Yousuf A. Khan
@yousufakhan.bsky.social
Group Leader @Stanford. RNA focused ML/AI, cryoEM/ET, and biophysics. Formerly:DeepMind AlphaFold,EvoscaleAI, Churchill Scholar@Cambridge_Uni & seen on Netflix
Pinned
Yousuf A. Khan
@yousufakhan.bsky.social
· Aug 27
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
www.yousufakhan.com
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
www.yousufakhan.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
October 24, 2025 at 10:32 PM
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
October 13, 2025 at 6:20 PM
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
www.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
www.yousufakhan.com
August 27, 2025 at 1:52 AM
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
www.yousufakhan.com
Reposted by Yousuf A. Khan
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...
August 1, 2025 at 3:27 PM
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...
Reposted by Yousuf A. Khan
Going deep on 2A peptides:
www.cell.com/cell-reports...
(Trying to pick between GSG:T2A, GSG:P2A, and furin site:GSG:T2A)
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...
www.cell.com
July 23, 2025 at 2:19 AM
Going deep on 2A peptides:
www.cell.com/cell-reports...
(Trying to pick between GSG:T2A, GSG:P2A, and furin site:GSG:T2A)
www.cell.com/cell-reports...
(Trying to pick between GSG:T2A, GSG:P2A, and furin site:GSG:T2A)
Reposted by Yousuf A. Khan
PSA = Google Colab Pro free for one year for academic use (US only):
blog.google/outreach-ini...
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
July 22, 2025 at 12:33 AM
PSA = Google Colab Pro free for one year for academic use (US only):
blog.google/outreach-ini...
blog.google/outreach-ini...
Reposted by Yousuf A. Khan
Key numbers in cell biology
Having a sense of scale helps to think more rigorously and realistically about biological systems.
Having a sense of scale helps to think more rigorously and realistically about biological systems.
July 9, 2025 at 11:14 AM
Key numbers in cell biology
Having a sense of scale helps to think more rigorously and realistically about biological systems.
Having a sense of scale helps to think more rigorously and realistically about biological systems.
Reposted by Yousuf A. Khan
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
July 3, 2025 at 12:01 PM
ICYMI: New online: SNARE disassembly requires Sec18/NSF side loading
Reposted by Yousuf A. Khan
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...
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...
www.nature.com
July 2, 2025 at 7:59 PM
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...
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)
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)
July 2, 2025 at 9:24 PM
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)
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)
Reposted by Yousuf A. Khan
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
This award will enable us to determine high-resolution structures of viral protein synthesis inside infected cells
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...
June 20, 2025 at 9:46 AM
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
This award will enable us to determine high-resolution structures of viral protein synthesis inside infected cells
Reposted by Yousuf A. Khan
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! ⬇️
June 12, 2025 at 1:44 PM
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! ⬇️
Reposted by Yousuf A. Khan
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
December 20, 2024 at 1:27 PM
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
Reposted by Yousuf A. Khan
someone said we need a meme
May 12, 2025 at 3:35 PM
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...
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...
www.cell.com
May 10, 2025 at 2:31 AM
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...
www.cell.com/cell/fulltex...
Reposted by Yousuf A. Khan
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...
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...
www.biorxiv.org
May 5, 2025 at 1:01 PM
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...
Reposted by Yousuf A. Khan
March 31, 2025 at 8:27 PM
Reposted by Yousuf A. Khan
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!
April 13, 2025 at 4:37 PM
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!
Reposted by Yousuf A. Khan
🚀 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.
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.
April 10, 2025 at 6:05 PM
🚀 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.
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.
Reposted by Yousuf A. Khan
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
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 ...
www.biorxiv.org
April 9, 2025 at 8:59 AM
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
Let me walk you through it 🧵 1/9
Reposted by Yousuf A. Khan
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...
March 26, 2025 at 5:39 PM
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
From 2010 to 2016 (latest data I have ), NIH research contributed to EVERY drug approved by the FDA
March 23, 2025 at 1:35 AM
Exactly
Reposted by Yousuf A. Khan
The @nytimes.com just discovered parallel computing.
March 17, 2025 at 6:11 PM
The @nytimes.com just discovered parallel computing.
Reposted by Yousuf A. Khan
Repost to make an American sad
March 15, 2025 at 3:27 PM
Repost to make an American sad