Bogdan Toader

Targeted disruption of phage liquid crystalline droplets abolishes antibiotic tolerance of bacterial biofilms

led by @abultarafder.bsky.social

Great collaboration with @pearce-maths.bsky.social and @geiselbiofilm.bsky.social

www.biorxiv.org/cgi/content/...

How can we best use AI in science?

Myself and 9 other research fellows from @imperial-ix.bsky.social use AI methods in domains from plant biology (🌱) to neuroscience (🧠) and particle physics (🎇).

Together we suggest 10 simple rules @plos.org 🧵

doi.org/10.1371/jour...

Today, we release Franca, a new vision Foundation Model that matches and often outperforms DINOv2.
The data, the training code and the model weights are open-source.

This is the result of a close and fun collaboration
@valeoai.bsky.social (in France) and @funailab.bsky.social (in Franconia)🚀

openreview.net/forum?id=8tQ...

good link:
openreview.net/forum?id=8tQ...

Our entrance into protein design! Inverse folding steered by external sources of information, and for multiple conformations. By the amazing @kaiyi94.bsky.social and @kjamali.bsky.social!
Download our code and try it yourself. 🥳

Thanks! I did not try it on symmetric structures. However, preconditioning influences the speed of convergence to a minimum (good or not), rather than which minimum it converges to, so it's not clear to me whether it will avoid the problem you mention without running it.

Exciting study from @kiranrpatil.bsky.social and colleagues. Hannah Ochner from the group performed cryo FIB imaging.

Congrats!

“Achieving individual tomograms of cells where any features are at 10 Å resolution or better is well-beyond both current capabilities and reasonable predictions of future improvements.”
:(

Postdoctoral Scientist - Structural Studies - Dr Sjors Scheres - LMB 2640 - Cambridgeshire job with MRC Laboratory of Molecular Biology (LMB) | 12840844 Postdoctoral Scientist Starting Salary: £41,344 Fixed term: 3 years MRC Laboratory of Molecular Biology, Cambridge, UK We are looking for a postdoc...

We have a 3-year funded postdoc position to work on structures of #amyloid filaments. If you are an expert in protein biochemistry, structural biology or #cryoEM / #cryoET, this could be for you! Feel free to email me with any questions. Come join us! 🤩

www.nature.com/naturecareer...

We also present a solution to the problem, showing how we can efficiently estimate 2nd order information and largely mitigate the poor conditioning, opening the door for efficient, SGD-based high resolution cryo-EM methods.

We show the numerical conditioning of cryo-EM reconstruction is increasingly poor at high resolution such that SGD has no real hope of resolving high resolution structures.

Ever wonder why SGD, which works so well for ab initio cryo-EM, never seems to get to high resolution on its own? Well, we have the answer: conditioning!

Work on SGD for high-resolution cryo-EM refinement from my previous postdoc finally published in @actacrystd.iucr.org

with Roy Lederman and @marcusabrubaker.bsky.social

📜 Paper: journals.iucr.org/paper?S20597...
💻 Code: github.com/bogdantoader...
💾 Data: doi.org/10.5281/zeno...

Structure of the virulence-associated Neisseria meningitidis filamentous bacteriophage MDAphi

Out in @pnas.org

Congrats @janboehning.bsky.social @abultarafder.bsky.social Miles Graham @mathieucoureuil.bsky.social
@mrclmb.bsky.social @hopitalnecker.bsky.social

www.pnas.org/doi/10.1073/...

spent some time this evening updating the teamtomo.org site - if you're interested in cryo-EM + Python you might want to take a look around!

This has been a long journey, but it's now out in final form. @kjamali.bsky.social

academic.oup.com/bioinformati...

🔥New Night Science paper!!
Discovery happens when your initial plans fall apart but it requires you to have a particular mindset: it's not extraverted, orderly, neurotic or agreeable that's the most important – discovery requires an OPENNESS to new ideas and unexpected insights.

Molecular mechanism of Mad2 conformational conversion promoted by the Mad2‐interaction motif of Cdc20 During mitosis, unattached kinetochores trigger the spindle assembly checkpoint by promoting the assembly of the mitotic checkpoint complex, a heterotetramer comprising Mad2, Cdc20, BubR1, and Bub3. ...

Our study of Mad2 conformational changes is out in final form.

A fun collaborative project to work that uses NMR and MD. @connyyu.bsky.social

onlinelibrary.wiley.com/doi/full/10....

We're on the cover of @science.org this week. Awesome work by @florentwaltz.bsky.social. #CryoET is reaching crazy resolutions inside cells, and this is just the beginning. Fantastic interpretation of the proton motive force by @verenaresch.bsky.social. Always a pleasure making #SciArt with you!🧪🧶🧬🌾

Chao has shown that disease-causing tau mutations V337M and R406W both lead to the formation of filaments with the #Alzheimer fold in human brain. Could one use these mutations to speed up models for tau filament formation in AD?

Structural biology inside multicellular specimens using electron cryotomography
by @idocaspy.bsky.social @zhexinwang.bsky.social

out now in Quarterly Reviews of Biophysics
doi.org/10.1017/S003...

Thou Shalt Not Overfit Venting my spleen about the persistent inanity about overfitting.

Overfitting, as it is colloquially described in data science and machine learning, doesn’t exist. www.argmin.net/p/thou-shalt...

The Mathematics of Artificial Intelligence: In this introductory and highly subjective survey, aimed at a general mathematical audience, I showcase some key theoretical concepts underlying recent advancements in machine learning. arxiv.org/abs/2501.10465

The MRC LMB @mrclmb.bsky.social is hiring a ML+Bio tenure track group leader!

Optimal transport made multimodal and computationally tractable for atlas-scale single-cell data, exciting!

Exciting update on the CryoET Data Portal! A new annotation set from Mart Last & team is now live. They’ve doubled available annotations with >1,800 tomograms of Chlamydomonas reinhardtii which now have almost fully dense labels, and all can be visualized in the browser using Neuroglancer.

200bn Weights of Responsibility The Stress of Working in Modern AI

The blog post of the late Felix Hill is powerful. Stress for AI researchers today is real.

I did not know Felix Hill and I am sorry for those who did.
This story is perhaps a reminder for students, postdocs, founders and researchers to take care of their well being.

medium.com/@felixhill/2...

Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate structures of biomolecules in their native context. However, challenges remain in the efficient production...

More than 1'800 tomograms available for the community. Towards visual proteomics using our favorite organism Chlamy!

Check out the preprint: www.biorxiv.org/content/10.1...

Find it on EMPIAR (11830) and fully annotated on the CZI data portal: cryoetdataportal.czscience.com

#TeamTomo

Cool idea to computationally enhance tomogram quality