BSc in Genetics at @UABBarcelona MSc in Bioinformatics at @UPFBarcelona PhD in Structural Bioinformatics at @dundeeuni Postdoctoral Research Fellow at @ucl
London, England, UK
Joined July 2020
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Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
The scientific programme for 3D-BioInfo 2026 is live! 🧬And today is the last chance to take advantage of the discounted registration rate!
🔗Register: iscb.org/3dbioinfo2026/regis…
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
Our bioRxiv paper introduces ECIFP: a scalable interaction fingerprint that maps the landscape of ligand binding modes.
✅ Identified binding modes for 9k+ ligands
✅ Analysis of 48k+ binding sites from 21k+ proteins
✅ Open-source & interpretable
more:
biorxiv.org/content/10.64898…
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
I'm 6 months into this fellowship, and it's been brilliant. If you've got ideas at the intersection of AI and science and want to take a shot at making them real then I can't think of a better opportunity. 8 DAYS LEFT TO APPLY TO JOIN COHORT 2. @encode_pillarvc @ARIA_research
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
Excited to announce the release of our open-source protein family language model, ProFam-1, designed to generate functional protein variants and predict fitness using in-context example sequences. 1/n
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
🎄✨ Season’s Greetings from PDBe ✨🎄
The PDBe wishes you a very Merry Christmas and a Happy New Year. We are delighted to share our jointly designed EMDB/PDBe Christmas card with you. It has been a busy year, and we look forward to seeing you in the New Year.
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
New Research: COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices frontiersin.org/articles/10.… #FrontiersIn #Bioinformatics
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
In short: individual NMD efficiency is a key factor in health & disease. 🔑
Huge thanks to @FranSupek & the @GenomeDataLab at @IRBBarcelona @PCB_UB! 🙏
#NMD #Bioinformatics #CancerResearch #Genomics #PhD #tumorevolution
8/8
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
Clinically, this is huge:
⬇️ Lower NMD efficiency correlated with ⬆️better survival 👍, higher CD8+ T-cell infiltration🥷, and improved predictive models of immunotherapy response 🛡️🤺!
7/8
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
Variable NMD efficiency shapes tumor evolution by influencing selective pressures on TSGs like TP53 (⬆️ positive selection in driver nonsense mutations for turmors with ⬆️ NMD activity). 🧬
6/8
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
2️⃣👶Our analysis of inherited rare variants points to the chromatin modifier KDM6B as a key gene that can tune an individual's NMD efficiency. 🌡️
5/8
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
What drives this variability? 🤔
1️⃣ Somatic alterations in tumors. A common chromosome 1q gain (affecting NMD genes like SMG5 and SMG7) is linked to⬇️ lower NMD efficiency in ~25% of cancers.
4/8
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
🧠 Nervous system & reproductive tissues: ⬇️ Lower NMD activity.
🩸Gastrointestinal tissues: ⬆️ Higher NMD activity, especially in hypermutated (MSI) tumors.
3/8
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
⚙️We developed 2 methods to measure individual-level NMD efficiency (iNMDeff) in TCGA & GTex datasets. This was done using allele-specific expression (ASE) of germline variants & transcript expression of endogenous NMD targets. 📊
2/8
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
🚨 My PhD paper is officially published in @GenomeBiology! 📜🚀
We quantified the efficiency of a key cellular mRNA QC pathway (NMD) 🧬across thousands of human tumors & healthy tissues, revealing its activity is highly variable!
🧵1/8 👇
🔗genomebiology.biomedcentral.…
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @BSC_CNS. Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
🧬💻BSC creates a computational method that reveals previously hidden connections between diseases
Researchers observed positive interactions, in which one disease favours the onset of another, such as between asthma and Parkinson's disease; and negative interactions, in which some groups of patients with one disease may be protected from developing others, such as between cancer and Huntington's disease
➡ bsc.es/4kh
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
🌹Meet #ROSIE, our new AI that predicts spatial multi-protein expression straight from routine H&E images.
Built on a large co‑staining dataset (>1k samples, 16M+ cells). It enables cell phenotyping & tissue structure insights w/o extra assays.
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
Explore 🧭 a residue’s structural environment in the context of its linked annotations. Colour-coding 🖍️residues in the sequence points you to places of interest, go and discover.
Try yourself: wwwdev.ebi.ac.uk/pdbe/entry/…
#PDBeBeta #ResidueLevelInsights #PDBeValidation #ARISE #IUCr
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
🧬 🔨 Residue-level insights powered by AI. Explore insight for specific amino acids from primary literature #TextMining
🔍 Check out the ⭐ Text Annotations (AI) ⭐ tab on the new #PDBeBeta pages!
🔗 wwwdev.ebi.ac.uk/pdbe/entry/…
#AIinBiology #Biology #Science #ARISE #IUCr
Dr Javier Sánchez Utgés @javierutges.bsky.social retweeted
We were thrilled to represent PDBe (PDBe.org) at #ISMBECCB2025.
A great opportunity to connect with users, collaborators & fellow data enthusiasts alongside our @emblebi colleagues!
Thanks to everyone who chatted with us about proteins, RNA, DNA, ligands & more!
