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Dominik Hrebik

@dhrebik.bsky.social

1.4K followers 1.3K following 72 posts

Postdoc @JohnBriggsGroup @MaxPlanck Institute of Biochemistry in Martinsried | PhD from PlevkaLab | #StructuralBiology of #Viruses #HIV | #CryoEM | #Memes Twitter/X: @F4ustus

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Dominik Hrebik @dhrebik.bsky.social · Mar 3

I am very happy to announce that we solved the in-virus #cryoEM structure of the #HIV matrix protein. The structure helped us to resolve a long mystery in HIV biology. A🧵1/5
Read more in Nature: www.nature.com/articles/s41... 🧪

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Dominik Hrebik @dhrebik.bsky.social · 9d

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

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Reposted by Dominik Hrebik

Max Planck Institute of Biochemistry @mpibiochem.bsky.social · 13d

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/

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Reposted by Dominik Hrebik

Ben Engel @cellarchlab.com · 13d

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/🧵

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Reposted by Dominik Hrebik

cryoEM papers @cryoempapers.bsky.social · 13d

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

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Reposted by Dominik Hrebik

Sofya Garushyants @garushyants.bsky.social · 23d

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!

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Dominik Hrebik @dhrebik.bsky.social · 23d

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?

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Oli Clarke @olibclarke.bsky.social · 25d

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

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Reposted by Dominik Hrebik

Bloom lab @jbloomlab.bsky.social · Sep 4

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...

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 ...

www.biorxiv.org

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Dominik Hrebik @dhrebik.bsky.social · Sep 4

Congrats Martin! Well deserved.

Reposted by Dominik Hrebik

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 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...

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Reposted by Dominik Hrebik

Bronwyn Lucas @bronwynalucas.bsky.social · Aug 30

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...

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...

www.biorxiv.org

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Reposted by Dominik Hrebik

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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Dominik Hrebik @dhrebik.bsky.social · Aug 27

Congratulations! Such an amazing and user friendly tool.

Reposted by Dominik Hrebik

Kyle Harrington @kyleharrington.com · Aug 26

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...

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...

doi.org

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Reposted by Dominik Hrebik

Science Magazine @science.org · Aug 14

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

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Reposted by Dominik Hrebik

Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · Jul 26

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

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Reposted by Dominik Hrebik

Max-Planck-Gesellschaft @maxplanck.de · Aug 1

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.

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

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Reposted by Dominik Hrebik

Oded Rechavi @odedrechavi.bsky.social · Jul 31

🥂This was the highlight of my year. The "instigators", led by local master of the ceremony @svobodalab.bsky.social will never forget the privilege of organizing it and i think every participant will treasure the experience forever ❤️ @nature.com @josiegz.bsky.social www.nature.com/articles/d41...

Scientific bedlam at the world’s weirdest and wildest research conference

Woodstock Bio2 + Night Science aimed to encourage collaborations through creativity. The walk-on music for presentations was fun, too.

www.nature.com

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Reposted by Dominik Hrebik

Harry Low’s Lab @lowlab.bsky.social · Jul 28

Please RT! Call for Fellows! If you’re a structural biologist and wanting to start your lab by applying for an external Fellowship then we at Imperial may be excited to host you. Synthetic biologists too.. Please submit expression of interest with details below 🙏

www.imperial.ac.uk/media/imperi...

www.imperial.ac.uk

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Dominik Hrebik @dhrebik.bsky.social · Jul 25

Congratulations!

Reposted by Dominik Hrebik

Oded Rechavi @odedrechavi.bsky.social · Jul 18

When the reviewers' identities are revealed

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Reposted by Dominik Hrebik

Stephen Royle @steveroyle.bsky.social · Jul 14

Check out our lab's latest paper. Laura Downie found that the Lamin B Receptor (LBR) can be used to inducibly label all kinds of membrane contact sites in live cells
doi.org/10.1371/jour...

Nondisruptive inducible labeling of ER-membrane contact sites using the Lamin B receptor

ER-membrane contact sites are often distorted by existing labeling methods. This study develops an inducible labeling system called LaBeRing that uses the Lamin B receptor to fluorescently tag a varie...

doi.org

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Reposted by Dominik Hrebik

Nitzan Tal @nitzantal.bsky.social · Jul 13

📢Preprint out!
Excited to share my final work from the @soreklab.bsky.social!

We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.

Found 3 new families targeting immune signaling!

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Reposted by Dominik Hrebik

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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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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