Yago Arribas
@yarribas.bsky.social
Immunologist. Mass spectrometry. Decoding non-coding but coding genome. Català a París.
Pinned
Yago Arribas
@yarribas.bsky.social
· Dec 12
Transposable element exonization generates a reservoir of evolving and functional protein isoforms
Transposable element exonization by unannotated splicing events produces stable protein isoforms with acquired functions that are subject to evolutionary selection.
www.cell.com
Not easy to describe the emotions of seeing our work published in @cellpress.bsky.social ! We explored how novel isoforms emerge during evolution through the exonization of Transposable Elements. Exonized TEs modify the functions and structures of host proteins.
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Yago Arribas
@biorxivpreprint.bsky.social Endogenous retroelements promote tolerance to dietary antigens @belkaidlab.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 11, 2025 at 3:43 AM
@biorxivpreprint.bsky.social Endogenous retroelements promote tolerance to dietary antigens @belkaidlab.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Yago Arribas
🚨🚨🚨 New review article on #microexons from the lab! A comprehensive recap of the current state of the field by @tahneema.bsky.social.
www.annualreviews.org/content/jour...
www.annualreviews.org/content/jour...
September 1, 2025 at 10:20 AM
🚨🚨🚨 New review article on #microexons from the lab! A comprehensive recap of the current state of the field by @tahneema.bsky.social.
www.annualreviews.org/content/jour...
www.annualreviews.org/content/jour...
Reposted by Yago Arribas
Many transcriptome regions are translated but not known to encode proteins. They remain poorly annotated and thus under studied, partly due to the lack of terminology for these features.
In @natmethods.nature.com we propose using "Translon" for any region decoded by the ribosome
In @natmethods.nature.com we propose using "Translon" for any region decoded by the ribosome
September 1, 2025 at 3:37 PM
Many transcriptome regions are translated but not known to encode proteins. They remain poorly annotated and thus under studied, partly due to the lack of terminology for these features.
In @natmethods.nature.com we propose using "Translon" for any region decoded by the ribosome
In @natmethods.nature.com we propose using "Translon" for any region decoded by the ribosome
Reposted by Yago Arribas
🧬🚨PREPRINT🚨- The first placental isoform reference from long-read seq & supporting data! We demonstrate how tissue-specific assembly improves transcript quantification with short-read data from multi-ancestry birth studies & reveals placenta-mediated effects of gestational diabetes on birth weight🫄
Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function
The placenta plays a critical role in fetal development and mediates maternal metabolic effects on offspring health outcomes. Despite its importance, the placenta remains understudied in large-scale g...
doi.org
July 2, 2025 at 1:08 PM
🧬🚨PREPRINT🚨- The first placental isoform reference from long-read seq & supporting data! We demonstrate how tissue-specific assembly improves transcript quantification with short-read data from multi-ancestry birth studies & reveals placenta-mediated effects of gestational diabetes on birth weight🫄
Reposted by Yago Arribas
Excited to see this out in @science.org today!! www.science.org/doi/10.1126/...
May 1, 2025 at 6:17 PM
Excited to see this out in @science.org today!! www.science.org/doi/10.1126/...
Reposted by Yago Arribas
"The main fates after gene duplication are gene loss, redundancy, subfunctionalization and neofunctionalization".
In our new review, @fedemantica.bsky.social and I argue we are missing the most prevalent one: specialization. And the same applies to alternative splicing! 1/7
tinyurl.com/45k7kbmp
In our new review, @fedemantica.bsky.social and I argue we are missing the most prevalent one: specialization. And the same applies to alternative splicing! 1/7
tinyurl.com/45k7kbmp
March 18, 2025 at 1:53 PM
"The main fates after gene duplication are gene loss, redundancy, subfunctionalization and neofunctionalization".
In our new review, @fedemantica.bsky.social and I argue we are missing the most prevalent one: specialization. And the same applies to alternative splicing! 1/7
tinyurl.com/45k7kbmp
In our new review, @fedemantica.bsky.social and I argue we are missing the most prevalent one: specialization. And the same applies to alternative splicing! 1/7
tinyurl.com/45k7kbmp
Reposted by Yago Arribas
Excited to share my first post & see the second part of my PhD work published! Our study on mTNBC highlights that baseline clonal expansion of dysfunctional CD8 cells is linked to better response to chemoimmunotherapy.
More here: www.sciencedirect.com/science/arti...
#CD8 #TCellExhaustion #TNBC
More here: www.sciencedirect.com/science/arti...
#CD8 #TCellExhaustion #TNBC
Continuous replenishment of the dysfunctional CD8 T cell axis is associated with response to chemoimmunotherapy in advanced breast cancer
Chemotherapy combined with immune checkpoint blockade has shown clinical activity in breast cancer. Response, however, occurs in only a low proportion…
www.sciencedirect.com
March 10, 2025 at 5:54 PM
Excited to share my first post & see the second part of my PhD work published! Our study on mTNBC highlights that baseline clonal expansion of dysfunctional CD8 cells is linked to better response to chemoimmunotherapy.
More here: www.sciencedirect.com/science/arti...
#CD8 #TCellExhaustion #TNBC
More here: www.sciencedirect.com/science/arti...
#CD8 #TCellExhaustion #TNBC
Reposted by Yago Arribas
Nuevo número de la Revista de la @sebbm.bsky.social dedicado al “Genoma no codificante” coordinado por Crisanto Gutiérrez @cbm-csic-uam.bsky.social entrevista a Jordi Camí, @prbb.org y presidente del #CEEI con artículos+contenido interesante
Editora: @inmayruela.bsky.social
sebbm.es/revista/nume...
Editora: @inmayruela.bsky.social
sebbm.es/revista/nume...
El genoma no codificante
sebbm.es
March 10, 2025 at 5:40 PM
Nuevo número de la Revista de la @sebbm.bsky.social dedicado al “Genoma no codificante” coordinado por Crisanto Gutiérrez @cbm-csic-uam.bsky.social entrevista a Jordi Camí, @prbb.org y presidente del #CEEI con artículos+contenido interesante
Editora: @inmayruela.bsky.social
sebbm.es/revista/nume...
Editora: @inmayruela.bsky.social
sebbm.es/revista/nume...
Reposted by Yago Arribas
🌸Happy Women's Day! 💪👩🔬
As we wrap up our campaign, we celebrate the incredible contributions of women in science and beyond. 🌟
A big shoutout to the amazing women of the #yefis Task Force! ✨
Let’s keep inspiring and empowering each other. 💜
#WomensDay #WomenInScience #WomenInStem
As we wrap up our campaign, we celebrate the incredible contributions of women in science and beyond. 🌟
A big shoutout to the amazing women of the #yefis Task Force! ✨
Let’s keep inspiring and empowering each other. 💜
#WomensDay #WomenInScience #WomenInStem
March 8, 2025 at 10:18 AM
🌸Happy Women's Day! 💪👩🔬
As we wrap up our campaign, we celebrate the incredible contributions of women in science and beyond. 🌟
A big shoutout to the amazing women of the #yefis Task Force! ✨
Let’s keep inspiring and empowering each other. 💜
#WomensDay #WomenInScience #WomenInStem
As we wrap up our campaign, we celebrate the incredible contributions of women in science and beyond. 🌟
A big shoutout to the amazing women of the #yefis Task Force! ✨
Let’s keep inspiring and empowering each other. 💜
#WomensDay #WomenInScience #WomenInStem
1/ We saw an update on the PDAC neoantigen vaccine (Sethna et al., 2025). A remarkable effort in showing long-lived T cell protection in PDAC + an exhaustive look at the T cells. One question intrigued me: Were the selected neoantigens different between the 8 responder and 8 non-responder patients?
March 7, 2025 at 3:29 PM
1/ We saw an update on the PDAC neoantigen vaccine (Sethna et al., 2025). A remarkable effort in showing long-lived T cell protection in PDAC + an exhaustive look at the T cells. One question intrigued me: Were the selected neoantigens different between the 8 responder and 8 non-responder patients?
Merck & Co. digs into 'junk DNA' for cancer clues in new Epitopea deal
firstwordpharma.com/story/5936238
firstwordpharma.com/story/5936238
FirstWord
firstwordpharma.com
February 20, 2025 at 7:18 PM
Merck & Co. digs into 'junk DNA' for cancer clues in new Epitopea deal
firstwordpharma.com/story/5936238
firstwordpharma.com/story/5936238
I am very happy to share that last week, I had the opportunity to present my research at the Winter Meeting of the Catalan Society of Immunology. But I feel even more honored to have presented in a session chaired by my first mentor in immunology, Dolores Jaraquemada.
February 9, 2025 at 2:58 PM
I am very happy to share that last week, I had the opportunity to present my research at the Winter Meeting of the Catalan Society of Immunology. But I feel even more honored to have presented in a session chaired by my first mentor in immunology, Dolores Jaraquemada.
Reposted by Yago Arribas
Registration is now open for the next ImmunoSchool!
This year’s theme: "10 Years of Discovery in Immunotherapy." We’ve put together a stellar lineup of speakers—don’t miss it!
Free registration @ bit.ly/3WFj0Hc
#ImmunoSchool #Immunotherapy #CancerResearch
This year’s theme: "10 Years of Discovery in Immunotherapy." We’ve put together a stellar lineup of speakers—don’t miss it!
Free registration @ bit.ly/3WFj0Hc
#ImmunoSchool #Immunotherapy #CancerResearch
February 3, 2025 at 3:18 PM
Registration is now open for the next ImmunoSchool!
This year’s theme: "10 Years of Discovery in Immunotherapy." We’ve put together a stellar lineup of speakers—don’t miss it!
Free registration @ bit.ly/3WFj0Hc
#ImmunoSchool #Immunotherapy #CancerResearch
This year’s theme: "10 Years of Discovery in Immunotherapy." We’ve put together a stellar lineup of speakers—don’t miss it!
Free registration @ bit.ly/3WFj0Hc
#ImmunoSchool #Immunotherapy #CancerResearch
Reposted by Yago Arribas
Thrilled to introduce our Cell Reports @cellreports.bsky.social article, showing how the iconic 'Hallmarks of Cancer' are located in the space of real human primary tumors. A team effort co-led by Eduard Porta, Matthew H. Bailey, and yours truly #SpatialBiology #Visium
www.cell.com/cell-reports...
www.cell.com/cell-reports...
January 25, 2025 at 5:07 PM
Thrilled to introduce our Cell Reports @cellreports.bsky.social article, showing how the iconic 'Hallmarks of Cancer' are located in the space of real human primary tumors. A team effort co-led by Eduard Porta, Matthew H. Bailey, and yours truly #SpatialBiology #Visium
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Reposted by Yago Arribas
Top 4 things to know about doing science:
1. You need to have someone you can talk to
2. One-on-one discussions are the best
3. Think about discussions as improvisations and use the ‘yes, and’ rule
4. Create a safe space so both of you feel open to saying seemingly silly things
1. You need to have someone you can talk to
2. One-on-one discussions are the best
3. Think about discussions as improvisations and use the ‘yes, and’ rule
4. Create a safe space so both of you feel open to saying seemingly silly things
January 13, 2025 at 1:52 AM
Top 4 things to know about doing science:
1. You need to have someone you can talk to
2. One-on-one discussions are the best
3. Think about discussions as improvisations and use the ‘yes, and’ rule
4. Create a safe space so both of you feel open to saying seemingly silly things
1. You need to have someone you can talk to
2. One-on-one discussions are the best
3. Think about discussions as improvisations and use the ‘yes, and’ rule
4. Create a safe space so both of you feel open to saying seemingly silly things
Reposted by Yago Arribas
The last Cell issue of the year is online. This one is a doozy if you like interferons (as I do!) or transposons and ERVs (and who doesn't?!) There's also cool stem cell and dev bio in this issue, immune responses to Zika during pregnancy... cancer, plants... cool stuff! www.cell.com/cell/issue?p...
December 27, 2024 at 1:43 PM
The last Cell issue of the year is online. This one is a doozy if you like interferons (as I do!) or transposons and ERVs (and who doesn't?!) There's also cool stem cell and dev bio in this issue, immune responses to Zika during pregnancy... cancer, plants... cool stuff! www.cell.com/cell/issue?p...
Reposted by Yago Arribas
The final chapter of my PhD thesis is now out! 🎉 We compared the latest gene regulatory network (#GRN) inference methods for #single-cell multimodal datasets and evaluated their performance across various tasks. Hard to believe this journey started in March 2021 and has finally reached this point 😅🥳
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
December 23, 2024 at 8:49 AM
The final chapter of my PhD thesis is now out! 🎉 We compared the latest gene regulatory network (#GRN) inference methods for #single-cell multimodal datasets and evaluated their performance across various tasks. Hard to believe this journey started in March 2021 and has finally reached this point 😅🥳
Reposted by Yago Arribas
MAETi: Mild acid elution in a tip enables quantitative immunopeptidome profiling from 25,000 cells https://www.biorxiv.org/content/10.1101/2024.12.20.628848v1
December 22, 2024 at 7:18 AM
MAETi: Mild acid elution in a tip enables quantitative immunopeptidome profiling from 25,000 cells https://www.biorxiv.org/content/10.1101/2024.12.20.628848v1
Reposted by Yago Arribas
WeekendRead! @cicacanesso.bsky.social @danmucida.bsky.social @victora.bsky.social &co show @science.org that cDC1s & Rorgt APCs drive peripheral Tregs to dietary antigens, & that helminth infections increase the ratio of inflammatory cDC2 preventing tolerance induction!
Identification of antigen-presenting cell–T cell interactions driving immune responses to food
The intestinal immune system must concomitantly tolerate food and commensals and protect against pathogens. Antigen-presenting cells (APCs) orchestrate these immune responses by presenting luminal ant...
www.science.org
December 21, 2024 at 3:52 PM
WeekendRead! @cicacanesso.bsky.social @danmucida.bsky.social @victora.bsky.social &co show @science.org that cDC1s & Rorgt APCs drive peripheral Tregs to dietary antigens, & that helminth infections increase the ratio of inflammatory cDC2 preventing tolerance induction!
Reposted by Yago Arribas
🔬 New insights into protein diversity published in @cellpress.bsky.social: researchers led by Dr. Amigorena have identified over 1,000 unannotated protein isoforms derived from transposable element exonization.
Read full publication ⤵️
www.cell.com/cell/fulltext/S0092-8674%2824%2901328-X
Read full publication ⤵️
www.cell.com/cell/fulltext/S0092-8674%2824%2901328-X
December 20, 2024 at 9:40 AM
🔬 New insights into protein diversity published in @cellpress.bsky.social: researchers led by Dr. Amigorena have identified over 1,000 unannotated protein isoforms derived from transposable element exonization.
Read full publication ⤵️
www.cell.com/cell/fulltext/S0092-8674%2824%2901328-X
Read full publication ⤵️
www.cell.com/cell/fulltext/S0092-8674%2824%2901328-X
Reposted by Yago Arribas
To generate HLA-restricted, TAA-binding TCRs (normally eliminated by central tolerance), Abdelfattah et al. (1) mutated a TAA peptide of interest by a single amino acid, (2) used the mutant peptide to expand and identify endogenous reactive [...] acir.org/journal-art... @harvardmed.bsky.social
December 17, 2024 at 12:30 PM
To generate HLA-restricted, TAA-binding TCRs (normally eliminated by central tolerance), Abdelfattah et al. (1) mutated a TAA peptide of interest by a single amino acid, (2) used the mutant peptide to expand and identify endogenous reactive [...] acir.org/journal-art... @harvardmed.bsky.social
Reposted by Yago Arribas
Al 1990 va néixer l'ACCC (llavors l'Associació Catalana de Periodisme Científic), com anuncia la nota de premsa compartida aquí per @xavierduran.bsky.social, membre de la 1a Junta Directiva.
📖 Descobreix tota la història de l'ACCC a accc.cat/lassociacio/#historia
📖 Descobreix tota la història de l'ACCC a accc.cat/lassociacio/#historia
December 12, 2024 at 10:15 AM
Al 1990 va néixer l'ACCC (llavors l'Associació Catalana de Periodisme Científic), com anuncia la nota de premsa compartida aquí per @xavierduran.bsky.social, membre de la 1a Junta Directiva.
📖 Descobreix tota la història de l'ACCC a accc.cat/lassociacio/#historia
📖 Descobreix tota la història de l'ACCC a accc.cat/lassociacio/#historia
Reposted by Yago Arribas
How does the immune system make "decisions" at mucosal barriers? My new perspective explores how seeing strategic cell interactions through the lens of game theory could reveal fresh insights into mucosal immune homeostasis and disease. 🧵 1/7
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Organismal mucosal immunology: A perspective through the eyes of game theory
In complex organisms, functional units must interact cohesively to maintain homeostasis, especially within mucosal barriers that house diverse, specia…
www.sciencedirect.com
December 15, 2024 at 11:48 AM
How does the immune system make "decisions" at mucosal barriers? My new perspective explores how seeing strategic cell interactions through the lens of game theory could reveal fresh insights into mucosal immune homeostasis and disease. 🧵 1/7
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Yago Arribas
#NotOnlyParasites! 2 Cell papers by @edchuong.bsky.social lab & Amigorena lab demonstrate that transposable elements #TEs can exonize giving rise to functional (often shorter) proteins with distinct functions: eg a decoy short IFNAR2 that inhibits #interferon signaling! www.cell.com/cell/fulltex...
Transposable element exonization generates a reservoir of evolving and functional protein isoforms
Transposable element exonization by unannotated splicing events produces stable protein isoforms with acquired functions that are subject to evolutionary selection.
www.cell.com
December 12, 2024 at 5:36 PM
#NotOnlyParasites! 2 Cell papers by @edchuong.bsky.social lab & Amigorena lab demonstrate that transposable elements #TEs can exonize giving rise to functional (often shorter) proteins with distinct functions: eg a decoy short IFNAR2 that inhibits #interferon signaling! www.cell.com/cell/fulltex...
And more TEs! Exciting to see this field growing! 😊
I’m excited to share our latest study led by @giuliapasquesi.bsky.social out today in @cellpress.bsky.social , uncovering a new way transposons have been repurposed for human interferon signaling! Read on for a thread on cryptic splice variants, decoy receptors, and viruses (1/N) 👇🧵 #TESky 🧪
Regulation of human interferon signaling by transposon exonization
Transposable element exonization can yield functional protein isoforms as seen for primate-specific IFNAR2.
www.cell.com
December 12, 2024 at 8:14 PM
And more TEs! Exciting to see this field growing! 😊