Tomàs Montserrat Ayuso
@tmontsay.bsky.social
💻 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
🎓 Associate Lecturer in Bioinformatics @ UVic-UCC
📚 Author of biologydatascience.com
🔬 Exploring genomics, data science, and the frontiers of biology
Pinned
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...
www.biorxiv.org
🧵 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!
🚨 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!
Reposted by Tomàs Montserrat Ayuso
🌍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
🙌 Excellent work and insightful discussions!
@annaesteveco.bsky.social #CNAG
November 6, 2025 at 9:19 AM
🌍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
🙌 Excellent work and insightful discussions!
@annaesteveco.bsky.social #CNAG
Reposted by Tomàs Montserrat Ayuso
🧵 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!
🚨 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!
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...
www.biorxiv.org
July 31, 2025 at 6:21 AM
🧵 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!
🚨 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!
🧵 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!
🚨 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!
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...
www.biorxiv.org
July 31, 2025 at 6:21 AM
🧵 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!
🚨 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!
Reposted by Tomàs Montserrat Ayuso
🧬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
🗣️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
May 26, 2025 at 9:43 AM
🧬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
🗣️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
Reposted by Tomàs Montserrat Ayuso
🌍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
🧬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
May 22, 2025 at 10:21 AM
🌍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
🧬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
Reposted by Tomàs Montserrat Ayuso
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?
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?
Male XIST expression in cardiac pseudo-glia does not induce X chromosome inactivation https://www.biorxiv.org/content/10.1101/2025.04.09.648005v1
April 15, 2025 at 7:40 PM
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?
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?
Reposted by Tomàs Montserrat Ayuso
🌟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
🚀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
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
media.tenor.com
February 19, 2025 at 1:33 PM
🌟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
🚀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
Reposted by Tomàs Montserrat Ayuso
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/...
www.encodeproject.org/single-cell/...
Single cell – ENCODEHomo sapiens clickable body map
www.encodeproject.org
January 7, 2025 at 9:29 PM
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/...
www.encodeproject.org/single-cell/...
Reposted by Tomàs Montserrat Ayuso
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/
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/
December 25, 2024 at 11:48 PM
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/
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/
Reposted by Tomàs Montserrat Ayuso
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.
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.
Delighted to see this research now out. Thank you to @willmacnair.bsky.social, @gocastelobranco.bsky.social, @rebeccakssmith.bsky.social, @sjaekel.bsky.social, charles ffrench-Constant, Dheeraj Malhotra and many more not on bluesky for making it happen.
December 20, 2024 at 6:02 PM
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.
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.
Reposted by Tomàs Montserrat Ayuso
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
regeneration-repair.ed.ac.uk/personalised...
#CRM
December 20, 2024 at 4:09 PM
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
regeneration-repair.ed.ac.uk/personalised...
#CRM
Reposted by Tomàs Montserrat Ayuso
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
December 13, 2024 at 12:50 PM
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
Reposted by Tomàs Montserrat Ayuso
Also filter on markers like MALAT1, cell intronic mapping reads cf. bmcgenomics.biomedcentral.com/articles/10....
December 13, 2024 at 2:42 PM
Also filter on markers like MALAT1, cell intronic mapping reads cf. bmcgenomics.biomedcentral.com/articles/10....
Reposted by Tomàs Montserrat Ayuso
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
December 12, 2024 at 9:44 AM
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
Reposted by Tomàs Montserrat Ayuso
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
December 12, 2024 at 10:32 AM
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
Reposted by Tomàs Montserrat Ayuso
chatomics! Bioinformatics is NOT Just Statistics! 🚨 The p-value is small in this example, but is it biologically meaningful?
December 11, 2024 at 2:15 PM
chatomics! Bioinformatics is NOT Just Statistics! 🚨 The p-value is small in this example, but is it biologically meaningful?
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
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...
bmcgenomics.biomedcentral.com
December 3, 2024 at 8:38 AM
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
Reposted by Tomàs Montserrat Ayuso
The distribution of ~ 2 trillion immune cells in the human body.
December 2, 2024 at 2:46 PM
The distribution of ~ 2 trillion immune cells in the human body.
Reposted by Tomàs Montserrat Ayuso
ChatGPT and similar LLM systems will help you save time here when used judiciously 👇
Non-native English speakers need 50% more time to write a paper
When they do, they face a 2.5 times higher chance of being rejected because of language
journals.plos.org/plosbiology/...
When they do, they face a 2.5 times higher chance of being rejected because of language
journals.plos.org/plosbiology/...
November 24, 2024 at 8:45 AM
ChatGPT and similar LLM systems will help you save time here when used judiciously 👇
Reposted by Tomàs Montserrat Ayuso
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
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
November 26, 2024 at 9:30 AM
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
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