Sign in

Yousuf A. Khan

@yousufakhan.bsky.social
1.5K followers 259 following 76 posts

Group Leader @Stanford. RNA focused ML/AI, cryoEM/ET, and biophysics. Formerly:DeepMind AlphaFold,EvoscaleAI, Churchill Scholar@Cambridge_Uni & seen on Netflix

PostsRepliesMedia
Reposted by Yousuf A. Khan
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026
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
217975
Yousuf A. Khan @yousufakhan.bsky.social · 16/06/2026
Realized I forgot to use #CryoEM tag to disseminate our cool structure of the 2C:RNA holoenzyme complex !
061
Yousuf A. Khan @yousufakhan.bsky.social · 11/06/2026
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)
2158
Yousuf A. Khan @yousufakhan.bsky.social · 01/06/2026
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!
100
Reposted by Yousuf A. Khan
Dimitry Tegunov @dtegunov.bsky.social · 03/05/2026
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:
6313118
Yousuf A. Khan @yousufakhan.bsky.social · 24/04/2026
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)
100
Reposted by Yousuf A. Khan
Mohammed AlQuraishi @moalquraishi.bsky.social · 13/03/2026
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
124490
Yousuf A. Khan @yousufakhan.bsky.social · 13/03/2026
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...
nature.com
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...
000
Yousuf A. Khan @yousufakhan.bsky.social · 03/12/2025
It's all about RNA baby! Ribose found on Bennu www.nature.com/articles/s41...
nature.com
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...
020
Yousuf A. Khan @yousufakhan.bsky.social · 24/10/2025
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
194
Yousuf A. Khan @yousufakhan.bsky.social · 13/10/2025
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...
news.stanford.edu
Stanford researchers receive NIH High-Risk, High-Reward grants
This year’s awardees are researching cancer treatments, age-related disease, and much more.
030
Yousuf A. Khan @yousufakhan.bsky.social · 27/08/2025
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
yousufakhan.com
Yousuf A. Khan (YAK) Lab - RNA Research at Stanford University
Yousuf A. Khan (YAK) Lab - Studying RNA folding, interactions, and cellular effects using Molecular and Cellular Physiology, Structural Biology, and Machine Learning at Stanford University
3174
Reposted by Yousuf A. Khan
Ahmad Jomaa @jomaalab.bsky.social · 01/08/2025
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...
48328
Reposted by Yousuf A. Khan
Alex Rubinsteyn @alexr.bsky.social · 23/07/2025
Going deep on 2A peptides: www.cell.com/cell-reports... (Trying to pick between GSG:T2A, GSG:P2A, and furin site:GSG:T2A)
cell.com
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...
12511
Reposted by Yousuf A. Khan
Sergey Ovchinnikov @sokrypton.org · 22/07/2025
PSA = Google Colab Pro free for one year for academic use (US only): blog.google/outreach-ini...
blog.google
New Google Colab features for higher education
Google Colab offers free Colab Pro for students, interactive slideshows and AI controls in notebooks.
0227
Reposted by Yousuf A. Khan
Nikolai Slavov @slavov-n.bsky.social · 09/07/2025
Key numbers in cell biology Having a sense of scale helps to think more rigorously and realistically about biological systems.
010329
Reposted by Yousuf A. Khan
Nature Structural & Molecular Biology @natsmb.nature.com · 03/07/2025
ICYMI: New online: SNARE disassembly requires Sec18/NSF side loading
go.nature.com
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.
042
Reposted by Yousuf A. Khan
Hiten Madhani @hitenmadhani.bsky.social · 02/07/2025
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...
nature.com
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...
0408
Yousuf A. Khan @yousufakhan.bsky.social · 02/07/2025
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)
23910
Reposted by Yousuf A. Khan
Chris H. Hill @chillzaa.bsky.social · 20/06/2025
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
7486
Reposted by Yousuf A. Khan
Oli Clarke @olibclarke.bsky.social · 12/06/2025
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! ⬇️
At left, a reconstruction of the vault cap with C39 symmetry imposed; at right, the reconstruction after identifying the correct symmetry, with the three non-equivalent protomers highlighted.
211227
Reposted by Yousuf A. Khan
Lena Steckelberg @lenasteckelberg.bsky.social · 20/12/2024
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
713739
Reposted by Yousuf A. Khan
Gina El Nesr @ginaelnesr.bsky.social · 12/05/2025
someone said we need a meme
1296
Yousuf A. Khan @yousufakhan.bsky.social · 10/05/2025
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...
cell.com
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...
020
Reposted by Yousuf A. Khan
Arne Elofsson @handle.invalid · 05/05/2025
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...
biorxiv.org
Limits of deep-learning-based RNA prediction methods
Motivation: In recent years, tremendous advances have been made in predicting protein structures and protein-protein interactions. However, progress in predicting the structure of RNA, either alone or...
18631
Reposted by Yousuf A. Khan
Grigorieff Lab @UMassChan and @HHMI @grigoriefflab.bsky.social · 31/03/2025
www.biorxiv.org/content/10.1... NEW PREPRINT ALERT! Thanks to all involved!
26224
Reposted by Yousuf A. Khan
Juan S. Bonifacino @juanbonifacino.bsky.social · 13/04/2025
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!
58779
Reposted by Yousuf A. Khan
Akshay Agrawal @akshaykagrawal.bsky.social · 10/04/2025
🚀 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.
0313
Reposted by Yousuf A. Khan
Haselbach Lab @haselbachlab.bsky.social · 09/04/2025
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
biorxiv.org
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 ...
27325
Yousuf A. Khan @yousufakhan.bsky.social · 09/04/2025
A 100 BILLION protein language model has dropped... www.nature.com/articles/s41...
nature.com
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...
010
Reposted by Yousuf A. Khan
Alice Ting @aliceyting.bsky.social · 26/03/2025
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...
1178
Yousuf A. Khan @yousufakhan.bsky.social · 23/03/2025
Exactly
011
Reposted by Yousuf A. Khan
Carl T. Bergstrom @carlbergstrom.com · 17/03/2025
The @nytimes.com just discovered parallel computing.
NY Times graphic.

Conventional computer: One task starts after another completes

AI computing: tasks are divided into small parts and happen at the same time.
701197181
Reposted by Yousuf A. Khan
Mark @quigonsmith.bsky.social · 15/03/2025
Repost to make an American sad
59825
Reposted by Yousuf A. Khan
Utrecht Virology Lab @utrechtvirology.bsky.social · 16/03/2025
More picornavirus research from us! 😄
1186
Reposted by Yousuf A. Khan
Mara Duncan @mcduncanlab.bsky.social · 16/03/2025
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.
onlinelibrary.wiley.com
Enhancing Yeast Transformation: Achieving up to a Tenfold Increase Through a Single Adjustment in the Lithium Acetate–Polyethylene Glycol Method
In red are the proposed improvements to the classical yeast transformation protocol.
32912
Reposted by Yousuf A. Khan
Waggoner Lab @labwaggoner.bsky.social · 13/03/2025
Cryo-EM reveals mechanisms of natural RNA multivalency @science.org www.science.org/doi/10.1126/...
0205
Reposted by Yousuf A. Khan
Chaitanya K. Joshi @chaitjo.bsky.social · 10/03/2025
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 👇
1449
Yousuf A. Khan @yousufakhan.bsky.social · 04/03/2025
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
021
Reposted by Yousuf A. Khan
Jake Wintermute @synbio1.bsky.social · 03/03/2025
I know that the mRNA is larger than the protein it codes for but I don't believe it
917041
Reposted by Yousuf A. Khan
Leslie Rissler @ljrissler.bsky.social · 03/03/2025
NSF plans to reinstate all probationary employees who were fired on 18 Feb! NSF’s decision. 👏🏻👏🏻❤️
8592149
Reposted by Yousuf A. Khan
Alice Ting @aliceyting.bsky.social · 26/02/2025
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
310531
Reposted by Yousuf A. Khan
David Buchanan @retr0.id · 24/02/2025
they call me 007 0 lines of code 0 commits 7 open issues
433387275
Reposted by Yousuf A. Khan
Jeremy Berg @jeremymberg.bsky.social · 22/02/2025
A US Senator Joins the Fray. Thank you @murray.senate.gov ! More of this, please! www.murray.senate.gov/senator-murr...
murray.senate.gov
Senator Murray Blasts Trump & Elon for Illegally Paralyzing Lifesaving Research Again, Threatening to Extinguish Ongoing and Groundbreaking Work - Senator Patty Murray
ICYMI: Murray Blasts Trump and Musk Decimating HHS, Risking Americans’ Health and Livelihoods Washington, D.C. — U.S. Senator Patty Murray (D-WA), Vice Chair of the Senate Appropriations Committee and...
932196
Reposted by Yousuf A. Khan
Gabriel Rocklin @grocklin.bsky.social · 19/02/2025
Send this to your reps! And more reporting on this please!
069
Yousuf A. Khan @yousufakhan.bsky.social · 16/02/2025
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!
020
Reposted by Yousuf A. Khan
Martin Vögele @martinvoegele.bsky.social · 15/02/2025
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.
Sunlight shining through the glass roof of the convention center.From affinity to activity: Ligand efficacy prediction through binding thermodynamics.
1364
Reposted by Yousuf A. Khan
Sonja Welsch @sonjawelsch.bsky.social · 04/02/2025
In case you wondered what it looks like "in real life" when the FluScreen of a Krios cryoEM is retracted/inserted: here you go. ❄️🔬
2476