Dominik Hrebik

GitHub - swing-research/icecream: 🍦Icecream: a self-supervised framework for cryo-ET reconstruction 🍦Icecream: a self-supervised framework for cryo-ET reconstruction - swing-research/icecream

We just released version v0.3.1 of 🍦Icecream!
Importantly, this fixes a bug in missing wedge correction. Please update, and let us know how it works for you!
#CryoET #TeamTomo

github.com/swing-resear...

It’s been a while since I put together the Structural Virology starter pack, and I’m sure some new folks have joined Bluesky since then. There’s still plenty of space to fill, so if you’d like to be added to the list just let me know.

#virology #cryoEM

go.bsky.app/Qxv95BL

TomoCPT is a transformer-based solution that reformulates particle detection in cryo-ET as a centroid-prediction task using Gaussian labels #CryoET #ParticlePicking #SubTomogramAveraging doi.org/10.1107/S205...

Visually, the cell contains a surprisingly low amount of ribosomes when I compare it to tomograms from other organisms I have seen before (bacteria, eukaryota). Is that a known feature of Archaea?

Enabling options for review: from training and transparency to author-centered AI tools - openRxiv Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...

Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n

openrxiv.org/enabling-rev...

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...

Glad to see our antibody design paper finally out in
@nature.com
(and congrats to lead authors and everyone involved )!
At Xaira we are excited about pushing antibody design further to bind harder targets and make drugs for unmet medical needs.
Paper:
www.nature.com/articles/s41...

At some point, Doppio will replace relion's gui. Already you can do more in Doppio than in relion! 🤩

Celebrate #NationalCatDay with the cats of RCSB PDB!

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...

Measurement of atomic scattering factors by cryo-electron microscopy www.biorxiv.org/content/10.1101/2025.10.24.683059v1 #cryoEM

Bending the rules: curvature’s impact on cell biology - BMC Biology Curvature is a ubiquitous feature in biology, shaping structures at every scale and playing diverse roles in processes ranging from membrane dynamics to tissue organization. In this review, we first introduce briefly the fundamental concepts and mathematical principles of curvature. The second section explores how membrane curvature is perceived by molecular sensors and integrated into cellular responses. The third section examines the effects of curvature on cellular processes and behaviors at the cell-scale, providing a detailed discussion of the underlying mechanisms. Finally, we offer insights into emerging perspectives and highlight the future challenges in unraveling the multifaceted roles of curvature in biology.

A Review BMC Biology from the Mechanobiology Collection introduces the fundamental concepts of curvature, discusses its effect on cellular processes and behaviors at the cell-scale, and offers insights into emerging perspectives on the roles of curvature in biology.

#MedSky

Icecream: High-Fidelity Equivariant Cryo-Electron Tomography www.biorxiv.org/content/10.1101/2025.10.17.682746v1 #cryoEM

This comic is becoming increasingly realistic.
m.xkcd.com/3056/

𝗖𝘂𝗿𝗶𝗼𝘂𝘀 𝗵𝗼𝘄 𝘄𝗲 𝘂𝘀𝗲 𝗵𝗶𝗴𝗵-𝘁𝗲𝗰𝗵 𝘁𝗼 𝗮𝗱𝘃𝗮𝗻𝗰𝗲 𝗼𝘂𝗿 𝗿𝗲𝘀𝗲𝗮𝗿𝗰𝗵?
Then join us at our Open Day and get exciting sneak peaks behind the scenes of one of Europe’s largest life science campuses in Martinsried.

Find out more (in German): mpi.lineupr.com/tdot/

Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on!

#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵

gapTrick - Structural characterisation of protein-protein interactions using AlphaFold pubmed.ncbi.nlm.nih.gov/40985612/ #cryoEM

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

Very impressive results and interesting approach. One can now wonder if the theoretical size limit still holds true. Has anyone tried to look at, e.g. lysozyme in cryoEM?

This one is a bit of a departure from the usual and definitely a work in progress!

We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.

Read on for details... 1/x

Determinants of human versus mosquito cell entry by the Chikungunya virus envelope proteins Chikungunya virus (CHIKV) infects both humans and mosquitoes during its transmission cycle. How the virus’s envelope proteins mediate entry in cells from such different species is unclear. MXRA8 is a ...

In new study led by Xiaohui Ju, we define how mutations to Chikungunya virus envelope proteins affect entry in human vs mosquito cells.

Sheds light on functional constraints & enables us to make loss-of-tropism mutants, which could be of use for vaccines.

www.biorxiv.org/content/10.1...

Congrats Martin! Well deserved.

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

Leopard-EM: An extensible 2DTM package to accelerate in situ structural biology The ability to generate high-resolution views of cells with cryogenic electron microscopy (cryo-EM) can reveal the molecular mechanisms of biological processes in their native cellular context. The re...

First pre-print from the Lucas Lab led by Matthew Giammar and @joshdcryoem.bsky.social online today! We develop a new, extensible Python implementation of 2DTM and apply it to build pixel size optimization, constrained search and characterize molecular motions in situ 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

Congratulations! Such an amazing and user friendly tool.

A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...

Better ML for cryo-ET starts with better benchmarks.

We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.

The result: community models beat expert tools.

Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...

Researchers have developed a #DeepLearning system called BioEmu that rapidly generates diverse protein conformations, enabling fast, accurate insights into protein flexibility and function.

Learn more this week in Science: https://scim.ag/3JdQVD4

New preprint: In situ Architecture of #Plasmodesmata.

Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.

🔗 doi.org/10.1101/2025...

🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM

Open Call for Expressions of Interest in Max Planck Directorships: Expressions of interest can be submitted until 31 October 2025.

Director at Max Planck - a unique position! The Open Call for Expressions of Interest in Max Planck Directorships is open now and can be submitted by the 31st of October 2025. ➡️ mpg.de/directors - Please share the Open Call among potential candidates.