Nacho Molina
banner
molinalab.bsky.social
Nacho Molina
@molinalab.bsky.social
Group leader of the Stochastic Systems Biology Lab at IGBMC - CNRS - University of Strasbourg. Models of gene regulation based on biophysics-informed deep learning: https://www.igbmc.fr/molina
Pinned
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
Reposted by Nacho Molina
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👇
August 18, 2025 at 1:00 PM
Reposted by Nacho Molina
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...
August 18, 2025 at 12:23 PM
Reposted by Nacho Molina
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....
August 7, 2025 at 4:20 PM
Reposted by Nacho Molina
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.
July 23, 2025 at 7:44 AM
Reposted by Nacho Molina
#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!
July 18, 2025 at 12:04 PM
Reposted by Nacho Molina
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
July 17, 2025 at 10:31 AM
Reposted by Nacho Molina
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
June 11, 2025 at 12:30 PM
Reposted by Nacho Molina
🚨 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...
June 3, 2025 at 12:59 PM
Reposted by Nacho Molina
🟦 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...
May 31, 2025 at 1:11 PM
For Spanish speakers, this is a fantastic podcast about science and much more!
¡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!
🚨NUEVO EPISODIO🚨
S02E05 Apocalipsis en la historia (parte I)

Spotify
open.spotify.com/episode/7CJs...

YouTube
youtu.be/fTa3DROe1vE

iVoox
go.ivoox.com/rf/148751814

Y Apple Podcasts o cualquier app que te guste. ¡Amárrate al asiento, que hoy el programa va lleno de desastres! #podcast
May 29, 2025 at 5:26 PM
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
May 28, 2025 at 9:45 PM
Reposted by Nacho Molina
‼️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
May 27, 2025 at 1:45 PM
Reposted by Nacho Molina
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
May 21, 2025 at 3:44 PM
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
May 21, 2025 at 8:31 PM
Reposted by Nacho Molina
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
May 19, 2025 at 6:55 PM
Reposted by Nacho Molina
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...
www.biorxiv.org
May 3, 2025 at 6:27 PM
Reposted by Nacho Molina
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 🤩?
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
May 19, 2025 at 9:44 PM
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
May 19, 2025 at 6:55 PM
🚨 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...
May 17, 2025 at 5:00 PM
Reposted by Nacho Molina
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...
www.biorxiv.org
May 9, 2025 at 10:49 AM
Reposted by Nacho Molina
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....
May 8, 2025 at 3:19 PM
Reposted by Nacho Molina
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!
April 30, 2025 at 8:34 AM
Reposted by Nacho Molina
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...
April 23, 2025 at 3:26 PM
Reposted by Nacho Molina
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...
www.biorxiv.org
April 17, 2025 at 12:34 PM
Reposted by Nacho Molina
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!
🚨 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
April 10, 2025 at 10:19 AM