Bogdan Toader
@btoader.com
Applied mathematician developing computational imaging tools
#CryoET #TeamTomo
Postdoc in Scheres & Bharat labs @ MRC Laboratory of Molecular Biology, Cambridge
btoader.com
#CryoET #TeamTomo
Postdoc in Scheres & Bharat labs @ MRC Laboratory of Molecular Biology, Cambridge
btoader.com
Pinned
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...
with Roy Lederman and @marcusabrubaker.bsky.social
📜 Paper: journals.iucr.org/paper?S20597...
💻 Code: github.com/bogdantoader...
💾 Data: doi.org/10.5281/zeno...
Excellent thread with links to tools whose development relied on the Chlamy dataset
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍
[Maybe long thread ahead]
January 10, 2026 at 10:52 AM
Excellent thread with links to tools whose development relied on the Chlamy dataset
Reposted by Bogdan Toader
The latest issue is now online www.cell.com/molecular-ce...
January 8, 2026 at 4:59 PM
The latest issue is now online www.cell.com/molecular-ce...
Reposted by Bogdan Toader
Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
December 19, 2025 at 4:45 PM
Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
Reposted by Bogdan Toader
Postdoc opportunity with Michel Goedert and myself to work on #cryoEM/#cryoET structures of #amyloids. Feel free to email me with any questions you might have.
mrc.tal.net/vx/mobile-0/...
mrc.tal.net/vx/mobile-0/...
Postdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752 - Medical Research Council
Location: Cambridge. Vacancy: Postdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752. Closing Date: 04/01/2026, 23:55
mrc.tal.net
December 10, 2025 at 2:28 PM
Postdoc opportunity with Michel Goedert and myself to work on #cryoEM/#cryoET structures of #amyloids. Feel free to email me with any questions you might have.
mrc.tal.net/vx/mobile-0/...
mrc.tal.net/vx/mobile-0/...
Join ML wizard Kiarash to develop BioML methods that work
I’m excited to announce that I will be starting my research group on computational enzyme design at the Generative Biology Institute, Oxford, UK (@eitoxford.bsky.social)! PhD applications are open, deadline is Jan 8th (www.chem.ox.ac.uk/genbio-dtp). Email [email protected] with any questions!
GenBio DTP
Optional supporting text
www.chem.ox.ac.uk
December 9, 2025 at 5:47 PM
Join ML wizard Kiarash to develop BioML methods that work
Reposted by Bogdan Toader
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
November 7, 2025 at 10:44 AM
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Reposted by Bogdan Toader
October 31, 2025 at 10:52 AM
Join our group to optimise Relion’s optimisation algorithms!
We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated.
mrc.tal.net/vx/appcentre...
mrc.tal.net/vx/appcentre...
Quick Check Needed
mrc.tal.net
October 31, 2025 at 8:33 AM
Join our group to optimise Relion’s optimisation algorithms!
Reposted by Bogdan Toader
Very excited to be able to talk about something I've been working on for a while now - we're working with Commonwealth Fusion Systems, IMO the leading fusion startup in the world, to take our work on AI and tokamaks and make it work at the frontier of fusion energy. deepmind.google/discover/blo...
Google DeepMind is bringing AI to the next generation of fusion energy
We’re announcing our research partnership with Commonwealth Fusion Systems (CFS) to bring clean, safe, limitless fusion energy closer to reality with our advanced AI systems. This partnership...
deepmind.google
October 16, 2025 at 1:55 PM
Very excited to be able to talk about something I've been working on for a while now - we're working with Commonwealth Fusion Systems, IMO the leading fusion startup in the world, to take our work on AI and tokamaks and make it work at the frontier of fusion energy. deepmind.google/discover/blo...
Reposted by Bogdan Toader
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.
The main additions are some further comparisons to yet more unmixing algorithms, in which we find that our algorithm is still the most accurate.
September 16, 2025 at 7:43 AM
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.
The main additions are some further comparisons to yet more unmixing algorithms, in which we find that our algorithm is still the most accurate.
Reposted by Bogdan Toader
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
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
August 31, 2025 at 6:44 PM
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
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
Reposted by Bogdan Toader
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👇
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👇
August 14, 2025 at 6:52 PM
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👇
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👇
Reposted by Bogdan Toader
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...
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
August 12, 2025 at 4:05 PM
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...
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...
Reposted by 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/...
led by @abultarafder.bsky.social
Great collaboration with @pearce-maths.bsky.social and @geiselbiofilm.bsky.social
www.biorxiv.org/cgi/content/...
July 29, 2025 at 9:35 AM
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/...
led by @abultarafder.bsky.social
Great collaboration with @pearce-maths.bsky.social and @geiselbiofilm.bsky.social
www.biorxiv.org/cgi/content/...
Reposted by Bogdan Toader
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...
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...
July 25, 2025 at 10:58 AM
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...
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...
Reposted by Bogdan Toader
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)🚀
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)🚀
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.
July 21, 2025 at 2:58 PM
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)🚀
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)🚀
Reposted by Bogdan Toader
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. 🥳
Download our code and try it yourself. 🥳
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…
July 15, 2025 at 7:18 AM
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. 🥳
Download our code and try it yourself. 🥳
Reposted by Bogdan Toader
Exciting study from @kiranrpatil.bsky.social and colleagues. Hannah Ochner from the group performed cryo FIB imaging.
Congrats!
Congrats!
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
Read more here: buff.ly/4FsVFsS
@kiranrpatil.bsky.social @indraroux.bsky.social
July 1, 2025 at 10:04 AM
Exciting study from @kiranrpatil.bsky.social and colleagues. Hannah Ochner from the group performed cryo FIB imaging.
Congrats!
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.”
:(
:(
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
July 1, 2025 at 9:53 AM
“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.”
:(
:(
Reposted by Bogdan Toader
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...
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
June 25, 2025 at 2:01 PM
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...
www.nature.com/naturecareer...
Reposted by Bogdan Toader
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.
June 24, 2025 at 9:31 PM
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.
Reposted by Bogdan Toader
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.
June 24, 2025 at 9:31 PM
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.
Reposted by Bogdan Toader
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...
with Roy Lederman and @marcusabrubaker.bsky.social
📜 Paper: journals.iucr.org/paper?S20597...
💻 Code: github.com/bogdantoader...
💾 Data: doi.org/10.5281/zeno...
June 24, 2025 at 9:31 PM
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...
with Roy Lederman and @marcusabrubaker.bsky.social
📜 Paper: journals.iucr.org/paper?S20597...
💻 Code: github.com/bogdantoader...
💾 Data: doi.org/10.5281/zeno...
June 24, 2025 at 5:43 PM
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...
with Roy Lederman and @marcusabrubaker.bsky.social
📜 Paper: journals.iucr.org/paper?S20597...
💻 Code: github.com/bogdantoader...
💾 Data: doi.org/10.5281/zeno...
Reposted by Bogdan Toader
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/...
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/...
June 23, 2025 at 10:26 AM
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/...
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/...