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
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
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
PLOS Biology@plosbiology.org · 2mo ago#Biofilm matrices containing filamentous phages help #Pseudomonas aeruginosa tolerate antibiotics. @abultarafder.bsky.social @tbharat-lab.bsky.social &co show that #nanobody disruption of #phage Pf4 #LiquidCrystalline droplets restores #antibiotic susceptibility @plosbiology.org 🧪 plos.io/4xkd6Mw
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...
Applications and prospects of cryo-electron tomography in drug discovery and understanding disease
Cryo-electron tomography (cryo-ET) is emerging as a transformative tool for structural biology. Unlike methods based on purified molecules, cryo-ET en…
sciencedirect.com
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
Oxygen gradients reshape cross-feeding through emergent spatial organization of gut commensal bacteria
Microbial interactions unfold within environments structured by physical transport and chemical gradients. Yet most mechanistic studies rely on well-mixed systems that mask the reciprocal influences of environmental heterogeneity on metabolism and ecology. Here, we investigate how the physical environment modulates the interaction between the gut commensal Bacteroides thetaiotaomicron and Escherichia coli . In anoxic liquid culture, cell-resolved isotope imaging and genetic perturbations reveal exploitative cross-feeding, where E. coli consumes diffusible sugars released by B . thetaiotaomicron during starch degradation. When exposed to intestinal-like oxygen gradients in microfluidics, the interaction is restructured by spatial organization. The species self-organize into complementary niches: E. coli locally depletes sugars and oxygen, thereby expanding the anoxic niche required by B. thetaiotaomicron . A reactive transport model confirms that this organization arises from coupled feedback between physical transport and metabolic reaction rates. Together, our results reveal how physical structure and chemical gradients convert an exploitative cross-feeding interaction into a dynamic niche-construction process that generates emergent spatial organization and stabilizes coexistence. ### Competing Interest Statement The authors have declared no competing interest.
biorxiv.org
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.
Carter Lab@carter-lab.bsky.social · 4mo agoExcited to share our work on the structure and function of cytoplasmic lattices within mouse embryos. A collaborative effort with @niakanlab.bsky.social and work led by @kashishsingh.bsky.social and @inaharasimov.bsky.social . It is now out on BioRxiv: www.biorxiv.org/content/10.6...
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
Training a force field for proteins and small molecules from scratch
Force fields for molecular dynamics are usually developed manually, limiting their transferability and making systematic exploration of functional forms challenging. We developed a graph neural networ...
arxiv.org
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/...
Research Group Leader Tenure Track - Structural Studies - LMB 2775 - Medical Research Council
Location: Cambridge. Vacancy: Research Group Leader Tenure Track - Structural Studies - LMB 2775. Closing Date: 16/03/2026, 23:55
mrc.tal.net
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
Ricardo D. Righetto@lifeonthewedge.bsky.social · 7mo agoThis 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]
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/...
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
Join ML wizard Kiarash to develop BioML methods that work
Kiarash Jamali@kjamali.bsky.social · 8mo agoI’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 kiarash.jamali@eit.org with any questions!
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...
Join our group to optimise Relion’s optimisation algorithms!
Sjors Scheres@sjorsscheres.bsky.social · 9mo agoWe 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...
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
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.
Multispectral live-cell imaging with uncompromised spatiotemporal resolution - Nature Photonics
A tree-like arrangement of dichroic mirrors and multiple cameras coupled with an iterative spectral unmixing algorithm enables multispectral imaging of live cells in up to eight spectral channels with...
nature.com
James Manton@jamesdmanton.bsky.social · 2y agoWe've recently updated our multispectral microscopy manuscript to clarify a few points (particularly regarding SNR) and add eight supplementary figures. Courtesy of Sjoerd Stallinga, we now also have a derivation of the appropriate Cramér–Rao lower bound! www.biorxiv.org/content/10.1...
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...
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...
cell.com
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)🚀
Andrei Bursuc@abursuc.bsky.social · last yr.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.
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 · last yr.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!