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Nacho Molina @molinalab.bsky.social · Aug 21

Congratulations, Arnaud!

Reposted by Nacho Molina

Arnaud Krebs @arnaudkr.bsky.social · Aug 18

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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Reposted by Nacho Molina

kasitc.bsky.social @kasitc.bsky.social · Aug 18

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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Reposted by Nacho Molina

Schubeler Lab @schubelerlab.bsky.social · Aug 7

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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Reposted by Nacho Molina

Yad Ghavi-Helm @yghavi.bsky.social · Jul 23

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.

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Reposted by Nacho Molina

Arnaud Krebs @arnaudkr.bsky.social · Jul 18

#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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Reposted by Nacho Molina

EMBL Events @events.embl.org · Jul 17

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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Reposted by Nacho Molina

Slavov Laboratory @slavovlab.bsky.social · Jun 11

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

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Reposted by Nacho Molina

Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · Jun 3

🚨 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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Reposted by Nacho Molina

Nikolai Slavov @slavov-n.bsky.social · May 31

🟦 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 · May 29

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

Saúl Ares @omeuxeito.bsky.social · May 29

¡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!

Podcast de la Vaca Esférica @lavacaesferica.bsky.social · May 29

🚨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

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Nacho Molina @molinalab.bsky.social · May 28

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 · May 27

‼️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

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Reposted by Nacho Molina

EMBL Events @events.embl.org · May 27

‼️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

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Nacho Molina @molinalab.bsky.social · May 22

Very cool, Lars! Congrats!

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Reposted by Nacho Molina

Lars Velten @larsplus.bsky.social · May 21

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

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Nacho Molina @molinalab.bsky.social · May 21

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 · May 19

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...

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Reposted by Nacho Molina

Nacho Molina @molinalab.bsky.social · May 19

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...

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Nacho Molina @molinalab.bsky.social · May 20

Thanks!

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Reposted by Nacho Molina

Selin Jessa @selinjessa.bsky.social · May 3

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

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Nacho Molina @molinalab.bsky.social · May 19

Thanks!

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Reposted by Nacho Molina

Dr Zeinab Rekad 🔬🧬🧪 @zeinabrekad.bsky.social · May 19

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 · May 19

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...

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Nacho Molina @molinalab.bsky.social · May 19

a man with long hair and a mustache is wearing a pink unicorn shirt

ALT: a man with long hair and a mustache is wearing a pink unicorn shirt

media.tenor.com

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Nacho Molina @molinalab.bsky.social · May 19

Muchas gracias!!!

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Nacho Molina @molinalab.bsky.social · May 19

Finally, if you've made it this far, you might be interested in testing the code. Feedback is very welcome! github.com/MolinaLab-IG...

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Nacho Molina @molinalab.bsky.social · May 19

HiddenFoot also works with Fiber-seq data! It reveals chromatin structure and nucleosome occupancy heterogeneity at single-molecule resolution driven by TF binding.

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