Robert Castelo

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

[Robert Castelo @robertclab]

@JaviRo92 @anigwei @electricscat Ara després de dinar ho he tornat a provar i m'ha funcionat, no sé què he fet diferent. En fi, creuem els dits q el tràmit arribi a bon port.

[Robert Castelo @robertclab]

@parejorejo @Imanol_arbelaiz @JaimeObregon Lo he vuelto a intentar después de comer y ahora ha funcionado. No sabría decir qué he hecho de forma distinta a esta mañana. En cualquier caso, gracias por los consejos!

[Robert Castelo @robertclab]

@JaviRo92 @anigwei @electricscat Jo estic igual, aquí una conversa amb algú q se n'ha sortit. Si trobes la solució fes-m'ho saber si us plau 🙏

[Robert Castelo @robertclab]

@parejorejo @Imanol_arbelaiz @JaimeObregon A mí me sigue dando el mismo error con certificado electrónico, tanto en Mac como en Windows. Algún otro consejo?

[Robert Castelo @robertclab]

@parejorejo @Imanol_arbelaiz @JaimeObregon La grabación está hecha desde una ventana de incógnito para intentar evitar q pille nada de la sesión anterior. Desde este mismo sistema accedo sin problemas a los trámites de la agencia tributaria e incluso puedo abrir mi carpeta de expedientes del mismo ministerio de industria.

[Robert Castelo @robertclab]

@parejorejo @Imanol_arbelaiz @JaimeObregon A mí me sigue dando el mismo error con certificado electrónico, tanto en Mac como en Windows. Algún otro consejo?

[Guillem Dels Comptesclars @Comptesclares]

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. 🧵

[Biomedicina BCN @the_prbb]

🔴 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

[Biomedicina BCN @the_prbb]

📣 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

[Vega Shah @dr_alphalyrae]

cell sorting using flow cytometry https://t.co/r1MHgh4aHm

[Heng Li @lh3lh3]

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 https://t.co/y5ZTr9btE6

[Lior Pachter @lpachter]

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/

[Alex Rives @alexrives]

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.

[Michael 英泉 Eisen @mbeisen]

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).

[Manuel Ansede @manuelansede]

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:
https://t.co/ToMju4YGEl Por @Nunodomin

[European Research Council (ERC) @ERC_Research]

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.
https://t.co/YavrW4P8FJ

[Manuel Fernández Navas @nolo14]

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".

👉 https://t.co/K9sdUbvc1h

[Steven Salzberg 💙💛 @StevenSalzberg1]

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: https://t.co/83cv4HqVMB

[Neila Campos @piquiliguardi]

@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.

[Steven Salzberg 💙💛 @StevenSalzberg1]

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 https://t.co/2wszLFcjlH

[Heng Li @lh3lh3]

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.