Bogdan Toader

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...

1/7 Excited to share GuideFlip! We use guided discrete flow matching to co-design protein sequences and structures for flexible interactions, with experimental validation across three systems: α-synuclein, RBX1 and active-state GPCR nanobodies.

We have 2 new preprints on @biorxivpreprint.bsky.social that describe reconstitution of #Alzheimers paired helical filaments in experimental model systems: one in human brain organoids and one in murine primary cultures. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...

Structural basis of biofilm formation mediated by the Pseudomonas aeruginosa fibrillar adhesin CdrA led by @olivia--smith.bsky.social Collaboration with @alexbateman1.bsky.social , Andres Floto and @geiselbiofilm.bsky.social labs

Disrupting phage liquid crystalline droplets restores antibiotic susceptibility in Pseudomonas aeruginosa biofilms out in @plosbiology.org by @abultarafder.bsky.social and team. Exciting collaboration with @geiselbiofilm.bsky.social @pearce-maths.bsky.social and others

We're happy to announce our new preprint! 🐸 easymode: general pretrained networks for cellular cryo-ET. Segment ~20 cellular features – ribosomes, microtubules, mitochondria, nuclei & more – with zero model training. 🔗 doi.org/10.64898/202... 🧵👇

Sub-cellular chemical mapping using correlated cryogenic electron and mass spectrometry imaging online @natmethods.nature.com, led by Hannah Ochner, collaboration with @catfranco.bsky.social and @kiranrpatil.bsky.social labs doi.org/10.1038/s415...

Applications and prospects of cryo-electron tomography in drug discovery and understanding disease Review article by @camilaclemente.bsky.social in our lab www.sciencedirect.com/science/arti...

Oxygen gradients reshape cross-feeding through emergent spatial organization of gut commensal bacteria www.biorxiv.org/content/10.6... Use of isotope labels and cryo-CLEM-FIB-SIMS to study microbial communities by Hannah Ochner. Collaboration with @kiranrpatil.bsky.social @jmghigolab.bsky.social

Thrilled with the our results with @kjamali.bsky.social and @sjorsscheres.bsky.social from the recent binder competition! 🎉 2 of our 7 designs successfully bound to the target, with affinities ranking 2nd and 3rd overall. All of these designs targeted the disordered region of the protein.

Happy to share my first adventure in #TeamTomo in collaboration with the talented @inaharasimov.bsky.social. It was a fun experience experience with a lot of learning along the way.

Check out our pre-print, where we train a protein and small molecule force field from scratch with a graph neural network. We show comparable performance to existing, manually-tuned force fields on a range of tasks including binding free energy prediction. (1/4) arxiv.org/abs/2603.16770

We're excited to announce the beta-release of #RELION-5.1! 🥳 This release has important updates on our #amyloid processing pipeline, as described in this preprint: doi.org/10.64898/202... There are also some tweaks for #teamtomo. #OpenSoftwareAcceleratesScience

Join #EMBOCryoEM to get a comprehensive foundation in advanced single-particle and cellular tomography techniques – we'll cover the entire workflow from sample preparation to data collection and image processing. https://s.embl.org/cry26-01-bl Apply by: 11 May 2026 @embo.org

Please spread the word: the Structural Studies Division @mrclmb.bsky.social is looking for a new tenure-track, independent group leader with an exciting plan in any area of Structural (Molecular & Cell) biology, in discovery biology and/or methods development. 🥳 mrc.tal.net/vx/mobile-0/...

Cow Tools! We have lived alongside cows for nearly 10,000 years. We breed them and exploit them It is now, only now, that we have discovered THEY CAN USE TOOLS Here I describe our study (paper) www.sciencedirect.com/science/arti... in @currentbiology.bsky.social with @auersperga.bsky.social

Excellent thread with links to tools whose development relied on the Chlamy dataset

The latest issue is now online www.cell.com/molecular-ce...

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

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/...

Join ML wizard Kiarash to develop BioML methods that work

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...

Happy Halloween! 🎃 Here's a selection of some of our scariest gargoyles and grotesques 👀 #Halloween

Join our group to optimise Relion’s optimisation algorithms!

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...

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.

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

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👇

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...

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)🚀

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. 🥳

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.” :(

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!

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.

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...

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!