Rafa F Leiro
@rfleiro
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Structural Biology & Genome Integrity @ CNIO
Madrid, Spain
Joined July 2014
Our REPAIRome study finally out today in @ScienceMagazine !!! https://t.co/LOJHQa4Yqe
science.org
The analysis of DNA sequence outcomes provides molecular insights into double-strand break (DSB) repair mechanisms. Using parallel in-pool profiling of Cas9-induced insertions and deletions (indels)...
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Congratulations to all the people involved, also in @ChromDyn @rfleiro @gjmacintyre labs @CNIOStopCancer Specially leading authors @ErnestoLDA1811 Israel Salguero and @DanielGLL_ Very proud of you!!!
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@ScienceMagazine 🧬The human repairome, REPAIRome, will allow researchers around the world to check out how each of the 20,000 human genes affects DNA repair. Authors: @CortesLab @ErnestoLDA1811 Israel Salguero Daniel Giménez et al. Funding: @CienciaGob @AgEInves @Europarl_ES
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Researches at #cniostopcancer create the ‘human repairome’, a catalogue of DNA ‘scars’ that will help define personalised cancer treatments. Published in @ScienceMagazine https://t.co/Fu0UIIhMF6
cnio.es
You can always be judged by your scars. This is the idea that sums up one of the new breakthroughs in basic and biomedical research published today in the journal Science, an achievement of the...
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Our GPUs are always busy processing cool cryoEM data❄️, but we *really* wanted a to mess around designing protein binders. To avoid swamping our cluster (and our colleagues complains 😅), we built a small batch-based binder design pipeline. Hopefully you'll find it useful too!
We present BinderFlow, a modular & automated pipeline that makes de novo protein binder design more accessible, efficient, and user-friendly. Preprint by @Nayimcete, Twitterless Carlos, @LlorcaLab, and myself: https://t.co/OElkbCkETT Open source code: https://t.co/GL07gSBCpe
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We hope BinderFlow empowers more labs to explore generative protein design, making it a routine tool for both exploratory & production-level research. Everything is open source: https://t.co/GL07gSBCpe Read the full preprint here: https://t.co/OElkbCkETT
biorxiv.org
Deep learning has revolutionised de novo protein design, with new models achieving unprecedented success in creating novel proteins with specific functions, including artificial protein binders....
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BinderFlow is fully modular: - Swap in new backbone generators, sequence designers, or scoring tools - Add new strategies as they emerge We illustrate this with two refinement approaches: - Partial Diffusion - Sequence Diversity
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We also developed BFmonitor, a web dashboard for real-time tracking: - Visualise metrics (pLDDT, PAE, PyRosetta scores) - Compare candidates - Export sequences & structures ready for DNA synthesis
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Instead of running thousands of designs in a linear workflow, BinderFlow splits campaigns into parallelised batches, enabling: - Efficient GPU use - Live monitoring - Stopping once enough hits are reached - Coexistence with other GPU-intensive tasks (e.g., cryoEM)
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Designing artificial protein binders has huge potential in therapeutics & biotech. But current methods are computationally demanding and require deep expertise. BinderFlow lowers these barriers, democratising binder design for experts & non-specialists alike.
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We present BinderFlow, a modular & automated pipeline that makes de novo protein binder design more accessible, efficient, and user-friendly. Preprint by @Nayimcete, Twitterless Carlos, @LlorcaLab, and myself: https://t.co/OElkbCkETT Open source code: https://t.co/GL07gSBCpe
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beautiful work!
Pre-print out from the @SternbergLab with our contribution on the structural side. Great effort from Matt, Egill Tanner and the rest of the team leaded by awesome Sam! A 1 year effort on my side learning helical reconstruction by cryoEM... 👇
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Pre-print out from the @SternbergLab with our contribution on the structural side. Great effort from Matt, Egill Tanner and the rest of the team leaded by awesome Sam! A 1 year effort on my side learning helical reconstruction by cryoEM... 👇
1/16 New pre-print from the Sternberg Lab! We uncover how temperate phages can use RNA-guided transcription factors to remodel the flagellar composition of their bacterial host and enhance their fitness. Find the preprint and full story here: https://t.co/rh4PoOWn9l
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If you -have years of postdoc experience, -love doing basic/clinical research, -like sharing your knowledge, -enjoy working in scientifically stimulating environment, -are looking for a permanent position Join my lab at @CNIOStopCancer!
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We are delighted to share our collaborative work with Ibarra Lab @3M_Lab and Fernandez-Leiro Lab @rfleiro, in which we dissect autoregulatory mechanism of Twinkle helicase! Big thank you to Sjoerd Wanrooij @Wanrooij20 and other reviewers for a smooth process! @Greg_Ciesielski ;
nature.com
Nature Communications - The human mitochondrial helicase Twinkle is essential for maintaining mitochondrial DNA. Here, the authors combine biochemical and single-molecule approaches to show how...
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I'm excited to share our new publication in @Nature! We showed that under Ni-limited conditions, similar to those in nature, #methanogens shift electron flow from [NiFe]- to [Fe]-hydrogenase Hmd with the help of a newly discovered protein complex, Elp. https://t.co/DuOBEBR7To
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Excited to share our latest paper, published in Nature Communications! As first author from @3M_Lab, I’m proud of this collaborative effort with @LabMito and @rfleiro, where we dissect the autoregulatory mechanism of the mitochondrial helicase Twinkle. 🔗
nature.com
Nature Communications - The human mitochondrial helicase Twinkle is essential for maintaining mitochondrial DNA. Here, the authors combine biochemical and single-molecule approaches to show how...
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Congrats to MCB's Eva Nogales on her election to the Fellowship of the Royal Society! 👏🎉 @royalsociety @NogalesLab
https://t.co/BY0qV4UWSi
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Great tool for AUTOMATIC primer design for cloning using in vivo DNA assembly! awesome work with the group of Sebastian Hiller and Radu Leonte spearheading! Upload your plasmid map, click on what you want to do and download your primers and new map! https://t.co/WdcGzJ7ewi
academic.oup.com
Abstract. Molecular cloning through in vivo assembly (IVA) is an efficient homology-based approach that can achieve complex cloning operations in a single
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@CaixaResearch @zhang_imperial @CostaLabCrick @rfleiro @NogalesLab In the second part of session 5 Meindert Lamers from @LUMC_Leiden will talk about how to target bacterial DNA polymerases for the next generation of antibiotics. Registration for #CFM_MolMech still open at https://t.co/zZTYGYDf79
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