Computational biology @UCPH_Research/@IRBBarcelona: genetics & evolution of tumors & human populations. #ERC, #HorizonEU, #NNF, #DCS, #DFF funded. PI @FranSupek

Copenhagen & Barcelona
Joined June 2017
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Genome Data Science lab retweeted
Hot off the press – new study from the group: 🧬🤖 A DNA language model for predicting mutation risk trained on massive genomic data sets A mutation seen again and again across cancer genomes looks like a causal change. But sometimes the DNA site is simply very easy to mutate and so generates a hotspot 🔥. We built MutFormer AI model to separate these two possibilities: operating at single-nucleotide resolution, it separates “driver” from “passenger” hotspots. (awesome work by Ivan Galvan 🔝, Marcell Veiner @MarcellVeiner et al. 👏)
🤖 Made with AI
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Genome Data Science lab retweeted
My group is looking to recruit 2 postdocs👩‍💻👨‍🏫 on the "A-SOuRCCE" project: 1⃣ AI for Knowledge Graphs in Regulatory Genomics 2⃣ Agentic AI for Scientific Discovery in Genomics Ideal positions for recent bioinformatics/genomics/compbiol PhDs looking to pivot towards AI 🖥️🧠 & to do impactful science. Also great for computer science people looking to get into genomics. Apply via links below! 👇 Deadline in ~2 weeks (10.2.)
Delighted to share that our project on agentic AI for genomic science has been funded!🌟 We secured 1.7M € from @novonordiskfond in “Data Science Investigator: Distinguished”🙏 A-SOuRCCE stands for "AI for Single-cell Omics and Reproducible Cardiometabolic & Cancer Exploration"
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Genome Data Science lab retweeted
Our new preprint! Inhibiting nonsense-mediated mRNA decay makes tumors more visible to the immune system. In a 🐭 tumours blocking NMD reduced tumor burden, and NMDi + anti–PD-1 worked even better. A great team effort @FranSupek and @TheAnaJanic labs 👇🔗biorxiv.org/content/10.64898…
Excited to share our latest collaborative study of a frontier approach in cancer immunotherapy, targeting the Nonsense-Mediated mRNA Decay (NMD) pathway. Read more in a short 🧵+ link to preprint is below:
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Genome Data Science lab 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.…
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Genome Data Science lab retweeted
Fantastic to be in such great company!🤩 👏Congrats to 19 colleagues from my institutions (🇩🇰BRIC @UCPH_health and 🇪🇸@IRBBarcelona) in this year's Elsevier/Stanford top 2% most cited researchers list
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Paper by our Patricia feat. Ivan GF is now out in @GenomeMedicine! 🧩HR-deficiency mutational signature SBS3 decomposes into at least 2 signatures when analysed in a multi-modal manner (indel+SNV jointly) As WGS gets widely available, good to include indels in mutsig analyses✅
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Congrats to our CRISPy fresh doctor 👏👏 Marcel McCullough for successfully defending his PhD thesis: 🧬✂️Combinatorial Gene Editing in Human Cells to Model Deficiencies of DNA Repair in Cancer Thx to committee members @CeronLab @LValleResearch and @DSzuts for great discussion!
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Very cool collaborative work of our lab w/group of Lluis Ribas at @IRBBarcelona, spearheaded by the 2 Marinas 😀Marina Murillo and our alumna @msalvadoresf
In this fascinating preprint, the authors uncover an eye-opening feature of tRNA genes: they’re insanely prone to mutation. Analyzing somatic mutations in cancer tissues, they report that tRNA genes are up to 9 times more mutated than protein-coding genes. Interestingly, the known biology of tRNA biology seems to line up neatly with this observation. tRNA genes are hypermutable for three reasons: - they are heavily transcribed than most protein-coding genes—more transcription means more chances for damage. - they’re transcribed by RNA Polymerase III, which lacks the robust DNA repair machinery that is coupled with RNA polymerase II that transcribe protein-coding genes. - they’re prime targets for APOBEC3 enzymes—viral defense agents that mutate single-stranded DNA and seem to hit tRNA genes as innocent bystanders. But the most interesting finding is this: when the somatic mutations hit the anticodon region (that recognizes amino-acid), they make the tRNAs to insert the wrong amino acids during translation, misspelling proteins without any change to the underlying DNA or mRNA. It's like a stealth mode mutation that defies the central dogma of biology, rewriting the proteome without touching the genome! Paper: Murillo-Recio et al. bioRxiv. Characterization of Somatic Mutations in Human tRNA Genes Reveals Tumor-Specific Mutational Loads, and the Generation of tRNA Variants that Alter the Genetic Code. bioRxiv 2025
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Genome Data Science lab retweeted
🧵Ahmed’s @GenomeDataLab paper on evolution of chemotherapy resistance is out in @NatureComms! We developed DiffInvex - a method tracking how #cancer driver genes change under therapy, applied to ~10k genomes. Key insight: resistance often emerges through existing pathways. 1/5
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Genome Data Science lab retweeted
🚨 Big news! I'm thrilled to share that our latest research has just been published in Nature Communications 🎉 🔍 Title: DiffInvex identifies evolutionary shifts in driver gene repertoires during tumorigenesis and chemotherapy 📎 doi.org/10.1038/s41467-025-5… (1/4) ⬇️
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Genome Data Science lab retweeted
Great news – we received funding from the Independent Research Fund Denmark @DFF_raad! 🧬We will study #cancer driver mutations in tumor suppressor genes. In particular, we will focus on so-called "dominant negative" mutations, by combining #genomics, #AI & CRISPR gene editing
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Double PhD defense day in the lab 🤩 Congrats to our dr. Guille Palou @gpaloumarquez, fresh from the oven 🎊🥳 and similarly so our newly-minted dr. Ignasi Toledano @IgnasiToledano! Amazing defense both, bravo 👏👏
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Website for the Marie Curie "INTERACT" call for interdisciplinary PhD fellowships at UCph/DTU/DCS is now up 👇 interact-msca.ku.dk/ Applications open 20th December.
No less than 6⃣6⃣ PhD fellowships will be available to assorted groups at 🌆U of Copenhagen & to 🇩🇰DTU via the "INTERACT" call 🎓Applications open 20/12. Spread the word! Apply + join us👇 Maybe there is a Nobel prize in physics awaiting you as well 😁 linkedin.com/posts/biotech-r…
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Genome Data Science lab retweeted
Postdoc and PhD position in AI for cancer genomics at BRIC/UCPH. Only 5 days left to apply!
Replying to @FranSupek
➡️Postdoc in AI for Cancer Genomics at the Supek Group, BRIC candidate.hr-manager.net/App… ➡️PhD fellowship in AI for Cancer Genomics at the Supek Group, BRIC candidate.hr-manager.net/App… Deadline 14/11. For informal inquiries, drop me an email.
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The youngsters from lab are at @EMBLEvents DNA Replication symposium #EESreplication 🧬 Our alumna dr. Marina @msalvadoresf and PhD Marcell @MarcellVeiner gave talks on their recent work 👏-- identifying DNA replication origins by mutation patterns and neural nets🤖
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Genome Data Science lab retweeted
🔥PhD student & postdoc opportunity @GenomeDataLab! Are you keen on: - driving cutting-edge science @ interface of #AI and cancer #genomics? - working in a dynamic & supportive environment of @UCPH_BRIC? - joining the U of Copenhagen, top-3 ranked uni in EU? Apply below👇
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Genome Data Science lab retweeted
No less than 6⃣6⃣ PhD fellowships will be available to assorted groups at 🌆U of Copenhagen & to 🇩🇰DTU via the "INTERACT" call 🎓Applications open 20/12. Spread the word! Apply + join us👇 Maybe there is a Nobel prize in physics awaiting you as well 😁 linkedin.com/posts/biotech-r…
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EMBO DNA Replication symposium -> still in time to register to attend! 👏to our @MarcellVeiner and @msalvadoresf - they will have talks on using 🤖#AI and cancer mutation analysis to understand 🧬DNA replication in human cells👇 embl.org/about/info/course-a…
Deadline for abstracts approaching! Don't miss this exciting DNA Replication Symposium 🧬 Stellar speaker lineup! MANY talks selected from abstracts.
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