-binding complex homologous to eIF4F, the defining translation-initiation complex of eukaryotes. The viral cap-binding complex is required for viral protein synthesis and...

www.cell.com/cell/fulltex...

Super cool work!

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social
doi.org/10.1016/j.ce...
Read the thread👇 for the highlights of our findings.

Happy to share scHiCAR, an ultra-high throughout (millions of cells), low cost (5 cents/cell including NGS), and trimodal platform for integrated single-cell level analysis of mRNA, open chromatin, and 5-kb resolution looping with ground-truth data the same individual cell.

Massively parallel reporter assays: from barcodes to biology Nature Reviews Genetics, Published online: 10 February 2026; doi:10.1038/s41576-026-00944-4In this Journal Club, Fumitaka Inoue discusses a 2009 paper by Patwardhan et al. that introduced a massively parallel saturation-mutagenesis assay that leverages high-throughput DNA synthesis and sequencing to quantify the effects of single-nucleotide changes on regulatory element activity.

New online! Massively parallel reporter assays: from barcodes to biology

Why Seeing Still Matters in Biology - the Node or, Why all biologists needs data visualization Biology probes form and function of Life. Form is easy to grasp: cells under a microscope, subcellular

Why Seeing Still Matters in Biology

@helenajambor.bsky.social addresses why all biologists need data visualisation. Read and discuss this topic on the Node. ⬇️

#DataVis #BioVis

thenode.biologists.com/why-seeing-s...

Regulation of gene expression by alternative polyadenylation in health and disease Nature Reviews Genetics, Published online: 15 January 2026; doi:10.1038/s41576-025-00928-wAlternative 3′-end processing of nascent RNA, known as alternative polyadenylation (APA), increases transcript diversity and augments post-transcriptional modulation of gene expression. APA profiles are highly dynamic in response to cell growth, differentiation and extracellular cues, and dysregulated APA is a hallmark of human diseases.

FYI: New online! Regulation of gene expression by alternative polyadenylation in health and disease

Another domain boundary factor identified

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/...

The printed version lives on my desk. Wonderfully written!

Germline fate determination by a single ARGONAUTE protein in Ectocarpus | PNAS ARGONAUTE (AGO) proteins are a highly conserved family of RNA-binding proteins that play central roles in gene regulation and developmental process...

One protein. One pathway. A whole germline fate.

New paper from my postdoc @mpi-bio-fml.bsky.social out in PNAS:
Germline fate determination by a single ARGONAUTE protein in Ectocarpus www.pnas.org/doi/10.1073/...

orthogene: a Bioconductor package to easily map genes within and across hundreds of species www.biorxiv.org/content/10.64898/2026.01...