Nacho Molina

Hey! You can have a look at our new preprint on #CellCycle regulation and #Pluripotency! A little thread 100% human 0% AI slop is coming (bear with me the mistakes). Let's thank first @maulik_nariya, the fantastic postdoc that led this project: www.biorxiv.org/content/10.6...

It was a pleasure to collaborate on this beautiful piece of work led by Susan Mango: nature.com/articles/s41...

Interested in #CellCycle and #Pluripotency? 👇

Sign up now for the EMBO meeting 'quantitative biology to molecular mechanisms'. Fantastic speaker lineup and plenty of speakers slots selected from abstracts. Submit your abstract before Sept 11!

With a bit of delay, I am very happy to share that after more than 20 years building my scientific career across Europe, I have returned to my hometown, Madrid, as Full Professor at IE University. An exciting new step and much to build ahead. More here: www.linkedin.com/feed/update/...

So grateful to my buddy the great @davidemazza.bsky.social and all the contributors from our teams to this joint effort to unravel NF-κB–p53 crosstalk. Davide’s thread nicely explains the main findings — here’s a short side note from me 🧵👇 (1/n)

Read our new preprint where we uncover a hierarchy in human PIC assembly and establish a quantitative framework that connects factor exchange kinetics to the regulation of Pol II activity in living human cells. doi: doi.org/10.64898/202... By A. Oravecz and our collaborators @molinalab.bsky.social

This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

Now available in its final form @narjournal.bsky.social ! doi.org/10.1093/nar/... Find out how we can reconstruct enhancer activity in vivo in the Drosophila embryo using scRNAseq data and Optimal Transport.

#EMBLsinglemolecule was a blast! Happy to host the birth of single molecule genomics as a field and to think about the future with the microscopy crowd. Thanks to participants and organizers!

Carrying on with Session 4 on #EMBLSingleMolecule Day 3 🤓💪🏼 ➡️ 'Decoding Gene Regulation at the Single-Molecule Level through Biophysical Modeling of DNA Footprinting Data' 🎙️ Nacho Molina – Institute of Genetics and Molecular and Cellular Biology @molinalab.bsky.social @igbmc.bsky.social @embl.org

The talk by @andrewleduc.bsky.social at #SCP2025 is on YouTube: 𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧 youtu.be/adkY6txDyqs?...

🚨 Only a few more days to REGISTER for the TriRhena Gene Regulation Club in Freiburg. Whether you are new or an established researcher in the Basel-Freiburg-Strasbourg region, this is your meeting when working in transcription, chromatin & gene regulation! ✍️ www.ie-freiburg.mpg.de/gene-regulat...

🟦 Label-free single-cell proteomics (blue bars). 🟧 Multiplexed single-cell proteomics affords higher throughput (orange bars). ⬛️ Proteome depth & quantitative accuracy are comparable. We aim to make the 🟧 bars taller. www.parallelsq.org/psmtags www.biorxiv.org/content/10.1...

For Spanish speakers, this is a fantastic podcast about science and much more!

No doubt, this is one of the most exciting meetings of the year! And we will present our new method, HiddenFoot 😉: www.biorxiv.org/content/10.1...

‼️Last chance to join us in person for #EMBLSingleMolecule! Attend talks, network, socialise, and experience the atmosphere on the campus 🤩 🎫 Register by 3 Jun 👉🏼 http://s.embl.org/grg25-01-bl 🧬RNA processing 🧬Translation 🧬Transcription & chromatin regulation 🧬Method development 🧬Theory

Out @nature.com: Clonal tracing with somatic epimutations 🧬 Single cell methylome encodes cell state & clonal identity 🔨 EPI-Clone reads out both (+mutations, +RNA) at scale 🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations doi.org/10.1038/s415... 🧵

Just in case you missed this and it’s something that might interest you. #SingleMoleculeBiology, #Chromatin, #Transcription, #TF, #Nucleosome, #PolII, #Biophysics, #MachineLearning, #ComputationalBiology 👇

Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6

I'm neighboring the chromatin biology field at the moment and there is a lot I need to understand. Especially, the specific techniques/methodologies in use to study chromatin, however this one looks 🔥🔥🔥. Many congratulations 👏🏻 🎉 to all those involved! Hey #ChromatinSky people where are you at 🤩?

🚨 New preprint out! Do you think Single Molecule Footprinting and Fiber-seq are super cool but aren't sure how to unlock their full potential? HiddenFoot can help you: www.biorxiv.org/content/10.1...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

New research by @kasitc.bsky.social @molinalab.bsky.social @arnaudkr.bsky.social reveals limited RNA polymerase II pausing at mouse promoters compared to flies ➡️ www.embopress.org/doi/full/10....

US colleagues: Looking to launch or move your lab to France? The ARC Foundation is recruiting outstanding US-based scientists to lead research in oncology. Generous support & relocation help included. Details here: www.fondation-arc.org/projets/recr... Interested? Contact us!

Here is-🥳🥳😇 tremendous effort by @palmrinmoy.bsky.social brilliantly supported by @tamas-schauer.bsky.social &super help by federico,iliya,tsune,adam,@mamartirenom.bsky.social Very happy to see this come to fruition- Look forward to feedback from colleagues ! More 👉 www.cell.com/cell/fulltex...

1/2. I am pleased to announce that the preprint of our latest study characterizing mouse and human EEC development is now on BioRxiv. A great collaboration with the @molinalab.bsky.social and Maxime Mahe (not on bluesky) www.biorxiv.org/cgi/content/...

Send us your abstract before easter! Extended deadline! we got lots of cool stories already! We would also welcome submissions with a focus on Translation and life of RNA!

🚨3 weeks left to apply!🚨 We’re hiring 2 new Group Leaders at IGBMC – early career researchers welcome 🌟 We offer salary support for up to 3 years while you secure a permanent position in the French system. Come join an international research environment in Strasbourg! www.nature.com/naturecareer...

🚨 Last chance to submit abstract for 'Gene regulation: one molecule at a time' 🧬✍🏼 👉🏼 s.embl.org/grg25-01-bl ℹ️ #EMBLSingleMolecule will catalyse the emergence of a new generation of mechanistic models of the regulation of genes across each steps of the central dogma. 📅 Deadline: 8 April!

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...

Hey! Check out our latest publication. A great collaboration with @longchrom.bsky.social and a nice example of how a negative result, the absence of a response to a transcriptional perturbation, can actually reveal an intriguing gene-specific buffering mechanism. www.science.org/doi/10.1126/...

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

Come start your lab in beautiful Strasbourg 🇫🇷 www.nature.com/naturecareer...

Hey! This was the result of a fantastic collaboration with the @longchrom.bsky.social lab, where we found evidence for a gene-specific buffering mechanism to compensate for transcriptional perturbations.

Almost 17 years after opening our yeast cell division lab, our first transcription paper in mouse embryonic stem cells! www.science.org/doi/10.1126/...