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/...

With a bit of delay, I am delighted to share that I have started a new position as Full Professor at IE University. After more than 20 years building my scientific career across Europe, it is very… |...

With a bit of delay, I am delighted to share that I have started a new position as Full Professor at IE University. After more than 20 years building my scientific career across Europe, it is very sp...

linkedin.com

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)

Davide Mazza@davidemazza.bsky.social · 5mo ago

🧵 I’m very happy to share a new preprint from the @samuzambrano.bsky.social group and ours — a project driven by @emabiong.bsky.social, a PhD student bold enough to tackle a question at the interface of our two expertises: how the biological oscillators p53 and NF-κB talk to each other.

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

RNA polymerase II initiation factors show different dynamic behaviour upon induced transcription in live cells

Transcription by RNA polymerase II (Pol II) requires the ordered action of general transcription factors (GTFs) forming the pre-initiation complex (PIC). How these events unfold kinetically remains un...

doi.org

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👇

kasitc.bsky.social@kasitc.bsky.social · 12mo ago

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...

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.

Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms

Abstract. Enhancers play an essential role in developmental processes by regulating the spatiotemporal expression of genes. Characterizing their spatiotemp

doi.org

Yad Ghavi-Helm@yghavi.bsky.social · 2y ago

🚨Preprint alert! tinyurl.com/2zkmynsd Did you ever dream of reconstruction #spatial single-cell #enhancer activity in a multicellular organism using massively parallel enhancer-reporter assays? Then Spatial-scERA is the method for you! #spatialOMICs

#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?...

Quantification of gene expression control in a mammalian tissue at single cell resolution | SCP2025

YouTube video by Nikolai Slavov

youtu.be

🚨 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!

Saúl Ares@omeuxeito.bsky.social · last yr.

¡Nos ha salido un episodio tremendo! Catástrofes climáticas prehistóricas, volcanes y maremotos, y el colapso internacional de una sociedad globalizada... que tiene muchos elementos en común con la nuestra 🙈 ¡No te pierdas este episodio del #podcast @lavacaesferica.bsky.social!

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...

EMBL Events@events.embl.org · last yr.

‼️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

‼️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... 🧵

Clonal tracing with somatic epimutations reveals dynamics of blood ageing - Nature

The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing th...

doi.org

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

Nacho Molina@molinalab.bsky.social · last yr.

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

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

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...

biorxiv.org

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 🤩?

Nacho Molina@molinalab.bsky.social · last yr.

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

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

🚨 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...

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data

Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

biorxiv.org

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!

Recruiting international leaders in oncology from USA 2025

By offering a significant support, the call for proposal "Recruiting international leaders in Oncology from USA" wishes to allow the implantation in France of new scientific leader that will establish...

fondation-arc.org

Fondation ARC pour la recherche sur le cancer@fondationarc.bsky.social · last yr.

En réponse à la forte baisse des financements publics et à l'arrêt soudain de certains projets de recherche aux États-Unis, la Fondation ARC débloque 3,5 millions d’euros. Pour s'informer et candidater : www.fondation-arc.org/projets/recr...

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/...

Unraveling Enteroendocrine Cell lineage dynamics and associated gene regulatory networks during intestinal development

Enteroendocrine cells (EECs) are rare intestinal epithelial cells producing multiple hormones that regulate essential aspects of digestion and energy. EEC subtypes, their hormone repertoire and differ...

biorxiv.org

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!

EMBL Events@events.embl.org · last yr.

🚨 Poster deadline extended! #EMBLSingleMolecule 'Gene regulation: one molecule at a time' 🧬🔍 📅 15 – 18 July 📍 EMBL Heidelberg and Virtual ✍️ Submit by 27 April 👉🏼 s.embl.org/grg25-01-bl 🧬 RNA processing 🧬 Translation 🧬 Transcription & chromatin regulation 🧬 Method development 🧬 Theory

🚨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...

Call For Two Group Leader Positions - Strasbourg-Ville, Bas-Rhin (FR) job with IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) | 12837602

The Institute of Genetics, Molecular and Cellular Biology (IGBMC) is seeking two outstanding group leaders to establish independent research teams.

nature.com

🚨 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!