Associate Professor @UPFBarcelona. Computational genomics R/Bioc dvlpr. He/him, vi/vim. Mastodon: @robertclab@genomic.social. BlueSky: @robertclab.bksy.social

Barcelona
Joined January 2012
We’ve lost an icon. Margaret Hamilton, a computer science pioneer best known for her work at MIT leading development of the flight software for the Apollo missions to the moon, has died at 90. Read about her legacy via MIT News: news.mit.edu/2026/margaret-h…
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Robert Castelo retweeted
arXiv has updated our policy on rate limiting for all submitters. This update was made to fairly distribute moderator time & support the arXiv community of staff, volunteers, readers & authors. Please read our announcement to learn more: blog.arxiv.org/2026/10/01/up…
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Robert Castelo retweeted
ATENCIÓ ⚠️ Imatges de l'ensorrament del sostre de l'estació de Fabra i Puig de Barcelona. Les infraestructures d'aquest país, sobretot les depenents d'Espanya, són tan precàries, que s'enfonsen posant en risc la vida dels ciutadans.
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Robert Castelo retweeted
I resigned from Anthropic today. I spent the last three years doing pretraining research at both OpenAI and Anthropic. Neither company is acting responsibly. They are racing straight to self-improving superintelligence and gambling with our lives. More thoughts below.
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1/ 🥛🥛🥛 Avui estic de moltíssima mala llet. 
Les competències educatives dels nostres fills són l'única matèria primera que té aquest país. No tenim petroli: tenim escoles. I l'únic mirall extern que ens diu si eduquem bé o malament es diu PISA. Aquest any, Catalunya no tindrà mirall. L'hem trencat nosaltres. Millor dit, El GOVERN DE TOTHOM. Obro fil. 🧵
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🔴 TODAY‼️ PRBB-CRG conference 📋 Geospatial Data Science for Public Health Surveillance 🗣️ Paula Moraga - @KAUST_News 📆 July 27 - ⏰ 12:00 hosted by: @robertclab - @UPFbiomed 📍 #PRBB Maria Skłodowska-Curie room
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Robert Castelo retweeted
📣 New PRBB-CRG conference 📋 Geospatial Data Science for Public Health Surveillance 🗣️ Paula Moraga - @KAUST_News 📆 July 27 - ⏰ 12:00 hosted by: @robertclab - @UPFbiomed 📍 #PRBB Maria Skłodowska-Curie room
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Robert Castelo retweeted
cell sorting using flow cytometry xitter.cf/faavoredsoul/status/20…
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Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
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Arguably the most boring step in genomics is the first one: normalization. Settled science. Scale + log. Move on. Except that here's been a huge blind spot in the field. And it matters for AIxBio. A 🧵about what I think may be one of the most important papers I've written. 1/
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Today we're announcing ESMFold2, an open scientific engine to power prediction, design, and discovery across protein biology. The new model delivers state of the art performance on protein interactions, especially antibodies, a critical modality for therapeutics. We have designed and validated miniprotein binders and single chain antibodies across five therapeutic targets that are important in cancer and immunology. We are seeing very high success rates, and affinities at levels consistent with therapeutic activity. We’re also releasing an atlas of 6.8 billion proteins, and 1.1 billion predicted structures. ESMFold2 is built on a state of the art language model that has been trained on billions of protein sequences. A world model of protein biology emerges through language modeling. We’ve used the techniques of mechanistic interpretability developed to understand large language models to understand the concepts ESM uses to represent proteins. The model’s representation space has a compositional organization of features across scales, levels of complexity, and abstraction, that reflects and mirrors the understanding of protein biology developed through a century of empirical science. This understanding emerges without prior knowledge, just from language modeling of protein sequences. Language models are becoming a powerful substrate to understand and program biology. The design of protein interactions is one of the most fundamental problems in biophysics, and has critical implications for the discovery of new medicines. A simple gradient based search with the model was able to discover high-affinity protein binders. I'm excited by the potential this has to accelerate basic science and the understanding of proteins. And especially for the new avenues it opens up for therapeutic design and medicine.
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Venter was an abrasive dick, but his general "we can just do things" attitude was transformative in modern genomics. He went against the plodding consensus, and succeeded time after time, first with EST sequencing, then with shotgun sequencing of bacteria and most famously with shotgun sequencing of flies and humans. I will never forget sitting behind Francis Collins and Eric Lander (the chief honshos of the public human genome project) at the CSHL Biology of Genomes meeting in 1998 right when Venter's Celera was announced, and seeing them panicking because they knew he was going to succeed and make them look like fools (which, despite their massaging of the press, he ultimately did).
I came back to the United States, hearing about a very sad news: Craig Venter passed away today. He is a pioneer, successfully sequenced the first Human genome, and tried to create Synthetic Cells. We lost a giant in Science. RIP. @JCVenterInst
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Robert Castelo retweeted
Barbacid ocultó sus intereses empresariales cuando anunció una supuesta 'curación' del cáncer de páncreas, como revelamos en EL PAÍS el 6 de febrero. La Academia de Ciencias de EE UU acaba de retractar su estudio por esa turbia maniobra: elpais.com/ciencia/2026-04-2… Por @Nunodomin
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The number of grant applications is rising sharply. Our capacity for their evaluation isn’t. ERC President Maria Leptin explains why stricter resubmission limits are being introduced for 2027 calls and what this mean for applicants. link.europa.eu/xF7kjc
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Robert Castelo retweeted
Me ha encantado este texto. Creo que da en el clavo en muchas cosas.  Lo que digo siempre: "Tarea que pueda ser copiada, merece ser copiada". 👉 f.mtr.cool/rcwrfpnxhb
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In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/…
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Replying to @joseledecastro
Seguramente algo tendrá que cambiar, pero también es verdad que la tesis doctoral es un medio (para la formación de un investigador/a), no un fin. También salimos a hacer deporte y corremos durante 1 hora, a pesar de que un coche haría el mismo recorrido en 5 min.
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we just published (in G3) the genome of the oldest living thing on Earth: the bristlecone pine, which can live 5,000 years or more. Do we know yet what allows it to live so long? No, but the genome is a great place to start ucdavis.edu/climate/news/unl…
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Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs.
New preprint on longcallD: a unified framework for joint calling and phasing of small, structural and mosaic variants from long reads. Improved SV calling and competitive small variant calling. Supervised by @lh3lh3 , co-work with @QianAlvinQin1, @wwliao88 and @irahall9.
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Wow! Detecten les 5 bases de l'ADN i l'ARN a les mostres de l'asteroide Ryugu! Adenina, guanina, citosina, timina i uracil són l'alfabet amb què s'escriuen els llibres d'instruccions de la vida (ADN i ARN). Què significa aquesta troballa? Fil...
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