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Reposted by Bogdan Toader

James Manton @jamesdmanton.bsky.social · 22d

The final version of our multispectral microscopy manuscript is now online at Nature Photonics: www.nature.com/articles/s41...

The main additions are some further comparisons to yet more unmixing algorithms, in which we find that our algorithm is still the most accurate.

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Tanmay Bharat @tbharat-lab.bsky.social · Aug 31

Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging

Congrats Hannah Ochner and authors on this important paper! Strong collaboration with @kiranrpatil.bsky.social

www.biorxiv.org/cgi/content/...
@mrclmb.bsky.social @wellcometrust.bsky.social

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Max Seitzer @maxseitzer.bsky.social · Aug 14

Introducing DINOv3 🦕🦕🦕

A SotA-enabling vision foundation model, trained with pure self-supervised learning (SSL) at scale.
High quality dense features, combining unprecedented semantic and geometric scene understanding.

Three reasons why this matters👇

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Sjors Scheres @sjorsscheres.bsky.social · Aug 12

Sofia Lövestam's vault structure is now online in Structure @cellpress.bsky.social. 🥳

How beautifully explorative is #cryoEM! We never planned to do this. The vaults just came down with #amyloids from human brain tissue, and Sofia decided to have a closer look.

www.cell.com/structure/fu...

Cryo-EM structure of the vault from human brain reveals symmetry mismatch at its caps

Lövestam and Scheres present a cryo-EM structure of vault particles, found during tau filament extraction from progressive supranuclear palsy (PSP) brain tissue. They reveal a symmetry shift at the va...

www.cell.com

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Tanmay Bharat @tbharat-lab.bsky.social · Jul 29

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/...

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Marcus Ghosh @marcusghosh.bsky.social · Jul 25

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...

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Yuki Asano @yukimasano.bsky.social · Jul 21

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)🚀

Andrei Bursuc @abursuc.bsky.social · Jul 21

1/ Can open-data models beat DINOv2? Today we release Franca, a fully open-sourced vision foundation model. Franca with ViT-G backbone matches (and often beats) proprietary models like SigLIPv2, CLIP, DINOv2 on various benchmarks setting a new standard for open-source research.

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Bogdan Toader @btoader.com · Jul 15

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

All-atom inverse protein folding through discrete flow matching

The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein...

openreview.net

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Bogdan Toader @btoader.com · Jul 15

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

All-atom inverse protein folding through discrete flow matching

The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein...

openreview.net

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Sjors Scheres @sjorsscheres.bsky.social · Jul 15

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. 🥳

Kai Yi @kaiyi94.bsky.social · Jul 14

Excited to share our paper at #ICML: All-atom inverse protein folding through discrete flow matching with @kjamali.bsky.social and @sjorsscheres.bsky.social : openreview.net/forum?id=8tQdw…. If you are at ICML, let’s connect and talk generative models&protein design!

OpenReview

Promoting openness in scientific communication and the peer-review process

https://openreview.net/forum?id=8tQdw…

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Bogdan Toader @btoader.com · Jul 12

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.

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Tanmay Bharat @tbharat-lab.bsky.social · Jul 1

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

Congrats!

MRC Toxicology Unit @mrc-tu.bsky.social · Jul 1

Researchers in the Patil Lab have discovered that certain species of gut bacteria can absorb PFAS. Boosting these species in our gut microbiome could be a new way to protect us from the harmful effects of PFAS.

Read more here: buff.ly/4FsVFsS

@kiranrpatil.bsky.social @indraroux.bsky.social

3D rendering of a bacterium with flagella cut open to show clumps of PFAS molecules inside along with the bacteria's own cellular machinery.

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Bogdan Toader @btoader.com · Jul 1

“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.”
:(

Josh Dickerson @joshdcryoem.bsky.social · Jun 28

Check out our recent review discussing the merits of tilt series vs single micrographs for in situ cryo-EM! www.sciencedirect.com/science/arti...

To tilt or not to tilt? Strategies for in situ cryo-EM data collection

Recent breakthroughs in single-particle cryogenic electron microscopy (cryo-EM) and protein structure prediction have transformed our ability to resol…

www.sciencedirect.com

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Sjors Scheres @sjorsscheres.bsky.social · Jun 25

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...

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...

www.nature.com

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Marcus Brubaker @marcusabrubaker.bsky.social · Jun 24

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.

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Marcus Brubaker @marcusabrubaker.bsky.social · Jun 24

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.

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Marcus Brubaker @marcusabrubaker.bsky.social · Jun 24

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!

Bogdan Toader @btoader.com · Jun 24

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...

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Bogdan Toader @btoader.com · Jun 24

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...

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Tanmay Bharat @tbharat-lab.bsky.social · Jun 23

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/...

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Alister Burt @alisterburt.bsky.social · May 30

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!

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Joe Greener @jgreener64.bsky.social · Apr 8

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

academic.oup.com/bioinformati...

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Itai Yanai @itaiyanai.bsky.social · Apr 2

🔥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.

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Joe Greener @jgreener64.bsky.social · Mar 31

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....

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. ...

onlinelibrary.wiley.com

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Ben Engel @cellarchlab.com · Mar 20

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!🧪🧶🧬🌾

Science Magazine @science.org · Mar 20

In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.

Learn more in this week's issue: scim.ag/3FA3Ygq

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Sjors Scheres @sjorsscheres.bsky.social · Mar 13

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?

Chao Qi @qcxy8886.bsky.social · Mar 13

Happy to share our latest publication on
@naturesmb.bsky.social Natural Structure & Molecular Biology, we show tau filaments show Alzheimer fold in mutants V337M and R406W.
thanks @sjorsscheres.bsky.social and Michel Goedert's support. 🥳
rdcu.be/edqzW
rdcu.be/edoGv

Mutant tau filaments from some inherited frontotemporal dementias show the Alzheimer fold

Nature Structural & Molecular Biology - Frontotemporal dementias can be caused by mutations in MAPT, which encodes the protein tau; the mutant protein forms harmful aggregates in the brain....

rdcu.be

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