James Kirk! And lots of interesting research: royalsociety.org/news/2025/11...

This is quite interesting, they used a conservative method instead of allele frequency (not there yet maybe), but then it is good enough for the questions they asked. www.cell.com/cell/fulltex...

A nice paragraph!
"Viral emergence and pandemic preparedness in a One Health framework"
www.nature.com/articles/s41...

This is crazy, I think I may have accidentally activated this model API call and then cancelled it. All input tokens, what a waste!

Pacman!

This is pretty cool! FigTree can still handle a genealogy of two million cells.

Glad that I found some recent literature that shares my concerns, and I would want this to be part of the modelling effort. DNA/Protein/Genomic Language modelling bros for "designing new synthetic life", please, let's slow down a little bit.
doi.org/10.1007/s101...

This immediately has "side effects", another problem would be in human genomes and many other multicellular organisms genomic elements of viral origin actually play important roles.

I saw similar statement for other models, such as ESM3. It is like it is that easy and the developed models actually work well. But I agree safe AI indeed needs to be taken seriously particularly when they are developed for life/biomedical sciences.

This is exciting! A working open source version (reproduction following AF3' Nature paper) was released by bytedance
github.com/bytedance/Pr...

Tried one model: gp120-CD4-CCR5 for HIV-1 cell entry.

It looks like it can capture some of the known conformation (five seeds, AF3 left, Protenix right).

I am a computational scientist with multiple screens! And Mac systems? A tree on the left side?

A good #academichumor to start your morning with a strong cup of Italian coffee.

The mRNA vaccine with full length spike protein and a natural signal peptide is indeed superior in many ways!
www.nature.com/articles/s41...

This actually highlighted some of the characteristics of viral glycoproteins, 1), can be highly disordered in some regions, (so low pTM and, pLDDT, if so low, could also mean prediction failure); 2) can be heavily glycosylated.
www.nature.com/articles/s41...

As Eddie pointed out: this [fur farming] could be the source of next pandemic. @eddieholmes.bsky.social

I am pretty concerned too if there is no science-based control measures.
www.science.org/doi/full/10....

A Journey Through the Virosphere, by Prof. Edward Holmes
www.youtube.com/watch?v=c5VD...