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Nacho Molina

@molinalab.bsky.social
1.7K followers 1.2K following 111 posts

Group leader of the Stochastic Systems Biology Lab at IGBMC - CNRS - University of Strasbourg. Models of gene regulation based on biophysics-informed deep learning: www.igbmc.fr/molina

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Nacho Molina @molinalab.bsky.social · 24/09/2026
Interested in #CellCycle and #Pluripotency? 👇
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Tineke Lenstra @tinekelenstra.bsky.social · 17/08/2026
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!
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Nacho Molina @molinalab.bsky.social · 24/09/2026
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...
biorxiv.org
Comparison of cell-cycle gene expression dynamics and mRNA kinetics across mouse and human pluripotent systems
Cell-cycle remodeling is fundamental to pluripotency and lineage commitment, yet whether its transcriptional and post-transcriptional architecture is conserved across species and developmental states ...
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Nacho Molina @molinalab.bsky.social · 15/06/2026
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/...
linkedin.com
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...
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Samuel Zambrano @samuzambrano.bsky.social · 26/02/2026
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)
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László Tora @tlaszlo.bsky.social · 24/12/2025
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
doi.org
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...
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Arnaud Krebs @arnaudkr.bsky.social · 18/08/2025
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👇
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kasitc.bsky.social @kasitc.bsky.social · 18/08/2025
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...
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Schubeler Lab @schubelerlab.bsky.social · 07/08/2025
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....
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Yad Ghavi-Helm @yghavi.bsky.social · 23/07/2025
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.
doi.org
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
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Arnaud Krebs @arnaudkr.bsky.social · 18/07/2025
#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!
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EMBL Events @events.embl.org · 17/07/2025
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
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Slavov Laboratory @slavovlab.bsky.social · 11/06/2025
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?...
youtu.be
Quantification of gene expression control in a mammalian tissue at single cell resolution | SCP2025
YouTube video by Nikolai Slavov
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Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · 03/06/2025
🚨 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...
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Nikolai Slavov @slavov-n.bsky.social · 31/05/2025
🟦 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...
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Nacho Molina @molinalab.bsky.social · 29/05/2025
For Spanish speakers, this is a fantastic podcast about science and much more!
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Nacho Molina @molinalab.bsky.social · 28/05/2025
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...
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EMBL Events @events.embl.org · 27/05/2025
‼️Last chance to join us in person for #EMBLSingleMolecule! Attend talks, network, socialise, and experience the atmosphere on the campus 🤩 🎫 Register by 3 Jun 👉🏼 s.embl.org/grg25-01-bl 🧬RNA processing 🧬Translation 🧬Transcription & chromatin regulation 🧬Method development 🧬Theory
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Lars Velten @larsplus.bsky.social · 21/05/2025
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... 🧵
doi.org
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...
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Nacho Molina @molinalab.bsky.social · 21/05/2025
Just in case you missed this and it’s something that might interest you. #SingleMoleculeBiology, #Chromatin, #Transcription, #TF, #Nucleosome, #PolII, #Biophysics, #MachineLearning, #ComputationalBiology 👇
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Nacho Molina @molinalab.bsky.social · 19/05/2025
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
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Selin Jessa @selinjessa.com · 03/05/2025
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 🧬🖥️
biorxiv.org
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...
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Dr Zeinab Rekad 🔬🧬🧪 @zeinabrekad.bsky.social · 19/05/2025
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 🤩?
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Nacho Molina @molinalab.bsky.social · 19/05/2025
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
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Nacho Molina @molinalab.bsky.social · 17/05/2025
🚨 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...
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Erik van Nimwegen @erikvannimwegen.bsky.social · 09/05/2025
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...
biorxiv.org
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...
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Molecular Systems Biology @molsystbiol.org · 08/05/2025
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....
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Manuel Mendoza @longchrom.bsky.social · 30/04/2025
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!
fondation-arc.org
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...
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ME Torres-Padilla @metorrespadilla.bsky.social · 23/04/2025
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...
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Gradwohl Gérard @pancint.bsky.social · 17/04/2025
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/...
biorxiv.org
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...
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Arnaud Krebs @arnaudkr.bsky.social · 10/04/2025
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!
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Manuel Mendoza @longchrom.bsky.social · 09/04/2025
🚨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...
nature.com
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.
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EMBL Events @events.embl.org · 01/04/2025
🚨 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!
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Arnaud Krebs @arnaudkr.bsky.social · 02/04/2025
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...
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Nacho Molina @molinalab.bsky.social · 31/03/2025
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/...
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 29/03/2025
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
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Manuel Mendoza @longchrom.bsky.social · 22/03/2025
Come start your lab in beautiful Strasbourg 🇫🇷 www.nature.com/naturecareer...
nature.com
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.
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Nacho Molina @molinalab.bsky.social · 20/03/2025
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.
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Manuel Mendoza @longchrom.bsky.social · 19/03/2025
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/...
This schematic illustrates the interplay between transcription coactivator perturbations (e.g., TIP60 or ATAC complex depletion) and RNA homeostasis. Perturbations lead to alterations in mRNA synthesis, which are counterbalanced by changes in mRNA export and cytoplasmic decay of specific transcripts, thereby maintaining RNA homeostasis.
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Mounia Lagha @laghalab.bsky.social · 16/03/2025
Don’t forget to register for this special conference. If you like gene regulation from single molecule approaches, please join us #EMBLSingleMolecule. Imaging and Omics and a bit of theory for lots of fun!
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Manuel Mendoza @longchrom.bsky.social · 28/02/2025
We're hiring! The Development & Stem Cells department at @igbmc.bsky.social, Strasbourg 🇫🇷 is recruiting a group leader working in cell & developmental biology. Our Integrated Structural Biology department also has an open call. More details below! + contact me for informal enquiries #sciencejobs
CALL FOR TWO GROUP LEADER POSITIONS
IGBMC 2025
The Institute of Genetics, Molecular and Cellular Biology (IGBMC), a
leading European research institute near Strasbourg, France, is seeking
two outstanding group leaders to establish independent research teams in
Development & Stem Cells & Integrated Structural Biology.CALL FOR TWO GROUP LEADER POSITIONS
IGBMC 2025
The Institute of Genetics, Molecular and Cellular Biology (IGBMC), a
leading European research institute near Strasbourg, France, is seeking
two outstanding group leaders to establish independent research teams in
Development & Stem Cells & Integrated Structural Biology.
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Samuel Zambrano @samuzambrano.bsky.social · 07/03/2025
The pro-EU demonstration 'una piazza per l'Europa', March 15th in Rome, is a great initiative but... www.comune.roma.it/partecipa/pu... Why not reproducing it in ALL Italian cities? Actually... Why not reproducing it in ALL European cities, from Madrid to Tallinn? (We the 🇪🇺 people are ready!)
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Alfonso Valencia @alfonsovalencia.bsky.social · 02/03/2025
PUBMED is down. This is disaster !! We do not have the system and organization to replace it. (EuroPMC is great but not a replacement) It is crystal clear that we cannot depend on critical systems provided by a single provider. European reaction has to include science and science infrastructures.
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David Suter @davidsuter.bsky.social · 13/02/2025
(6/6) #Epigenetics #StemCells Check out the preprint: www.biorxiv.org/content/10.1...
biorxiv.org
Mechanisms of gene regulation by SRCAP and H2A.Z
Discriminating regulatory functions of chromatin composition from those of chromatin-modifying complexes is a central problem in gene regulation. This question remains unexplored in the context of his...
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@tim_stasevich @tim-stasevich.bsky.social · 12/02/2025
Making intrabodies from antibodies just got easier! Learn how we made 𝟭𝟵 intrabodies to bind and light up peptides and histone modifications in live cells. And thanks to Academia, all sequences are freely available. (video credit: Yuko Sato @YukoSatoT2) (1/15) www.biorxiv.org/content/10.1...
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IGBMC @igbmc.bsky.social · 04/02/2025
Friday Lectures – Giacomo Cavalli Join us on Friday, 7th February at 3pm for a talk by Giacomo Cavalli, expert in Polycomb regulation and 3D genome architecture. He’ll explore how these mechanisms affect epigenetic inheritance and cancer development. Don’t miss it! #Epigenetics #Genomics #Cancer
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Mounia Lagha @laghalab.bsky.social · 18/01/2025
Come join us for this very first conference on single molecule approaches (both omics et imaging) to understand gene expression regulation. Lots of slots for young selected speakers!
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Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · 14/01/2025
The next TriRhena Gene Regulation Club takes place at IGBMC #Strasbourg. Save your seat & submit a talk. Strengthen your local #epigenetics network & collaborate with peers. 📅 5 Feb. 2025 | 14:00 🎟️ Free entry, registration required ✍️ Register by: 24. Jan. www.ie-freiburg.mpg.de/gene-regulat...
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Davide Mazza @davidemazza.bsky.social · 20/12/2024
We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, 🔬 focused: sciencedirect.com/science/arti... A big thank you to Tom Fillot for his efforts on this and to @hansen_lab @marcelonollmann for their help as editors.
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Peter Koo @pkoo562.bsky.social · 10/12/2024
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