Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

Realized I forgot to use #CryoEM tag to disseminate our cool structure of the 2C:RNA holoenzyme complex !

Yousuf A. Khan@yousufakhan.bsky.social · 2mo ago

Today my laboratory is thrilled to announce a major breakthrough in the fight against the common cold and other diseases like hand,foot, and mouth disease acute flaccid myelitis caused by picornaviruses. We present the first structure of picornaviral 2C, bound to ssRNA (1/n)

Today my laboratory is thrilled to announce a major breakthrough in the fight against the common cold and other diseases like hand,foot, and mouth disease acute flaccid myelitis caused by picornaviruses. We present the first structure of picornaviral 2C, bound to ssRNA (1/n)

Great to see such a spike in interest for the RNA design capabilities of yakRNA Design after my talk at @rnasociety.bsky.social . Thank you to everyone for the lovely feedback to me and the rest of the team! I'm so excited to see what people create with it!

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...

Recoding genomes with programmed ribosomal frameshifting - Nature Reviews Genetics

In this Journal Club, Yousuf A. Khan recounts a landmark study published in 1985 by Jacks and Varmus that documented programmed ribosomal frameshifting in retroviruses, which later inspired Yousu...

nature.com

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

Bio-essential sugars in samples from asteroid Bennu - Nature Geoscience

Samples returned from asteroid Bennu contain bio-essential sugars such as ribose and glucose that may have formed in the parent asteroid from brines containing formaldehyde, according to a geochemical...

nature.com

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...

Stanford researchers receive NIH High-Risk, High-Reward grants

This year’s awardees are researching cancer treatments, age-related disease, and much more.

news.stanford.edu

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)

Systematic identification and characterization of eukaryotic and viral 2A peptide-bond-skipping sequences

Rao et al. identified thousands of previously unknown 2A peptides across both viruses and eukaryotes using an HMMER analysis. The authors further identified a unique class of 2A peptides, class B, who...

cell.com

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

New Google Colab features for higher education

Google Colab offers free Colab Pro for students, interactive slideshows and AI controls in notebooks.

blog.google

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

SNARE disassembly requires Sec18/NSF side loading

Nature Structural & Molecular Biology, Published online: 02 July 2025; doi:10.1038/s41594-025-01590-wKhan et al. show that Sec18 uses both D1 and D2 AAA+ rings cooperatively, opening them laterally for SNARE substrate loading and for subsequent release of SNAREs.

go.nature.com

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...

Functional amyloid proteins confer defence against predatory bacteria - Nature

Escherichia coli uses curli fibres, oligomers of the functional amyloid CsgA, as a barrier to protect against the predatory bacteria Bdellovibrio bacteriovorus and Myxococcus xanthus in a mechanism th...

nature.com

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

The Lister Institute of Preventive Medicine@thelisterinstitute.bsky.social · last yr.

We are very proud to introduce our brand new 2025 #ListerFellows! This year there are eight Prize recipients. lister-institute.org.uk/a-warm-welco...

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

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.

While this paper looks interesting, let me just say (again) that (essentially all) NMR ensembles in the PDB are NOT thermodynamic ensembles or meant to represent these. They are "uncertainty ensembles" and using them to benchmark machine learning (or other) models of dynamics is not a good idea.

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...

The structure of human sweetness

A single taste receptor initiates our reactions to both sugars and artificial sweeteners, triggering a signaling process that drives our intense attraction to sweet foods. Single-particle cryo-EM reve...

cell.com

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 juan.bonifacino@nih.gov. 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

Structural basis for the ubiquitin chain recognition of the human 26S proteasome

Proteasomal degradation is a fundamental process for all eukaryotic life. A protein destined for degradation is first tagged with a polyubiquitin chain, which is selected by the proteasome. Different ...

biorxiv.org

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

xTrimoPGLM: unified 100-billion-parameter pretrained transformer for deciphering the language of proteins - Nature Methods

xTrimo protein general language model (xTrimoPGLM) is a unified pretraining framework and foundation model designed for various protein-related tasks, including protein understanding and generation or...

nature.com