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Tomàs Montserrat Ayuso

@tmontsay.bsky.social
458 followers 892 following 22 posts

💻 PhD Student @ Functional Genomics Team, CNAG 🎓 Associate Lecturer in Bioinformatics @ UVic-UCC 📚 Author of biologydatascience.com 🔬 Exploring genomics, data science, and the frontiers of biology

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Reposted by Tomàs Montserrat Ayuso
CNAG @cnag-eu.bsky.social · 06/11/2025
🌍Yesterday, our PhD student @tmontsay.bsky.social from the Functional Genomics Team presented his poster at #EMBOMobileGenome on 'A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses' 🙌 Excellent work and insightful discussions! @annaesteveco.bsky.social #CNAG
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Reposted by Tomàs Montserrat Ayuso
Tomàs Montserrat Ayuso @tmontsay.bsky.social · 31/07/2025
🧵 1/ 🚨 New preprint alert! Excited to share my first PhD paper, supervised by @annaesteveco.bsky.social at @cnag-eu.bsky.social: 📄 A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses 📄 Preprint: www.biorxiv.org/content/10.1... 🧬 Read on for the dataset & code!
biorxiv.org
A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses
Human endogenous retroviruses (HERVs) occupy nearly 8% of the human genome, yet their protein-coding potential remains largely unexplored. Like their exogenous counterparts, HERVs derive from ancestra...
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Tomàs Montserrat Ayuso @tmontsay.bsky.social · 31/07/2025
🧵 1/ 🚨 New preprint alert! Excited to share my first PhD paper, supervised by @annaesteveco.bsky.social at @cnag-eu.bsky.social: 📄 A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses 📄 Preprint: www.biorxiv.org/content/10.1... 🧬 Read on for the dataset & code!
biorxiv.org
A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses
Human endogenous retroviruses (HERVs) occupy nearly 8% of the human genome, yet their protein-coding potential remains largely unexplored. Like their exogenous counterparts, HERVs derive from ancestra...
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Reposted by Tomàs Montserrat Ayuso
CNAG @cnag-eu.bsky.social · 26/05/2025
🧬Great presentation by our Functional Genomics Team Leader, @annaesteveco.bsky.social, at #eshg2025! 🗣️She showcased our work on “Integrative multi-omics for undiagnosed Rare Diseases (Omics-RD)” 👏 Congratulations, Anna, and well done to the team behind this project! #RareDiseases #CNAG
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Reposted by Tomàs Montserrat Ayuso
CNAG @cnag-eu.bsky.social · 22/05/2025
🌍Today is #BiodiversityDay! 🧬At CNAG, we decode genomes to protect life on Earth and guide conservation efforts 🦉In the last two years, we have assembled nearly 50 reference genomes under the umbrella of @ebpgenome.bsky.social, @ergabiodiv.bsky.social, and @catbiogenoma.bsky.social #Biodiversity
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Gennady Gorin @goringennady.bsky.social · 15/04/2025
New preprint out! This is probably my most important paper. To my deep chagrin, it has no math. XIST is a non-coding RNA exclusive to XX females. It silences one of the X chromosomes. So what is it doing in male heart Schwann cells?
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Reposted by Tomàs Montserrat Ayuso
CNAG @cnag-eu.bsky.social · 19/02/2025
🌟Great News: CNAG is now on BlueSky! 🚀From Barcelona to the world, we’re bringing you the latest in genomics! Stay tuned for breaking news, cutting-edge technologies, groundbreaking research, and upcoming events 🔗https://www.cnag.eu #Genomics #Innovation #Research #BlueSky #CNAG
media.tenor.com
a blue sky with a butterfly and the word bluesky on it
ALT: a blue sky with a butterfly and the word bluesky on it
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Reposted by Tomàs Montserrat Ayuso
Anshul Kundaje @anshulkundaje.bsky.social · 07/01/2025
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/ www.encodeproject.org/single-cell/...
encodeproject.org
Single cell – ENCODEHomo sapiens clickable body map
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Reposted by Tomàs Montserrat Ayuso
Anshul Kundaje @anshulkundaje.bsky.social · 25/12/2024
Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
biorxiv.org
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
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Reposted by Tomàs Montserrat Ayuso
Will Macnair @willmacnair.bsky.social · 20/12/2024
So happy to see this work published! This is still the biggest single nuclei dataset of MS, and poses some fascinating questions. We found that the proportions of cell types across lesion types varied as expected, e.g. in active lesions we saw fewer oligos and more microglia.
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Institute for Regeneration and Repair @edinuni-irr.bsky.social · 20/12/2024
People living with multiple sclerosis #MS could be prescribed personalised treatment in future, helped by research published in Neuron today in which Prof Anna Williams and colleagues studied more than half a million brain cells. @mssocietyuk regeneration-repair.ed.ac.uk/personalised... #CRM
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Reposted by Tomàs Montserrat Ayuso
Anna Esteve Codina @annaesteveco.bsky.social · 13/12/2024
Huge effort from @anaconesa.bsky.social at @scb.iec.cat comparing long-read RNA technologies @pacbio.bsky.social @nanoporetech.com and softwares #sqanti3, #bambu, #talon, #isoquant, for isoform discovery, still challenging to disentangle real biology from artefacts
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Reposted by Tomàs Montserrat Ayuso
Lee Zamparo @lzamparo.bsky.social · 13/12/2024
Also filter on markers like MALAT1, cell intronic mapping reads cf. bmcgenomics.biomedcentral.com/articles/10....
bmcgenomics.biomedcentral.com
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
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Reposted by Tomàs Montserrat Ayuso
Anna Esteve Codina @annaesteveco.bsky.social · 12/12/2024
Brilliant presentation by @jamesasharpe.bsky.social at XII Jornades de Bioinformàtica i Genòmica by @scb.iec.cat about mechanistic dynamical models and #Turing patterns to go from genes to phenotypes
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Anna Esteve Codina @annaesteveco.bsky.social · 12/12/2024
Spreading our work at the XII Jornades de Bioinformàtica i Genòmica de la @scb.iec.cat @tmontsay.bsky.social about our recent discovery rdcu.be/d04Gz of pervasive presence of not completly lysed cells in reference cell atlases @humancellatlas.org compromising quality & model training
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Ming Tommy Tang @tommytang.bsky.social · 11/12/2024
chatomics! Bioinformatics is NOT Just Statistics! 🚨 The p-value is small in this example, but is it biologically meaningful?
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Tomàs Montserrat Ayuso @tmontsay.bsky.social · 03/12/2024
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8
bmcgenomics.biomedcentral.com
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
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Reposted by Tomàs Montserrat Ayuso
Nikolai Slavov @slavov-n.bsky.social · 02/12/2024
The distribution of ~ 2 trillion immune cells in the human body.
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Sophien Kamoun @kamounlab.bsky.social · 24/11/2024
ChatGPT and similar LLM systems will help you save time here when used judiciously 👇
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Julien Roux @julienroux.bsky.social · 26/11/2024
I created a starter pack including people working in #bioinformatics core facilities 🧬 🖥️ I am sure I missed a lot of relevant people, so if you'd like to be added or know people who should be in there, let me know! go.bsky.app/LfGCpSX
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