Simon Kozlov

Cyclic peptide structure prediction and design using AlphaFold2 Nature Communications - AfCycDesign: Cyclic offset to the relative positional encoding in AlphaFold2 enables accurate structure prediction, sequence redesign, and de novo hallucination of cyclic...

Great to have our manuscript with @sokrypton.org 's lab describing AfCyDesign finally out in @natcomms.bsky.social . Structure prediction, sequence redesign, de novo hallucination of cyclic peptides, and some binder design examples in this version.
rdcu.be/em0vA

In one court document from Aug. 23, 2018, the government owned up to its mistake, saying Mr. Subaihani had been removed to Iraq despite the court's order. Locating Mr. Subaihani was complicated because nobody knew where he had gone, or even if he had made it to Iraq. By September 2018, several weeks after Mr. Subaihani had been deported, a federal judge demanded ICE go to great lengths to find him.

ICE officials complied, explaining to the court that they were in touch with State Department staff in Iraq and in other countries he had transited through. They even called airline officials — Mr. Subaihani had been deported on a commercial flight — for more on his whereabouts. n late September, ICE officials notified the court that they had und evidence Mr. Subaihani had made it to Iraq. By October, Mr. Subaihani's attorneys had tracked him down with the help of an investigator, and set about working with ICE to get him back to the United States.

Oh wow great @haleaziz.bsky.social piece on a 2018 case in which Trump’s ICE screwed up and erroneously deported a guy. AND THEY BROUGHT HIM BACK because why wouldn’t they?

We’re in a much darker place now.

Free link:

www.nytimes.com/2025/04/15/u...

Curios how you connected revoked visa to jaywalking - in the stories I heard there were no explanations whatsoever.

Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org

🧬 Code will be released in a couple weeks

The best-run train line in US. Hit me up next time you’re in Boston!

Figure from the paper, showing BOOSTER-overexpressing poplar plants that are about twice as tall as the negative controls. Googly eyes (not from original paper) look at the taller plants.

BOOSTER, a newly identified orphan gene, supercharges photosynthesis and, when overexpressed, boosts height of poplars by up to 200% (at least in greenhouse)

To make it even more interesting, part of the gene seems derived from a poplar fungus-farming ant 🐜

Paper: www.cell.com/developmenta...

Biology is amazing

Yes, as long as all the code is in the Jupyter Notebook :(

💡💥Here’s a modest proposal I’ve been pondering for a while on how to change the PEER REVIEW process and start more community-driven SCIENCE FUNDING. Lots of feedback/discussion welcomed! Other variants of the idea might exist already—not claiming originality. (a long 🧵) (1/9)

What would be an economic model for this? Are there economic incentives for farmers to reduce nitrous oxide emissions already?

Fully accepting nothing may work out is a surprisingly effective way to work something out.

Here’s the catch: knowing this fights against acceptance.

A venture creation fund, where all companies stay small lol

Holy shit, @akosnyerges.bsky.social got a meaningful reply to a highly technical question. We are so back! bsky.app/profile/geno...

I would love for a social network to exist where questions like this get a meaningful discussion. I don’t think Twitter had it even if it’s best days, with a few exceptions when tweet randomly goes viral.
Can we make it work here? That would take the whole community to a next level.

Made a biotech founders starter pack, DM me to be added!

go.bsky.app/LWm8uPE

Noticed that whenever I see a tweet I like, the first thing I do is check if author is on BlueSky. Glad to be here!

Also struggling with looking silly when exercising - sometimes when I walk back from work, I’m thinking I could jog for a few minutes, but feel I’ll look silly doing it in my regular clothes when people around me are jogging all geared up

Wanted to ask for a while - what is a good resource describing the main drivers of how we were able to reduce emissions and bend the curve so far? Like, who are the main players and what are the incentives that worked? (Fully agree we should bend it more)