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Charlie Pugh

@cwjpugh.bsky.social
266 followers 1.2K following 12 posts

PhD candidate - Machine Learning and Genomics @CRG.eu with @jonnyfrazer.bsky.social and @MafaldaFigDias

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Reposted by Charlie Pugh
Ezequiel Galpern @eag91.bsky.social · 25/09/2026
🧬 What do deep-learning models for proteins actually learn? Our new review looks at how model predictions relate to fitness, folding stability and function. With @cwjpugh.bsky.social, Mafalda Dias & @jonnyfrazer.bsky.social 🔗 chemrxiv.org/doi/full/10....
chemrxiv.org
From sequences and structures to fitness, folding and function: challenges in the age of AI | ChemRxiv
Deep-learning models have transformed our ability to predict the phenotypic effects of sequence perturbations. Protein language models (pLMs) score the evolutionary propensity of any amino-acid substi...
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Charlie Pugh @cwjpugh.bsky.social · 05/08/2026
It was great to contribute to this new work from our group led by @eag91.bsky.social 1/2
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Reposted by Charlie Pugh
Ezequiel Galpern @eag91.bsky.social · 05/08/2026
1/ New preprint! with @solersanchisx.bsky.social @cwjpugh.bsky.social @federicobilleci.bsky.social @jonnyfrazer.bsky.social and Mafalda Dias, we introduce a scalable framework to improve stability prediction and separate folding from functional constraints. www.biorxiv.org/content/10.6...
biorxiv.org
Blending physics-based and inverse folding models to disentangle variant effects on stability and function
Protein sequences are constrained not only by the need to fold into stable structures, but also by specific functional requirements imposed by natural selection. Yet predictions of how amino-acid chan...
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Reposted by Charlie Pugh
Centre de Regulació Genòmica (CRG) @crg.eu · 15/06/2026
Mafalda Dias es finalista del premio Vanguardia de la Ciencia. Su línea de investigación está ayudando agilizar el diagnóstico de enfermedades raras, ofreciendo una evidencia adicional para médicos que ya tienen sospechas sobre ciertos genes implicados según los síntomas. ¡Vota ahora!
lavanguardia.com
“Diagnosticamos enfermedades raras analizando millones de años de evolución”
Vota a las finalistas del premio Vanguardia de la Ciencia
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Reposted by Charlie Pugh
Jonathan Frazer @jonnyfrazer.bsky.social · 23/10/2025
Applications are open for the @crg_eu PhD Programme! 20 fully funded positions — including one in our group through the Evolutionary Medical Genomics ITN. Join us to develop deep generative models of cross-species data to tackle open questions in disease genetics. www.crg.eu/en/content/t...
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Charlie Pugh @cwjpugh.bsky.social · 26/05/2025
New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n www.biorxiv.org/content/10.1...
biorxiv.org
From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models
Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...
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Reposted by Charlie Pugh
Isabelle Zane @isabellease.bsky.social · 22/05/2025
@cwjpugh.bsky.social at #VariantEffect25
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Reposted by Charlie Pugh
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 03/12/2024
Three BioML starter packs now! Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc Pack 3: go.bsky.app/NAKYUok DM if you want to be included (or nominate people who should be!)
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Reposted by Charlie Pugh
iseultleahy.bsky.social @iseultleahy.bsky.social · 28/11/2024
Thanks Charlie for opening the PhD Symposium! Many thanks to everyone involved in its organisation. #CRGPhDSymp2024
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