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Fran Supek

@fransupek.bsky.social
377 followers 490 following 54 posts

🧬Genetics geek, 🤖AI enthusiast. PI @GenomeDataLab studying DNA repair, mutations, epigenome & NMD. 2xERC, professor @bric-ucph.bsky.social, GL @irbbarcelona.org and BRIC/KU. 🎲Chaotic good.

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Fran Supek @fransupek.bsky.social · 16/07/2026
♨️Hot off the press, new study from our group: 🧬🤖 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 & so generates a hotspot🔥
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Fran Supek @fransupek.bsky.social · 10/07/2026
DNA mismatch repair (MMR) deficiency is an important driver of cancer genome instability. Yet it is usually treated as a binary label 0️⃣/1️⃣: MSI-high or not. Our new preprint -- fresh from the oven🔥 -- argues that this simple dichotomy obscures the underlying biology.
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Reposted by Fran Supek
CRUK Convergence Science Centre @crukconvergence.bsky.social · 08/06/2026
🔬 @fransupek.bsky.social ( @bric-ucph.bsky.social) - how #DNA repair defects drive cancer evolution 💻 Dr Syed Haider ( @icr.ac.uk ) - using large-scale cancer #genomics #data to uncover synthetic lethal interactions and identify new therapeutic vulnerabilities. More information 👉 buff.ly/JHRhnJi
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Reposted by Fran Supek
Bernardo Rodríguez Martín @bernardo-rodriguez.bsky.social · 03/06/2026
📢📢 Job opening between the Bioinformatics Unit and my group (REPBIO) at @crg.eu Interested in contributing to our efforts to leverage long-read sequencing technologies for human genome research? Join us in Barcelona: recruitment.crg.eu/content/jobs... Please repost😊
recruitment.crg.eu
Bioinformatician | CRG Online Recruitment Portal
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Fran Supek @fransupek.bsky.social · 26/03/2026
✂️🧬preprint! "Quantitative prediction of nonsense-mediated #mRNA decay across human genes by #genomic language #model & large-scale mutational scanning" Fantastic teamwork by @IgnasiToledano 👨‍🔬and @MarcellVeiner👨‍💻. We combine massive experiment and sequence AI to elucidate NMD👇
AI-generated cartoon of a computational biologist and wet-lab biologist collaborating on a research project
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Fran Supek @fransupek.bsky.social · 02/02/2026
On the heels of the release of #AlphaGenome, we have written up a review on 🧬genomic language models for DNA/RNA, out in EMBO @molsystbiol.org journal 🔖"The DNA dialect: a comprehensive guide to pretrained genomic language models" by Marcell Veiner👏 & yours truly👇 link.springer.com/article/10.1...
Figure 1: Data modalities of genomic language models. From review article "The DNA dialect: a comprehensive guide to pretrained genomic language models" by Veiner and Supek.
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Fran Supek @fransupek.bsky.social · 24/01/2026
We also have a PhD student position open. Application deadline 10.2. 👇 candidate.hr-manager.net/ApplicationI...
candidate.hr-manager.net
PhD fellowship in AI for Single-Cell Disease Genomics at the Supek Group, BRIC
We are offering a PhD fellowship in AI for Single-Cell Disease Genomics commencing 1 May 2026, or soon thereafter (flexible start date). The PhD project is part
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Fran Supek @fransupek.bsky.social · 22/01/2026
We're recruiting 2 postdocs👩‍💻👨‍🏫 on the "A-SOuRCCE" project: 1️⃣AI for Knowledge Graphs in Regulatory Genomics (auto extraction, organization and querying of knowledge) 2️⃣Agentic AI for Scientific Discovery in Genomics (LLMs for hypothesis generation and assessment) Apply below! 👇 Deadline soon: 10.2.
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Fran Supek @fransupek.bsky.social · 15/01/2026
Delighted to share that our project on agentic AI for genomic science has been funded!🌟 We secured 1.7M € from @novo-nordisk.bsky.social in “Data Science Investigator: Distinguished” - v grateful!🙏 A-SOuRCCE stands for "AI for Single-cell Omics and Reproducible Cardiometabolic & Cancer Exploration"
AI-generated cartoon to illustrate the central idea of the A-SOuRCCE project
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Fran Supek @fransupek.bsky.social · 02/01/2026
📢new study @genomedatalab.bsky.social When a cell divides, it copies 3 billion DNA letters. How does it know where to begin? ⁉️For years, the field debated if replication initiation was random or strict 📜Our preprint uses AI + mutation signatures to show it’s a precise, two-part system
AI-generated graphical summary of the DNA replication origins study
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Fran Supek @fransupek.bsky.social · 09/12/2025
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:
Figure summarizing NMD from a review article Supek, Lehner and Lindeboom (2021) Trends in Genetics.
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Fran Supek @fransupek.bsky.social · 18/11/2025
📣 Attention postdocs in the life sciences! Are you ready to take the big leap? Start your lab at the Biotech Research and Innovation Centre in Copenhagen! 🇩🇰 @bric-ucph.bsky.social Collegial atmosphere, cutting-edge science, core funding. (+the weather is wonderful, relative to Siberia😁) Apply!👇
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Fran Supek @fransupek.bsky.social · 18/11/2025
Congrats to colleagues from IRB!
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Fran Supek @fransupek.bsky.social · 29/09/2025
🛑Guille's @guillepalou.bsky.social no-nonsense 😉 paper is out in @springernature.com Genome Biology! We report variable activity of the NMD pathway (mRNA QC) across tissues & individuals: 🧠less active in the nervous system & in reproductive tissues 🩸more active in digestive tract, muscle, blood
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Fran Supek @fransupek.bsky.social · 28/09/2025
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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Fran Supek @fransupek.bsky.social · 04/09/2025
Thanks to organizers for inviting!
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Reposted by Fran Supek
IRB Barcelona @irbbarcelona.org · 08/07/2025
🧬New approach to decoding mutational signatures improves prediction of prognosis in #OvarianCancer. 📰 #GenomeMedicine ✍️ Patricia Ferrer-T Iván Galván-F & @fransupek.bsky.social ➡️ bit.ly/4nA579b 📌DOI: 10.1186/s13073-025-01497-7 @genomedatalab.bsky.social @bric-ucph.bsky.social 🧪
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Fran Supek @fransupek.bsky.social · 01/07/2025
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 Julian Ceron, Laura Valle and David Szuts for a great discussion!
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Fran Supek @fransupek.bsky.social · 03/06/2025
Join us at BRIC/FinsenLab -- start your group at the University of Copenhagen!
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Fran Supek @fransupek.bsky.social · 14/05/2025
🧵 Ahmed’s @genomedatalab.bsky.social paper on evolution of chemotherapy resistance is out @natcomms.nature.com! We developed DiffInvex - a method tracking how #cancer driver genes change under therapy using ~10k whole-genomes. Key insight: drug resistance often emerges through existing pathways 1/5
AI-generated illustration of DNA with mutations, cancer cells, and drugs applied to them
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Fran Supek @fransupek.bsky.social · 12/05/2025
Great news – we received funding from the Independent Research Fund Denmark (DFF)! 🧬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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