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Jan-Hannes Schaefer

@jhschaef.bsky.social
461 followers 497 following 81 posts

Structural Biology to the rescue. Postdoc at Scripps Research. jhschaefer.de ❄️🔬 🎹⛳

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Jan-Hannes Schaefer @jhschaef.bsky.social · 15/09/2026
Turns out it's "A hair in the Soup." Tailocins are recurrent contaminants in ex vivo amyloid extraction. We've updated the preprint and provided actionable recommendations to avoid overinterpreting contaminants. doi.org/10.64898/202...
doi.org
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Jan-Hannes Schaefer @jhschaef.bsky.social · 08/09/2026
Transthyretin doesn't exclusively unfold the way we thought. Under lysosomal pH (4-5), or with certain mutations, it takes an alternative route through a more expanded tetrameric transition state. And kinetic stabilizers work less well on it. @scripps.edu doi.org/10.1073/pnas...
Blender rendering of the diverging unfolding pathway of TTR
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bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 28/08/2026
Imaging large fields-of-view at high resolution in cryo-ET with square beam montaging www.biorxiv.org/content/10.64898/20…
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Jan-Hannes Schaefer @jhschaef.bsky.social · 13/08/2026
Thanks for highlighting our work. I hope it helps the community. Let me know if the Protocol works for you and what @cryosparc.bsky.social could improve.
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Eric Topol @erictopol.bsky.social · 06/08/2026
Against all odds, with an HHS that has defunded mRNA research programs, the FDA just approved the first mRNA flu vaccine
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Jon Agirre @glycojones.bsky.social · 04/08/2026
Some questions for our structural biology community: What protocols do you think would be useful to have? Do you prefer to watch step-by-step videos, or follow written instructions? Of course, not everything has to be a video, but certain workflows are simply best documented on video #protocols
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Jan-Hannes Schaefer @jhschaef.bsky.social · 19/06/2026
Bacteriophage tails co-enrich with ex vivo amyloids from amyloidosis patients. Cryo-EM reveals Siphoviridae tail tube protein in ALys and AL amyloid extract. Do phages interact with human amyloids? @landerlab.bsky.social @nanigrotjahn.bsky.social & Kelly Lab #cryoEM #b3d doi.org/10.64898/202...
blender rendering of amyloids with phage tail tubes
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Jan-Hannes Schaefer @jhschaef.bsky.social · 09/06/2026
New paper out in @actacrystf.iucr.org! We benchmarked cryoSPARC for amyloid helical reconstruction: ease of use over RELION, but amyloid-specific development still needed & software interoperability remains a problem. @landerlab.bsky.social Kelly Lab @scripps.edu doi.org/10.1107/S205...
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Harry M. Williams @harrywilliams.bsky.social · 22/05/2026
We are pleased to release an update to this pre-print! Includes (1) proof-of-principle experiments on ultrasonic excitation during plunge vitrification, (2) cryo-ET characterisation of the effect, (3) and insights into grid/ice quality following ultrasonic excitation during vitrification.
biorxiv.org
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Eric Topol @erictopol.bsky.social · 18/05/2026
This is the kind of work, published today, that should be fully supported and prioritized at the highest level. Currently, there is no vaccine vs the Ebola Bundibugyo virus, the source of a major outbreak www.pnas.org/doi/10.1073/...
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 16/05/2026
Try this new online training game from Leandro F. Estrozi designed for newcomers in structural biology, with a focus on cryo-EM and cryo-ET map interpretation: rico.ibs.fr/helixplo...
Screenshot of online game
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Jan-Hannes Schaefer @jhschaef.bsky.social · 06/05/2026
In our new work from the Kelly, Ye & @landerlab.bsky.social , we link ATTR cardiomyopathy to microangiopathy. Increased capillary permeability exposes components of the vascular basement membrane to misfolded TTR. Work led by Joe Donnelly. #amyloidosis #cryoem #b3d doi.org/10.1161/JAHA...
TTR amyloids rendered with Blender
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Jan-Hannes Schaefer @jhschaef.bsky.social · 07/04/2026
We identified the maltoside detergent DM as an effective and easy solution to address preferred orientation in cryo-EM. Helped me switch from graphene grids. Special congrats to Maria Rafiq! @landerlab.bsky.social @nanigrotjahn.bsky.social @wisemanlab.bsky.social #cryoEM doi.org/10.64898/202...
Blender Rendering of vitrified HA trimer with DM at the air-water interface
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Sjors Scheres @sjorsscheres.bsky.social · 18/03/2026
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
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Jan-Hannes Schaefer @jhschaef.bsky.social · 16/03/2026
Great to see one of my PhD projects out on bioRxiv. We report "A dual sensor regulates P-glycoproteins structural plasticity." Congrats to Michael Kamel for doing the heavy lifting from @arnemoeller.bsky.social & Urbatsch Lab. doi.org/10.64898/202... #b3d #cryoEM
ABC transporter Pgp in membrane. Blender Rendering
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Jan-Hannes Schaefer @jhschaef.bsky.social · 14/03/2026
For obvious reasons, we need a Paceometer! #endroadrage doi.org/10.1017/S193...
Pacometer vs. speedometer
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John Rubinstein @johnrubinstein.bsky.social · 06/03/2026
I've written a review on what I think is an extremely exciting direction in cryo-EM: Cryo-EM of endogenous membrane proteins in their native lipid bilayer Open access in Quarterly Reviews of Biophysics: doi.org/10.1017/S003...
Figure 1. Cryo-EM of abundant protein complexes in native membranes.Figure 2. Cryo-EM of membrane proteins in vesicles.Figure 3. 3D reconstruction of V-ATPase in native synaptic vesicle membranes.Figure 4. Generation of membrane vesicles for structure determination of proteins in their native lipid bilayer.
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ChimeraX @chimerax.ucsf.edu · 24/02/2026
The new ChimeraX CubeNTube plugin allows erasing parts of maps using cube, cylinder, and custom shapes and has undo. Created by Tamino Cairoli. Available from ChimeraX menu Tools / More Tools....
ChimeraX screenshot showing CubeNTube plugin.
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Hanjin Liu @liu-hanjin.bsky.social · 22/02/2026
Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...
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Jan-Hannes Schaefer @jhschaef.bsky.social · 19/01/2026
Thanks, I guess we all needed this.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 17/12/2025
In our new preprint, we show how fibril-dynamics of signaling component TIRAP supports sensitive & fast sensing of endotoxin LPS. Congrats to co-lead @arthurfelker.bsky.social. @piehlerlab.bsky.social @arnemoeller.bsky.social #TLR #cryoEM #blender doi.org/10.64898/202...
Blender rendering of TLR4 in membrane and TIRAP fibrils at the plamsma membrane. Blender rendering of TLR4 in membrane and TIRAP fibrils at the plamsma membrane. View from the cytosol.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 11/12/2025
Thanks to @actacrystf.iucr.org for highlighting our smart 2D selection tool CryoSift. You can test it yourself here cryosift.org
cryosift.org
CryoSift - Cryo-EM 2D Classifier
Automated cryo-EM 2D class evaluation and sorting with AI.
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Gabriel Rocklin @grocklin.bsky.social · 19/11/2025
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
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hamid13r.bsky.social @hamid13r.bsky.social · 25/11/2025
Just installed Doppio on our Linux machine. This is awesome work making relion more accessible and easy to run. I haven't tried submitting jobs yet but it is already making our live easier! I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!
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Jan-Hannes Schaefer @jhschaef.bsky.social · 07/11/2025
CryoSift is now out @actacrystf.iucr.org doi.org/10.1107/S205... Thanks to all involved. Happy processing!
doi.org
CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection
CryoSift is a CNN-based tool that assesses the quality of 2D class averages. The incorporation of CryoSift into cryoSPARC workflows enables automated particle-stack cleaning.
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IUCrJ @iucrj.iucr.org · 28/10/2025
Lauren Alexandrescu et al.: `Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale #ElectronMicroscopy #CryoEM #TimeResolvedStudies ... #IUCr journals.iucr.org/paper?S2052252525…
journals.iucr.org
`Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale
The development of methods for low-cost time-resolved cryo-EM using an on-grid mixing strategy is described.
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Anastasia Gusach @g-anastasia.bsky.social · 22/10/2025
Excited to share a new chapter of my scientific journey in Chris Russo's group — developing a way to freeze proteins faster than they diffuse, paving the way for cryo-EM without air–water interface damage.
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Structura Biotechnology @structurabio.bsky.social · 20/10/2025
🚀 Introducing fully automated data processing for repeat-target #cryoEM. Using new tools in #CryoSPARC, it is now possible to obtain resolutions & map quality equal to or better than manual processing, with zero user intervention. Preprint: www.biorxiv.org/content/10.1...
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Jan-Hannes Schaefer @jhschaef.bsky.social · 17/10/2025
Thanks @odedrechavi.bsky.social. Even without explicit coverage of structural biology, it did a great job as Reviewer #0 on my latest preprint. Highly recommend www.qedscience.com
qedscience.com
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
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Jan-Hannes Schaefer @jhschaef.bsky.social · 05/10/2025
Helical Reconstruction of Amyloids in cryoSPARC? We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social. Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
Amyloid reconstructions from cryoSPARC
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Meytal Landau @meytallandau.bsky.social · 26/09/2025
‪We had a fantastic time hosting the first Functional Amyloid Meeting @ DESY! #FFFatDESY2025 #FunctionalFibrilFriends landaulabcssb.bsky.social
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Oli Clarke @olibclarke.bsky.social · 26/09/2025
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup). A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
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Harry M. Williams @harrywilliams.bsky.social · 18/09/2025
❄️ NEW PRE-PRINT ❄️ Happy to see our latest work online. Here we present a super simple solution to the preferred orientation problem in single particle cryo-EM: the use of ultrasonic excitation during vitrification! Details in the 🧵 below... #cryoEM #structuralbiology
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Oli Clarke @olibclarke.bsky.social · 17/09/2025
Another successful approach to the same problem as HR-HAIR! 🤩 I wonder if a combo might be worth a try - use one frequency band to get perfectly centered particles using 2DTM, then re-estimate orientations using HR-HAIR with a non-overlapping frequency band?
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Jan-Hannes Schaefer @jhschaef.bsky.social · 13/09/2025
A great resource. One highlight for me is: "One of the best things about structural biology is visualizing what you are discovering."
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Oli Clarke @olibclarke.bsky.social · 13/09/2025
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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Jan-Hannes Schaefer @jhschaef.bsky.social · 05/09/2025
Magellon has taken off to explore your cryo-EM data! Now out in @iucrj.iucr.org doi.org/10.1107/S205... Congrats to all involved!
doi.org
Magellon – an extensible platform for cryo-EM data visualization, management and processing
This work presents a new cyberinfrastructure framework for cryo-EM structure determination, Magellon, which offers a robust and flexible approach to cryo-EM data management. We show the power of this ...
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Jan-Hannes Schaefer @jhschaef.bsky.social · 04/09/2025
Uninspired while making figures? Search no more. #science #art
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Jan-Hannes Schaefer @jhschaef.bsky.social · 29/08/2025
Our work on "Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned" is now out in Science Advances! Congrats to all involved. www.science.org/doi/10.1126/...
doi.org
Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned
The molecular comparison of related RabGEFs reveals adaptation mechanisms of a functional module for specific cellular tasks.
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Oli Clarke @olibclarke.bsky.social · 22/08/2025
Was lucky to see this presented at the NYC cryoEM meeting earlier this year - super cool stuff!
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David B. Sauer @davidbsauer.bsky.social · 15/08/2025
Di-Gembodies (dimerized nanobodies) for improved and duplexed CryoEM of small and challenging targets! A collaboration of @cmd.ox.ac.uk, STRUBI, @diamondlightsource.bsky.social, @rosfrankinst.bsky.social Out now in Nature Chemical Biology @natchembio.nature.com www.nature.com/articles/s41...
nature.com
Covalently constrained ‘Di-Gembodies’ enable parallel structure solutions by cryo-EM - Nature Chemical Biology
Disulfide-based dimerization of modified identical and heterologous nanobody scaffolds enables higher-order assembly for high-resolution cryo-electron microscopy structure determination that is widely...
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Eric Topol @erictopol.bsky.social · 06/08/2025
New @nature.com The possibility that lithium deficiency is a driver of Alzheimer's disease. Experimental model shows Li depletion impedes amyloid clearance, and repletion in humans could be achieved with low doses nature.com/articles/s41...
nature.com
Lithium deficiency and the onset of Alzheimer’s disease - Nature
Lithium has an essential role in the brain and is deficient early in Alzheimer’s disease, which can be recapitulated in mice and treated with a novel lithium salt that restores the physiological level.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 01/08/2025
Check out our new preprint from the @landerlab.bsky.social, Stagg-Lab and Cianfrocco-Lab: CryoSift - An accessible and automated CNN-driven tool for cryo-EM 2D class selection www.biorxiv.org/content/10.1... Happy testing: cryosift.org #cryoEM #CNN
CryoSift – An accessible and automated CNN-driven
tool for cryo-EM 2D class selection
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Basil Greber @bjgreber.bsky.social · 30/07/2025
Now out in Structure: Paper on high-resolution #cryoEM using the 100 kV Tundra cryo-TEM by Dimple Karia, Adrian Koh, @abhaykot.bsky.social, @lingboyu.bsky.social, @landerlab.bsky.social and many others. Happy to have contributed to this effort. Check it out: www.sciencedirect.com/science/arti...
sciencedirect.com
Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV
Cryoelectron microscopy (cryo-EM) has transformed structural biology by providing high-resolution insights into biological macromolecules. We report s…
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Saloni @scientificdiscovery.dev · 21/07/2025
Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good! There are also little quizzes and interactives. www.ebi.ac.uk/training/onl...
ebi.ac.uk
AlphaFold - A practical guide
AlphaFold - A practical guide
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Jan-Hannes Schaefer @jhschaef.bsky.social · 14/07/2025
Yet another great case study! Maybe most symmetric assemblies are not? And helical assemblies next @structurabio.bsky.social ?
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Jan-Hannes Schaefer @jhschaef.bsky.social · 25/06/2025
Provocative but there is truth to it! "Every time a scientist abdicates their work to an AI tool, that is a tacit admission that the work is not worth being done by the scientist." #LLM #science
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Alexey Amunts @amunts.bsky.social · 23/06/2025
Running Phenix and stuck? Now you can ask the new Phenix chatbot anything from the 600-page tutorial about how to run any program. Big thanks to Tom Willinger for making this happen! Try it out: phenix-online.org/version_docs...
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Jan-Hannes Schaefer @jhschaef.bsky.social · 24/06/2025
Exited to share my first PostDoc contribution! Like Magellan explored the globe, you can explore your cryoEM data with Magellon. Congrats to all involved. Scott Stagg Lab & Michael Cianfrocco Lab @landerlab.bsky.social www.biorxiv.org/content/10.1... 🌎❄️🔬
Magellon GUI for cryoEM
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