Jan-Hannes Schaefer
@jhschaef.bsky.social
Structural Biology to the rescue. Postdoc with Gabriel Lander at Scripps Research. PhD with Arne Moeller. #cryoEM ❄️🔬 🎹⛳
CryoSift is now out @actacrystf.iucr.org doi.org/10.1107/S205... Thanks to all involved. Happy processing!
November 7, 2025 at 4:58 PM
CryoSift is now out @actacrystf.iucr.org doi.org/10.1107/S205... Thanks to all involved. Happy processing!
Reposted by Jan-Hannes Schaefer
Lauren Alexandrescu et al.: `Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale ##ElectronMicroscopy##CryoEM##TimeResolvedStudies... ##IUCrhttps://journals.iucr.org/paper?S2052252525008838
`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.
journals.iucr.org
October 28, 2025 at 1:00 AM
Lauren Alexandrescu et al.: `Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale ##ElectronMicroscopy##CryoEM##TimeResolvedStudies... ##IUCrhttps://journals.iucr.org/paper?S2052252525008838
Reposted by Jan-Hannes Schaefer
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.
Chris Russo and Anastasiia Gusach have developed a new method to prepare #cryoEM samples that avoids protein damage during freezing
Read more: www2.mrc-lmb.cam.ac.uk/a-new-method...
#LMBResearch
Read more: www2.mrc-lmb.cam.ac.uk/a-new-method...
#LMBResearch
October 22, 2025 at 9:33 PM
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.
Reposted by Jan-Hannes Schaefer
🚀 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...
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...
October 20, 2025 at 2:32 PM
🚀 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...
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...
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
October 17, 2025 at 3:43 PM
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
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...
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...
October 5, 2025 at 4:16 AM
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...
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...
Reposted by Jan-Hannes Schaefer
We had a fantastic time hosting the first Functional Amyloid Meeting @ DESY! #FFFatDESY2025 #FunctionalFibrilFriends
landaulabcssb.bsky.social
landaulabcssb.bsky.social
September 26, 2025 at 3:18 PM
We had a fantastic time hosting the first Functional Amyloid Meeting @ DESY! #FFFatDESY2025 #FunctionalFibrilFriends
landaulabcssb.bsky.social
landaulabcssb.bsky.social
Reposted by Jan-Hannes Schaefer
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.
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.
September 26, 2025 at 2:28 AM
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.
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.
Reposted by Jan-Hannes Schaefer
❄️ 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
Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification https://www.biorxiv.org/content/10.1101/2025.09.14.676144v1
September 18, 2025 at 8:04 AM
❄️ 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
Reposted by Jan-Hannes Schaefer
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?
Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching www.biorxiv.org/content/10.1101/2025.09.11.675606v1 #cryoem
September 17, 2025 at 10:57 AM
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?
A great resource. One highlight for me is: "One of the best things about structural biology is visualizing what you are discovering."
Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...
10 Rules for a Structural Bioinformatic Analysis
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...
chemrxiv.org
September 13, 2025 at 3:35 PM
A great resource. One highlight for me is: "One of the best things about structural biology is visualizing what you are discovering."
Reposted by Jan-Hannes Schaefer
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
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
September 13, 2025 at 12:05 AM
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
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
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!
September 5, 2025 at 2:48 PM
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!
Been thinking about creating a collection of good protein structure figures, as inspiration for my own work.
#1 www.nature.com/articles/s41...
#1 www.nature.com/articles/s41...
September 4, 2025 at 1:09 AM
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/...
August 29, 2025 at 3:39 PM
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/...
Reposted by Jan-Hannes Schaefer
Was lucky to see this presented at the NYC cryoEM meeting earlier this year - super cool stuff!
August 22, 2025 at 9:37 PM
Was lucky to see this presented at the NYC cryoEM meeting earlier this year - super cool stuff!
Reposted by Jan-Hannes Schaefer
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...
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...
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...
www.nature.com
August 15, 2025 at 10:00 AM
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...
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...
Reposted by Jan-Hannes Schaefer
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...
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...
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.
nature.com
August 6, 2025 at 3:16 PM
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...
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...
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
Happy testing: cryosift.org #cryoEM #CNN
August 1, 2025 at 3:20 PM
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
Happy testing: cryosift.org #cryoEM #CNN
Reposted by Jan-Hannes Schaefer
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...
www.sciencedirect.com/science/arti...
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…
www.sciencedirect.com
July 30, 2025 at 9:50 PM
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...
www.sciencedirect.com/science/arti...
Reposted by Jan-Hannes Schaefer
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...
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
AlphaFold - A practical guide
AlphaFold - A practical guide
www.ebi.ac.uk
July 21, 2025 at 3:33 PM
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...
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
Yet another great case study! Maybe most symmetric assemblies are not? And helical assemblies next @structurabio.bsky.social ?
Working with symmetric or pseudosymmetric particles in #cryoEM?
This TRPV5 and CaM case study includes practical considerations for using symmetry relaxation and 3D classification when analyzing a pseudosymmetric particle in #CryoSPARC!
This TRPV5 and CaM case study includes practical considerations for using symmetry relaxation and 3D classification when analyzing a pseudosymmetric particle in #CryoSPARC!
July 14, 2025 at 2:35 PM
Yet another great case study! Maybe most symmetric assemblies are not? And helical assemblies next @structurabio.bsky.social ?
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
A few months ago, Nature published how-to guide for using ChatGPT to write your peer reviews in 30 minutes.
This is, of course, a horrible idea. Here’s my response with @jbakcoleman.bsky.social .
This is, of course, a horrible idea. Here’s my response with @jbakcoleman.bsky.social .
AI, peer review and the human activity of science
When researchers cede their scientific judgement to machines, we lose something important.
www.nature.com
June 25, 2025 at 5:45 PM
Reposted by Jan-Hannes Schaefer
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...
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...
June 23, 2025 at 5:15 AM
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...
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...
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... 🌎❄️🔬
June 23, 2025 at 11:28 PM
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... 🌎❄️🔬