📄 That's a wrap 📄 we're excited to share that the latest from @arnaudkr.bsky.social 's lab and Judith Zaugg's lab is at last online at doi.org/10.1038/s415.... Many thanks to my co-first @valentinabaderna.bsky.social and to @embl.org for the wonderful research environment.

Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency - Nature Genetics

This study uses single-molecule footprinting to quantify chromatin accessibility at enhancers and promoters in mouse embryonic stem cells and to dissect the contributions of transcription factor bindi...

doi.org

Valentina Baderna@valentinabaderna.bsky.social · last yr.

Happy to share the latest story from @arnaudkr.bsky.social's lab @embl.org! With @guidobarzaghi.bsky.social, we used Single Molecule Footprinting to quantify how often chromatin is accessible at enhancers after TF and chromatin environment changes! Check our preprint bit.ly/3XQMFxN + thread ⬇️ 1/11

"Together, these findings demonstrate that LLM hallucinations are infiltrating knowledge production at scale, threatening both the reliability and equity of future scientific discovery as human and AI systems draw on the existing literature" arxiv.org/abs/2605.07723

LLM hallucinations in the wild: Large-scale evidence from non-existent citations

Large language models (LLMs) are known to generate plausible but false information across a wide range of contexts, yet the real-world magnitude and consequences of this hallucination problem remain p...

arxiv.org

Read our @natgenet.nature.com News&Views on the impressive work by @muzumdarlab.bsky.social and @sstevenwang.bsky.social. How does the 3D genome guide Kras-driven cancers evolution? Find out with single-cell genome-wide chromatin tracing! 📖https://rdcu.be/eShAY

Muzumdar Lab@muzumdarlab.bsky.social · last yr.

💡 Cancer cells don’t just mutate—they reorganize their DNA in 3D space. Our new study shows how the genome’s folding pattern shifts as tumors progress, cell by cell 🧩🧬. It’s the first 3D genome atlas of cancer progression. Thread 👇

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇

5/2025 Issue ➡️ www.embopress.org/toc/17444292... tissue-specific huntingtin interactomes, gene product diversity evolution Cover: mammalian promoters characterised by low RNA pol II occupancy and high turnover @kasitc.bsky.social @molinalab.bsky.social @arnaudkr.bsky.social

Don't forget to checkout our annex pre-print bit.ly/3EkRqJh for a sense on our new 💻 tool FootprintCharter, for the unsupervised footprint quantification from single molecule data. Available on Bioconductor at bit.ly/3XLe8RC.

FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data

Single molecule footprinting profiles the heterogeneity of TF occupancy at cis-regulatory elements across cell populations at unprecedented resolution. The single molecule nature of the data in princi...

bit.ly

Valentina Baderna@valentinabaderna.bsky.social · last yr.

We developed FootprintCharter to classify molecules into accessible or nucleosome-occupied at TF motifs by unsupervisedly detecting TF and nucleosome footprints. FootprintCharter is distributed on Bioconductor at bit.ly/3XLe8RC. For more details, read our annex preprint at bit.ly/3EkRqJh. 3/11

Having a stressful day? Lay back, crack a beer open and read about how chromatin accessibility responds to perturbations of TF binding at the single molecule level bit.ly/3XQMFxN. I'm incredibly thankful to my PhD mentors @arnaudkr.bsky.social and Judith Zaugg for these super productive years!!

Cumulative TF binding and H3K27 Acetylation drive enhancer activation frequency

In eukaryotes, transcription factors (TFs) must continuously compete with nucleosomes to access their binding sites, leading to cell-to-cell variability in chromatin accessibility at regulatory region...

bit.ly

Valentina Baderna@valentinabaderna.bsky.social · last yr.

Happy to share the latest story from @arnaudkr.bsky.social's lab @embl.org! With @guidobarzaghi.bsky.social, we used Single Molecule Footprinting to quantify how often chromatin is accessible at enhancers after TF and chromatin environment changes! Check our preprint bit.ly/3XQMFxN + thread ⬇️ 1/11

The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...