We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better. Preprint: www.biorxiv.org/content/10.6... Code: github.com/warpem/miss-... 🧶 Thread:

Introducing yakRNA Design🚀, an RNA composer that makes synthetic, programmed RNAs at the touch of your fingers! The crazy part? Unlike other macromolecular design models, we didn't use ANY 3D RNA structures in our model🤯 (1/n)

New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

Check out our lab's latest "Journal Club" in Nature Review Genetics today where we talk about how molecular mechanisms can dynamically recode our genomes: www.nature.com/articles/s41...

It's all about RNA baby! Ribose found on Bennu www.nature.com/articles/s41...

Excited to announce the YAK lab's first paper and the discovery of the FIRST human cellular PRF signal to give access to two overlapping open reading frames (science.org/doi/10.1126/...)! Before we dive in, the story actually begins in a Nature from 11 years ago

Excited to announce that I have been selected to receive a High-Risk, High-Reward grant from the NIH to help support the research our lab does at the intersection of AI and molecular biology to study RNA. Read more about here: news.stanford.edu/stories/2025...

I'm extremely thrilled to announce that I will be starting as a group leader at Stanford this upcoming fall! My lab will be studying how RNAs exert themselves in the cell to induce a multitude of biological phenomena using ML, cryoEM/ET, and biochemistry! www.yousufakhan.com

Check out our new preprint on the discovery of a molecular switch in NAC that mediates nascent chain sorting on the ribosome and prevents mitochondrial protein mistargeting by SRP. A great collaboration with the Shan Lab @Caltech and the Qi Lab @UVA: www.biorxiv.org/content/10.1...

Going deep on 2A peptides: www.cell.com/cell-reports... (Trying to pick between GSG:T2A, GSG:P2A, and furin site:GSG:T2A)

PSA = Google Colab Pro free for one year for academic use (US only): blog.google/outreach-ini...

Key numbers in cell biology Having a sense of scale helps to think more rigorously and realistically about biological systems.

ICYMI: New online: SNARE disassembly requires Sec18/NSF side loading

Cool paper on bacterial amyloids as protection from predatory bacteria from the Whitely lab at CU Boulder. There are predatory fungi, so one wonders if a similar system exists in eukaryotes. www.nature.com/articles/s41...

Sharing some of my PhD work that just came out today. TLDR; We found a universal mechanism for all the many kinds of SNAREs are processed and recycled by a single molecular machine that is conserved in all eukaryotic life as we know it (1/5) www.nature.com/articles/s41... (1/5)

I'm thrilled and honoured to receive the 2025 Lister Prize, along with seven other fantastic biomedical scientists 🔬🦠🧬 This award will enable us to determine high-resolution structures of viral protein synthesis inside infected cells

1/x New story - the structure of the Vault cap, at 2.3Å! Matching a beautiful preprint from @sjorsscheres.bsky.social, we show that the cap of the vault particle has C13 symmetry, in contrast to the 39-fold symmetry of the body. Study lead by talented postdoc @huanli00.bsky.social from my group! ⬇️

Hi Bluesky, just in time for the holidays I am excited to share the latest pre-print from my group! We solved the 3D structure of a mysterious viral RNA that resists degradation by host nucleases. A short 🧵 &link below – please also check out the full video! #RNA #RNAbiology #RNASky #lovevirology

someone said we need a meme

The structure of the human sweetness receptor bound to sucralose, and aspartame!!! Who will design the protein binder that mimics this conformation? Protein sweetneer?? www.cell.com/cell/fulltex...

In this evaluation of AlphaFold3 (and other methods), we show that (i) accurate predictions are limited to RNA structures/complexes with structural similarity to PDB and (ii) that current methods are bad at estimating the accuracy of the predictions. www.biorxiv.org/content/10.1...

www.biorxiv.org/content/10.1... NEW PREPRINT ALERT! Thanks to all involved!

Our lab at the NIH (Bethesda, MD) is looking for postdoctoral fellows to join our team studying the molecular mechanisms of protein trafficking and their links to neurodevelopmental disorders starting on or after 10-1-2025. Send your application to [email protected]. Please share and repost!

🚀 We achieved a big milestone today: marimo just crossed 12200 GitHub stars — crossing Jupyter notebook, too. We launched marimo to the public just over a year ago. People are clearly hungry for a better environment for working with data, and we have a lot more planned still.

New Preprint: We have solved the structure of the proteasome in complex with two different ubiquitin chains: www.biorxiv.org/content/10.1... This work is spearheaded by PhD Student Sascha Amann Let me walk you through it 🧵 1/9

A 100 BILLION protein language model has dropped... www.nature.com/articles/s41...

We are hiring a new lab manager! Our wonderful lab manager Albert is headed off to grad school and we are looking to fill his position this summer. This is a great opportunity for a new graduate to spend a couple years immersed in research before applying to PhD or MD programs. 50% of the job is...

Exactly

The @nytimes.com just discovered parallel computing.

Repost to make an American sad

More picornavirus research from us! 😄

A slight modification to the standard yeast lithium acetate transformation protocol increases transformation efficiency substantially. Basically, 2 fold increase if you resuspend in 2M sorbitol after heat shock, and an additive increase with some sorbitol during heat shock.

Cryo-EM reveals mechanisms of natural RNA multivalency @science.org www.science.org/doi/10.1126/...

Introducing All-atom Diffusion Transformers — towards Foundation Models for generative chemistry, from my internship with the FAIR Chemistry team There are a couple ML ideas which I think are new and exciting in here 👇

I never felt such joy as I have until I temporarily upgraded to COOT 1, realized how terrible it is, and downgraded back to my old friend Coot 0.9. #CryoEM #TeamTomo

I know that the mRNA is larger than the protein it codes for but I don't believe it

NSF plans to reinstate all probationary employees who were fired on 18 Feb! NSF’s decision. 👏🏻👏🏻❤️

Today we report the directed evolution of HUH into rHUH, a sequence-specific covalent protein tag for RNA labeling. rHUH was hard to engineer: the initial HUH template had no RNA activity, so we started with RNA-DNA hybrids. 30 rounds of selection on the yeast surface were required, and 7 cycles of

they call me 007 0 lines of code 0 commits 7 open issues

A US Senator Joins the Fray. Thank you @murray.senate.gov ! More of this, please! www.murray.senate.gov/senator-murr...

Send this to your reps! And more reporting on this please!

I'm at BPS LA 2025. DM me to meet up to chat all things cryo, ML, RNA, and AAA+! Happy to meet people who I've spoken to!

Arrived at Los Angeles Convention Center for the @biophysicalsoc.bsky.social annual meeting #BPS25. Come see my talk about ligand efficacy prediction with ML and FEP on Monday February 17 at 4:50 pm in Petree Hall C.

In case you wondered what it looks like "in real life" when the FluScreen of a Krios cryoEM is retracted/inserted: here you go. ❄️🔬

Kiah was set to join our faculty at Howard Law School in the Fall. She was a dedicated, brilliant civil rights lawyer poised to make a powerful difference in our world. Our hearts are broken & we pray for her family & friends. www.kwch.com/2025/01/30/c...

I’m sad to learn that my law school classmate, Kiah Duggins, died in the DC plane crash last night. Kiah was an exceptionally talented civil rights lawyer and aspiring legal scholar. I hope you’ll read about her work and the causes she cared about, some of which I’ll 🧵 below. What an immense loss

Pretty sure this is a contaminant but do #CryoEM #TeamTomo people know exactly what this is? One of my many 3d classes

Ever wonder where Nobel Prize-winning AlphaFold got its training data? Read how pioneering crystallographer Helen Berman helped build the Protein Data Bank as a home for more than 200,000 protein structures that would come to shape AI and protein prediction ➡️