Guess what I found today. Online course contents for Experimental Design and Analysis with R at UC Davis (listed as Plant Sciences 205 at UC Davis). I took it back in 2017 when I was a PhD student, but now it is also online! I highly recommend. deruncie.github.io/PLS205_course/

every girl should have a balcony or a terrace or maybe even a secret garden hidden from the outside world

I don’t care where you stand on the death penalty, if the prosecutor’s office seeks to vacate a conviction and the victim’s family want the sentence commuted—the state should not execute that person. This headline is an indictment of Missouri.

We’ve had a busy few years.

PROTECT YOUR CARS: The City of Tampa has opened all of its parking garages for free so residents in low-lying and flood-prone areas can protect their cars ahead of Milton. 8.wfla.com/4gREeKu

A 1,000,000th reminder the crucial importance of basic research. Ambros and Ruvkun were looking into understanding nematode genetics and development, not looking for a drug, and ended up opening an entire new area in biology

MGnify Proteins – our vast database of protein sequences derived from metagenomic sequencing – is now accessible via the web (ebi.ac.uk/metagenomics/p…) and via Google Cloud BigQuery Public Datasets. For the full news, see ebi.ac.uk/about/news/upd…

2024 #NobelPrize laureate in chemistry David Baker has succeeded with the almost impossible feat of building entirely new kinds of proteins. In recent years, one incredible protein creation after the other has emerged from Baker’s laboratory. They range from new nanomaterials

This year’s chemistry laureates Demis Hassabis and John Jumper have developed an AI model, AlphaFold2, to solve a 50-year-old problem: predicting proteins’ complex structures. Check out two examples of protein structures determined using AlphaFold2. First up, a bacterial enzyme

Big shout out to those researchers who made their data available in PDB over the years The Chemistry Nobel Prize winners today relied on that open academic data to train their models We wouldn't have these advances if researchers hadn't made 200,000 protein structures available

And we got it!!!! This is a historical day for Bioinformatics! Since always we get comments about bioinformatics and computational biology being secondary disciplines in comparison to experimental disciplines. No more! Congrats to the Nobel winners!! Today we celebrate!!!

Clearly, we’re now in the golden age of biology: physiology/medicine Nobel to tiny RNAs; physics Nobel to neural networks; chemistry Nobel to protein structure prediction.

The Nobel prize website has a pretty well made 1-pager on how Alphafold works

For the first (and probably last) time in my life I understand the technical details of both the physics and chemistry Nobel prizes.

These laureates are VERY deserving. But an important addendum—no model could be trained without 40 years of Helen Berman and others’ work at the PDB, and we would not be certain of AF’s success without 30 years of John Moult and others’ work on CASP. Hats off to them as well 🥂

I'm thrilled to see the 2024 Nobel Prize in Chemistry going to the Computational Biology field of Protein Structure Prediction BCBHubCSIC I2SysBio ISCB News INB / ELIXIR-ES CSIC HiTSeq 2026 ELIXIR Europe

We have now made our model code and data for our viral genome language model, Protein Set Transformer, public. If you are interested in viruses, genome, and deep learning - do check it out! Link to preprint below. Happy for any feedback

PUBLIC DOMAIN ILLUSTRATIONS FROM THE NIH!!!

I think all jobs should be closed Election Day. It happens once every 4 years. Let us off of work!

The single worst thing about Trump to me will always be how much he's changed people. I've watched friends and relatives become entirely new, worse people in the wake of his political rise. Like it's not merely that he's a terrible guy, it's that he's ruined people.