Fernán Agüero

You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.

This saves some clicking around. Neat!

Amazing news that the 5th Virtual @chembiotalks.bsky.social attracted 450 participants from 50 countries.

If you are as excited as we are, already mark next year's date (29th of September, 2026) in your calendars and make sure to suggest your favorite speakers!

#ChemSky #ChemBio #DrugDiscovery

Test the activity of 300+ natural enzymes against 100+ substrates, discover 200+ new enzymatic reactions, and train machine learning models to predict which enzymes can do which reactions.

@aepaton.bsky.social @gabegomes.bsky.social @alisonnarayan.bsky.social

www.nature.com/articles/s41...

Yes, yes, Europe has its benefits. Walkable cities. Cultural heritage. Amazing food. Little gun violence. Healthcare. Governments that are not shut down. But the number of website pop-ups asking one to accept cookies renders the continent pretty much unlivable.

End GDP mania: how the world should really measure prosperity The obsession with economic output as a measure of human development puts sustainability on the back burner. Researchers can now help to devise better indicators.

The obsession with economic output as a measure of human development puts sustainability on the back burner

Time to end the GDP mania

Our editorial inspired by a @nature.com paper that looks at how the world should really measure prosperity
🧪 #SGDs #doughnuteconomics
www.nature.com/articles/d41...

See this? This = implanting mouse embryo. Usually this happens inside its mother and is invisible to us, but we can actually watch implantation ex vivo with the hope of understanding why implantation goes awry in embryos of older women. A 🧵...

💊Did you know that ChEMBL @chembl.bsky.social isn’t just for bioactivity data?

It also curates open-access info on approved drugs and clinical candidates.

Explore why ChEMBL should be a go-to resource if you work in pharma, biotech & AI drug discovery.

📖 pubs.acs.org/doi/10.1021/...

#PharmSky

Cool work to design phospho-tyrosine binder by the Baker lab. They show it works but success rate is low (<0.1%) and binders are not super strong (>500nM, likely related to cost of desolvating the phosphate) .
www.biorxiv.org/content/10.1...

How to rapidly search the world’s microbial DNA By making the world’s microbial DNA easier to explore, LexicMap helps researchers track outbreaks, study antibiotic resistance, and understand microbial diversity.

There are millions of openly available microbial genomes, but searching them can be slow.

Until now 🥁

Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more.

www.ebi.ac.uk/about/news/r...
🦠

So for >30y, it was thought that #MAPK cascade in #fission #yeast lacked a scaffold ! Like in #animals, or #budding yeast.

Well this changes today !

All hail #Sms1

Congrats @borissieber.bsky.social @sophiemartinlab.bsky.social and Team !!

my stand mixer is older than most of gen z and I think about that A LOT every time something I bought in the last 5 years breaks after 6 months.

How to freeze the =today() function once data has been entered I would like to use the =TODAY() function in a table in excel. However, once data has been entered into that table row, I would like it never to change dates again (effectively capturing the date t...

I was TODAY() years old when I learnt that using `Ctrl + ;` in Excel enters the current date into a cell.

I was breaking my mind trying to use TODAY() but then wanted the date to be fixed once I entered the rest of the data in a row.

stackoverflow.com/questions/31...

Understanding Life: Using Largescale Biodiversity Reference Genomes by Wellcome Connecting Science Conference dates: 27-29 October 2025, Join us for a series of focused workshops into the methods and technologies transforming genomics and biodiversity research.

Register for your place at #Biodiversity25 by 29 September! ⏰

Connect with experts tackling the same #BiodiversityResearch challenges as you🌱

Learn how to apply the latest genomics tools and approaches to transform your eukaryotic genome studies🧬

📎 bit.ly/4j3vAZ9
#BiodiversitySky

5 surprisingly hopeful things we learned about Alzheimer’s this year From a blood test to the unexpected role of lithium, these findings may lead to better diagnosis and treatment of the memory-robbing condition.

If you are like a lot of people, you might be anxious about the risk of getting dementia as you age.

From a blood test to the unexpected role of lithium, these findings may lead to better diagnosis and treatment of the memory-robbing condition.

GPU-accelerated homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

“When it comes to the AI technology industry, we refuse their frames, reject their addictive and brittle technology, and demand that the sanctity of the university both as an institution and a set of values be restored.”

zenodo.org/records/1706...

4/🧵

Make the most of the ChEMBL interface with our newest webinar! Before starting a new drug discovery project, it’s useful to compile existing data on compounds and targets of interest. Open access bioacti...

The ChEMBL team is providing a free “Drug Design” webinar chembl.blogspot.com/2025/09/make...

🧵 Thread with my favourite quotes from:

📝 Guest, O., Suarez, M., Müller, B., et al. (2025). Against the Uncritical Adoption of 'AI' Technologies in Academia. Zenodo. doi.org/10.5281/zeno...

1/🧵

Geographic distribution of human toxoplasmosis

DeepSeek-R1, now published in Nature, shows how reinforcement learning can turn AI into more than an imitator. By rewarding correct answers, it develops reasoning strategies on its own—achieving breakthroughs in math, coding, and STEM problem-solving. www.nature.com/articles/s41...

Why science needs outsiders - Works in Progress Magazine Science has forgotten that the greatest breakthroughs often come from outsiders who are able to take a fresh perspective.

Fun article about “outsider” scientists and their breakthroughs.

“Academia filters most funding, publishing, and hiring decisions through senior insiders, which favors ideas within existing paradigms.”

worksinprogress.co/issue/why-sc...

Chagas disease isn’t increasing in the US. Testing just lags behind Americans in the southern US often go years without knowing they’re infected with ‘kissing bug’ disease

News headlines have blasted in recent weeks that the carrier of the potentially deadly parasite Trypanosoma cruzi—the cause of Chagas disease—has been detected in 32 US states. cen.acs.org/biological-c... #chemsky 🧪

Join us for upcoming BSP Tryps Club meetings! Schedule here ⬇️

A timeline titled "The Golden Age of Antibiotics" shows when each antibiotic drug class was first available for medical use, with example antibiotics labeled. Classes are color-coded by their source: actinomycetes, other bacteria, fungi, or synthetic. Milestones include the first antibiotics (arsphenamines in 1910), as well as the discovery of many actinomycetes-derived antibiotics, such as streptomycin, and sulfonamides, penicillins, and tetracyclines. Data: Hutchings, Truman, Wilkinson (2019). Created by Saloni Dattani for Our World in Data.

This graphic shows about two-thirds of all antibiotic drug classes were developed during the "Golden Age of Antibiotics" from the early 1940s through the mid-1960s.

Since 1970, just 8 new classes of antibiotics have been approved.
ourworldindata.org/golden-age-a... (by @scientificdiscovery.dev)

Piqued my interest. Not a cardiologist, but what type of ECG data is used as input for training? Digital readings of electrical signals? (e.g. numbers in a plain text file) Or digital images of scanned ECGs?

While the github repo is apparently empty. Would love to peruse data out of curiosity.

How market design can feed the poor America's largest non-profit had a broken distribution system. University of Chicago economists fixed it.

Very interesting post on how the non-profit Feeding America implemented an auction system with its own currency which massively improved allocation of food to food banks.

www.worksinprogress.news/p/how-market...

YouTube video by ThePrimeTime DHH Is Right About Everything

Open Source is not a democracy. It's a meritocracy.
Absolute must-watch interview with David Heinemeier Hansson aka DHH, creator of Ruby on Rails.

www.youtube.com/watch?v=mTa2...

@biorxivpreprint.bsky.social There are some cool aspects to this new genetic study, so forgive my poking for fun:
1. HLA is associated control of virus infections (uh, duh?)
2. Is it even significant? (p = 9.1×10-851 )
www.biorxiv.org/content/10.1... @harvardmed.bsky.social

Interesting, didn't know about "raincloud plots". Here are my hot takes:

1. Raincloud plot is not a new plot, but 3 plots stacked (density, box plot, jittered 1d scatter).

Figure 2 from the linked article.

Abstract of the linked article

New paper for anyone working with data:
Better data viz - for free, in few clicks.

Below, all N = 111, M = 0.04, SD = 0.27.
One-sided t-tests vs. 0 yield: t(110) = 1.67, p = .049.

Use raincloud plots. Or risk wrong conclusions!
Plot w/ @jaspstats.bsky.social today!

🧪 📊 #PsychSciSky #StatsSky

🧵👇