iiinova — where your digital self keeps evolving

Nacho Molina @molinalab.bsky.social · 19/05/2025

Finally, if you've made it this far, you might be interested in testing the code. Feedback is very welcome! github.com/MolinaLab-IG... 6/6

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Nacho Molina @molinalab.bsky.social · 19/05/2025

HiddenFoot also works with Fiber-seq data! It reveals chromatin structure and nucleosome occupancy heterogeneity at single-molecule resolution driven by TF binding. 5/6

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Nacho Molina @molinalab.bsky.social · 19/05/2025

HiddenFoot resolves Pol II and nucleosome occupancy at the HIV-1 promoter, molecule by molecule. Under transcriptional inhibition (TLD), Pol II footprints vanish, while nucleosome occupancy at the +1 and −1 positions increases. 4/6

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Nacho Molina @molinalab.bsky.social · 19/05/2025

HiddenFoot infers pairwise interaction energies from single-molecule data and compares them to simulated equilibrium profiles to distinguish true TF–TF cooperativity from nucleosome-mediated co-binding. 3/6

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Nacho Molina @molinalab.bsky.social · 19/05/2025

HiddenFoot is a thermodynamics-based model that integrates known TF PWMs and nucleosome occupancy to efficiently evaluate all possible non-overlapping binding configurations. It fits model parameters using both stochastic gradient descent and MCMC. 2/6

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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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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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Nacho Molina @molinalab.bsky.social · 26/11/2024

3) Waves of RNA degradation rates and top predicted RBPs: Similarly, Zfp36l1, Tia1, Hnrnpl, Nudt21, Srsf1, and Fus have been linked to regulation of RNA stability or/and cell cycle... So, perhaps our predictions are not completely random! Happy to hear your feedback.

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Nacho Molina @molinalab.bsky.social · 26/11/2024

2) Waves of RNA export rates and top predicted RBPs: It seems that Nxf1, Hnrnpk, Taf15, Rbm10, Strap, and Ep300 may have a role in RNA export or/and cell cycle regulation.

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Nacho Molina @molinalab.bsky.social · 26/11/2024

1) Waves of transcription rates and top predicted TFs: Previous evidence shows that E2f4, Hmga1, Mybl1, and Hes1 are linked to cell cycle control and proliferation.

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Nacho Molina @molinalab.bsky.social · 19/11/2024

My favourite place for conferences!

A forest with a funny building in the background

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Nacho Molina @molinalab.bsky.social · 18/01/2024

Welcome! Avez-vous un compte en anglais ?

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Nacho Molina @molinalab.bsky.social · 17/01/2024

10X multiome allowed us to assess how chromatin accessibility changes throughout the cell cycle. Interestingly, dynamics within TF footprints reveal key cell cycle regulators.

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Nacho Molina @molinalab.bsky.social · 17/01/2024

Extending our biophysical model to single-nucleus transcriptomes shows clear waves of nuclear mRNA export!

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Nacho Molina @molinalab.bsky.social · 17/01/2024

Genome-wide, we've identified distinct waves of transcription and degradation during the cell cycle. Notably, postranscriptional regulation emerges as a key player in shaping mRNA accumulation.

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Nacho Molina @molinalab.bsky.social · 17/01/2024

Fitting a biophysical model to unspliced and spliced mRNA reads uncovers gene-specific transcription and degradation rates that dynamically change during the cell cycle:

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Nacho Molina @molinalab.bsky.social · 17/01/2024

We combined single-cell and single-nucleus sequencing with deep learning and biophysical modelling to analyse single-cell multiome data from mESCs. DeepCycle (doi.org/10.1038/s414...) is effective in sorting both single cells and nuclei according to their cell cycle progression:

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Nacho Molina @molinalab.bsky.social · 17/01/2024

Hey, I am new here! What better way to debut here than to share our recent bioRxiv preprint (the happiest moment during the publication process) on RNA metabolism and chromatin accessibility dynamics during the cell cycle: biorxiv.org/content/10.1... #CellCycle #GeneExpression #SingleCellMultiome

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Nacho Molina @molinalab.bsky.social · 15/01/2024

New year, new lab preprint! 🎉 I am so happy to share our latest work on RNA metabolism and chromatin accessibility dynamics during the cell cycle in mESCs: www.biorxiv.org/content/10.1101/202… #CellCycle #GeneExpression #SingleCellSequencing #DeepLearning #Biophysics @mauli...

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Nacho Molina @molinalab.bsky.social · 20/12/2022

Interested in developing new methods to analyse single-cell sequencing data combining generative deep learning with biophysical principles? Here at the @IGBMC you have a position! #PostdocPosition #ComputationalBiology #SingleCellBiology #DeepLearning #Biophysics (RT 🙏)

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Nacho Molina @molinalab.bsky.social · 01/06/2022

Hey, there are PhD positions on Computational Biophysics available in my lab! Interested? #PhDpositions #ComputationalBiology #ComputationalBiophysics jobrxiv.org/job/igbmc-27778-phd-pos…

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Nacho Molina @molinalab.bsky.social · 22/04/2022

I lived next to the @CERN for almost five years and never found time to visit it. I have finally resolved this anomaly!

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Nacho Molina @molinalab.bsky.social · 06/03/2022

A great talk from @Naefelix at #EESBioOsc studying circadian rhythms in human from post-mortem samples.

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Nacho Molina @molinalab.bsky.social · 06/03/2022

First in-person conference in two years! I think I forgot how to interact with people face-to-face 😅. #EESBioOsc

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Nacho Molina @molinalab.bsky.social · 28/10/2021

Last day of my short sabbatical at the @EMBLHeidelberg. I am going to miss the woods and the great science! Thanks @arnaud_kr to host me. I am very excited with the projects we have started. And thanks to the Theory@EMBL program for the support.

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Nacho Molina @molinalab.bsky.social · 09/04/2021

Do you want to do a PhD on #ComputationalBiology and #MachineLearning at the heart of Europe in a great and exciting scientific environment? We offer 2 PhD positions! Join our lab at the IGBMC! (Any help with dissemination is greatly appreciated):

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Nacho Molina @molinalab.bsky.social · 23/03/2021

And in collaboration with the Sexton lab to study chromatin dynamics in the context of TADs and its connections with function:

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Nacho Molina @molinalab.bsky.social · 23/03/2021

Today my second PhD student, Guilherme Oliveira, is defending his thesis! He has demonstrated to be a brilliant researcher. Here a preprint with his work on analyzing and modeling chromatin dynamics using Gaussian processes: www.biorxiv.org/content/10.1101/202…

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Nacho Molina @molinalab.bsky.social · 22/03/2021

Our latest stories online in @biorxivpreprint. 1) Chromatin dynamics + live-imaging + Gaussian processes: 2) Cell cycle + scRNAseq + deep learning: www.biorxiv.org/content/10.1101/202… #singlecell #deeplearning #cellcycle #chromatindynamics

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Nacho Molina @molinalab.bsky.social · 22/03/2021

We are also able to identify key TFs and their activity dynamics driven the observed gene expression dynamics around the cell cycle:

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Nacho Molina @molinalab.bsky.social · 22/03/2021

I am very excited with the new preprint of my team. A fantastic work of @arriba87 to estimate the cell cycle progression of single cells from scRNA-seq data: www.biorxiv.org/content/10.1101/202…

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Nacho Molina @molinalab.bsky.social · 17/12/2020

An amazing international PhD program at the heart of Europe. A great environment for research. Apply now! imcbio-phdprogram.unistra.fr

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Nacho Molina @molinalab.bsky.social · 07/05/2017

Vive la France! Long live Europe!

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Nacho Molina @molinalab.bsky.social · 23/03/2015

Estimación de los trasvases de voto en las elecciones andaluzas del 2015: molinalab.bio.ed.ac.uk/and2015.html

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Nacho Molina @molinalab.bsky.social · 22/03/2015

Estimación de la transferencia de voto en las andaluzas 2015. molinalab.bio.ed.ac.uk/and2015.html

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Nacho Molina @molinalab.bsky.social · 28/11/2012

Análisis cuantitativo (beta) sobre el trasvase de votos en las elecciones de Cataluña.

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