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Excited that CREME (Cis-Regulatory Element Model Explanations) is published in Nature Genetics! Work led by ShToneyan! tl;dr CREME interprets rules of gene regulation learned by genomic deep learning models using carefully designed in silico perturbations. rdcu.be/dT3kq

I've been looking forward to this release for a while: tangermeme v0.4.0 is out and asks "so... what did my model actually learn?" v0.4.0 moves past the individual components I've been building and shows how using them together can be very powerful. 1/ github.com/jmschrei/tange…

For me one of the biggest unsolved questions in biology: how do different phenotypes arise and how is this related to genomic sequence, different cell types and gene regulation? We address this question in our BAT wing project. biorxiv.org/content/10.110…

You still have a couple of weeks to submit an abstract for our next #LEGO meeting day in Paris! gt-lego.cnrs.fr/animation/lego…

Extensive binding of uncharacterized human transcription factors to genomic dark matter (Razavi et al., 2024) biorxiv.org/content/10.110… ▶️166 uncharacterized human TFs ▶️"Dark TFs", mainly bind closed chromatin enriched for transposable elements ▶️Some Dark TFs contain KRAB domain

Chromatin architecture mapping by multiplex proximity tagging [Delamarre et al. 2024] biorxiv.org/content/10.110… ▶️Nucleosome maps in 3D with Proximity Copy Paste (PCP) ▶️Connectivity of nucleosomes in S. cerevisiae ▶️Chromatin is predominantly organized in regular nucleosome arrays

Interesting preprint on nucleosome spacing from cfDNA [Johnston et al., 2024] biorxiv.org/content/10.110…. The authors refer to NRL changes 10n -> 10n-5 bp. Earlier we showed that NRL decrease in cancer is more complex & context-specific [Jacob et al., 2024] link.springer.com/article/10.118…

New preprint! "Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture", a tour de force project led by the amazing Yohsuke Fukai, in collaboration with Kurumizaka Lab (U Tokyo) and Umehara lab (RIKEN BDR). biorxiv.org/content/10.110…

How does chromatin linker length affect its emergent phase behavior? 🧬👩‍🔬 We explore this question via microscopy and MD simulations: Our new paper, in collaboration with the Rosen and Redding Labs, is out today!! 🔥 biorxiv.org/content/10.110…

Curious about alternative splicing? Kick off the year with our latest review in Current Opinion/Research in Structural Biology! authors.elsevier.com/sd/article/S09…

Ledidi turns any genomics ML model into a controllable sequence designer by inverting the normal ML paradigm. Now, it is significantly faster, flexible, and more powerful than before. Available on GitHub and installable with `pip install ledidi`

New preprint from our group on the genetic architecture of complex disease. Thread from 1st author Madison Chapel 👇. Here, I give a some context of why I am particularly excited about this.

The Borzoi manuscript is now out in Nature Genetics: doi.org/10.1038/s41588… Borzoi predicts RNA-seq profiles in many tissues & cell types from DNA sequence as its only input. With it, we can score the impact of genetic variants on a number of gene-regulatory functions. 1/

New (and hotly anticipated - at least by me) preprint from my group describing a better way to partition training data for genomic-trained models to solve the long-neglected problem of homology-based data leakage. Thread from first author Abdul Muntakim Rafi 👇

[SAVE THE DATE] MLCB 2025 is happening Sep 10-11 at the NY Genome Center—NYC! Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections! Submission deadline: Jun 1 Details: mlcb.github.io Spread the word—please RT!

What happens to bacterial genomes when they're cloned into yeast? Do they transcribe, do they get silenced, do they get packaged away from the rest of the DNA? This cool study congrats to the Koszul lab team at Pasteur for this great work science.org/doi/10.1126/sc…

#ResultatScientifique🔎| Prédire l’organisation et l’activité d’un ADN étranger dans une cellule hôte 🤝 CNRS 🌍 CNRS Ile-de-France Meudon Inserm Muséum national d'Histoire naturelle ✍️ Romain Koszul & Julien Mozziconacci 📕 Science Magazine | buff.ly/3CSj3st buff.ly/40GvJL2