Jan Philipp Kreysing
@jpkreysing.bsky.social
in cell cryo-ET and image processing enthusiast #teamtomo
PhD student in Martin Beck's group (@becklab.bsky.social) at the Max Planck Institute of Biophysics (@mpibp.bsky.social)
PhD student in Martin Beck's group (@becklab.bsky.social) at the Max Planck Institute of Biophysics (@mpibp.bsky.social)
Pinned
New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
Reposted by Jan Philipp Kreysing
We are excited to share our new preprint which is now available to read on biorXiv: doi.org/10.64898/202... 🎉🎉🎉
January 13, 2026 at 2:39 PM
We are excited to share our new preprint which is now available to read on biorXiv: doi.org/10.64898/202... 🎉🎉🎉
#teamtomo strikes again! Check out our new preprint on the enigmatic vault and its newly discovered association with membranes in situ.
It’s out! Using cryo-ET in Dicty cells, we take a fresh in situ look at vaults. Surprisingly, we uncover vaults associated with ER and NE membranes, and find that many vaults enclose ribosomes in defined orientations, opening new avenues to their cellular function! www.biorxiv.org/lookup/conte...
December 16, 2025 at 9:42 AM
#teamtomo strikes again! Check out our new preprint on the enigmatic vault and its newly discovered association with membranes in situ.
Reposted by Jan Philipp Kreysing
New paper out!
How can we force HIV genomes out of their capsid shells and what can we learn about HIV biology doing so?
Hint: capsid inhibitors actively re-route nuclear HIV complexes, and expose genomes via intriguing structural effects!
open access:
link.springer.com/article/10.1...
read below
How can we force HIV genomes out of their capsid shells and what can we learn about HIV biology doing so?
Hint: capsid inhibitors actively re-route nuclear HIV complexes, and expose genomes via intriguing structural effects!
open access:
link.springer.com/article/10.1...
read below
Lenacapavir-induced capsid damage uncovers HIV-1 genomes emanating from nuclear speckles - The EMBO Journal
Following cell entry, HIV-1 capsids enter the nucleus by passage through nuclear pores and reach nuclear speckles with subsequent uncoating of the reverse-transcribed genome and its integration into s...
link.springer.com
December 4, 2025 at 1:58 PM
New paper out!
How can we force HIV genomes out of their capsid shells and what can we learn about HIV biology doing so?
Hint: capsid inhibitors actively re-route nuclear HIV complexes, and expose genomes via intriguing structural effects!
open access:
link.springer.com/article/10.1...
read below
How can we force HIV genomes out of their capsid shells and what can we learn about HIV biology doing so?
Hint: capsid inhibitors actively re-route nuclear HIV complexes, and expose genomes via intriguing structural effects!
open access:
link.springer.com/article/10.1...
read below
Exciting new paper from my colleague @deglushk.bsky.social in the @becklab.bsky.social! It introduces a fast, robust tool for measuring membrane thickness in tomograms #TeamTomo.
Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
November 6, 2025 at 8:37 AM
Exciting new paper from my colleague @deglushk.bsky.social in the @becklab.bsky.social! It introduces a fast, robust tool for measuring membrane thickness in tomograms #TeamTomo.
Reposted by Jan Philipp Kreysing
Have you registered to the next EMBO Practical Course on In-situ structural biology by Cryo-FIB and Cryo-ET? 🧊 Join us in Frankfurt for hands-on training on cryo-techniques and networking with experts!
🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...
📍 Frankfurt | 📆 April 12–20, 2026
🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...
📍 Frankfurt | 📆 April 12–20, 2026
October 23, 2025 at 9:10 AM
Have you registered to the next EMBO Practical Course on In-situ structural biology by Cryo-FIB and Cryo-ET? 🧊 Join us in Frankfurt for hands-on training on cryo-techniques and networking with experts!
🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...
📍 Frankfurt | 📆 April 12–20, 2026
🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...
📍 Frankfurt | 📆 April 12–20, 2026
Reposted by Jan Philipp Kreysing
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Icecream: High-Fidelity Equivariant Cryo-Electron Tomography
Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...
www.biorxiv.org
October 23, 2025 at 11:13 AM
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Reposted by Jan Philipp Kreysing
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️
www.biorxiv.org/content/10.1...
#teamtomo
www.biorxiv.org/content/10.1...
#teamtomo
October 15, 2025 at 6:26 AM
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️
www.biorxiv.org/content/10.1...
#teamtomo
www.biorxiv.org/content/10.1...
#teamtomo
❓What if you could peek between your tilt series ❓ We are proud to introduce cryoTIGER -- deep-learning based tilt interpolation for enhanced reconstruction in cryo-ET. A great collaboration between Turoňová lab, @becklab.bsky.social, @hummerlab.bsky.social #teamtomo www.nature.com/articles/s42...
cryoTIGER: deep-learning based tilt interpolation generator for enhanced reconstruction in cryo electron tomography - Communications Biology
Deep learning-based interpolation using cryoTIGER enhances angular sampling in cryoET, improving 3D reconstructions, particle localization, and structural recovery without increasing electron dose.
www.nature.com
October 10, 2025 at 10:35 AM
❓What if you could peek between your tilt series ❓ We are proud to introduce cryoTIGER -- deep-learning based tilt interpolation for enhanced reconstruction in cryo-ET. A great collaboration between Turoňová lab, @becklab.bsky.social, @hummerlab.bsky.social #teamtomo www.nature.com/articles/s42...
More great cryo-ET benchmarking work from my colleagues Maarten Tuijtel, Tomáš Majtner, Beata Turoňová, & @becklab.bsky.social: Systematic study of how tilt increment choice affects downstream TM & STA. Preprint has the optimally balanced tilt increment. #TeamTomo www.biorxiv.org/content/10.1...
Optimal tilt-increment for cryo-ET
Cryo-electron tomography (cryo-ET) enables high-resolution, three-dimensional imaging of cellular structures in their native, frozen state. However, image quality is limited by a trade-off between ang...
www.biorxiv.org
August 23, 2025 at 9:18 AM
More great cryo-ET benchmarking work from my colleagues Maarten Tuijtel, Tomáš Majtner, Beata Turoňová, & @becklab.bsky.social: Systematic study of how tilt increment choice affects downstream TM & STA. Preprint has the optimally balanced tilt increment. #TeamTomo www.biorxiv.org/content/10.1...
Reposted by Jan Philipp Kreysing
We’re hosting the @embo.org Practical Course on In-situ structural biology by CryoFIB and CryoET in April 2026! 🧬❄️ You can expect hands-on training, cutting-edge methods, and a chance to work alongside leading experts in structural biology. 🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...
August 18, 2025 at 11:29 AM
We’re hosting the @embo.org Practical Course on In-situ structural biology by CryoFIB and CryoET in April 2026! 🧬❄️ You can expect hands-on training, cutting-edge methods, and a chance to work alongside leading experts in structural biology. 🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...
Reposted by Jan Philipp Kreysing
AI for Cryo-ET 🌟 Our new paper presents a deep-learning framework that cleans up faulty tilt series in a more automated, precise and powerful way! 💪 Read more here: www.sciencedirect.com/science/arti...
Automated removal of corrupted tilts in cryo-electron tomography
Cryo-electron tomography (cryo-ET) enables the visualization of macromolecular structures in their near-native cellular environment. However, acquired…
www.sciencedirect.com
July 25, 2025 at 10:14 AM
AI for Cryo-ET 🌟 Our new paper presents a deep-learning framework that cleans up faulty tilt series in a more automated, precise and powerful way! 💪 Read more here: www.sciencedirect.com/science/arti...
New from my colleagues Markus Schreiber & Beata Turoňová: TANGO, an #opensource tool for more holistic spatial analysis of cryo-ET particles. It can clean or cluster particles, analyze lattices, and identify patterns. #TeamTomo
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Twist and Scout: Analysis and Curation of Particles in Cryo-Electron Tomography Using TANGO
Cryo-electron tomography (cryo-ET) enables the visualization of cellular structures in near-native environments, but its potential for spatial analysis has been underutilized due to a lack of versatil...
www.biorxiv.org
July 23, 2025 at 8:14 AM
New from my colleagues Markus Schreiber & Beata Turoňová: TANGO, an #opensource tool for more holistic spatial analysis of cryo-ET particles. It can clean or cluster particles, analyze lattices, and identify patterns. #TeamTomo
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jan Philipp Kreysing
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Welcome to TomoGuide
A step-by-step Cryo-ET guide
tomoguide.github.io
May 6, 2025 at 4:27 PM
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Reposted by Jan Philipp Kreysing
🦠🧠 MemBrain update! 🧠🦠
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo
April 25, 2025 at 7:28 AM
🦠🧠 MemBrain update! 🧠🦠
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo
Looking for a tool to measure membrane thicknesses in tomograms (#TeamTomo)? Or curious about thickness differences within and across organelles? Check out my fellow @becklab.bsky.social PhD student @deglushk.bsky.social's excellent preprint:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
April 12, 2025 at 7:29 PM
Looking for a tool to measure membrane thicknesses in tomograms (#TeamTomo)? Or curious about thickness differences within and across organelles? Check out my fellow @becklab.bsky.social PhD student @deglushk.bsky.social's excellent preprint:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
April 11, 2025 at 9:04 AM
New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
Also, check out @sergiocruzleon.bsky.social's post for a cool video summary about our new heterochromatin preprint.
Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social
🔗 Preprint here tinyurl.com/3a74uanv
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social
🔗 Preprint here tinyurl.com/3a74uanv
April 11, 2025 at 8:45 AM
Also, check out @sergiocruzleon.bsky.social's post for a cool video summary about our new heterochromatin preprint.
Excited to share our latest work on nuclear pore complex scaffold integrity and its perturbation. Now out in Nature Cell Biology: rdcu.be/eg4i9
Great work by Reiya Taniguchi who just opened his own research group back in Japan! 🥳
Great work by Reiya Taniguchi who just opened his own research group back in Japan! 🥳
Nuclear pores safeguard the integrity of the nuclear envelope
Nature Cell Biology - Taniguchi et al. structurally analyse nuclear pore complex architecture in situ during differentiation, which is associated with mechanical constraints on the nuclear...
rdcu.be
April 9, 2025 at 3:49 PM
Excited to share our latest work on nuclear pore complex scaffold integrity and its perturbation. Now out in Nature Cell Biology: rdcu.be/eg4i9
Great work by Reiya Taniguchi who just opened his own research group back in Japan! 🥳
Great work by Reiya Taniguchi who just opened his own research group back in Japan! 🥳
Reposted by Jan Philipp Kreysing
Automated Removal of Corrupted Tilts in Cryo-Electron Tomography https://www.biorxiv.org/content/10.1101/2025.03.13.642992v1
March 15, 2025 at 7:17 AM
Automated Removal of Corrupted Tilts in Cryo-Electron Tomography https://www.biorxiv.org/content/10.1101/2025.03.13.642992v1
Reposted by Jan Philipp Kreysing
Reposted by Jan Philipp Kreysing
Fresh out of the press! ✨Check out our new paper on the violent entry of the HIV capsid into the nuclear pore — and how it cracks the gate! 🤯 💥 Incredible work from @becklab.bsky.social and @hummerlab.bsky.social 🤩 More here: www.biophys.mpg.de/2842024/hivcapsid-cracks-the-npc?c=2011019 🔗 #teamTOMO
January 17, 2025 at 4:34 PM
Fresh out of the press! ✨Check out our new paper on the violent entry of the HIV capsid into the nuclear pore — and how it cracks the gate! 🤯 💥 Incredible work from @becklab.bsky.social and @hummerlab.bsky.social 🤩 More here: www.biophys.mpg.de/2842024/hivcapsid-cracks-the-npc?c=2011019 🔗 #teamTOMO
So happy that my main PhD project on HIV-1 nuclear entry is now out in Cell. I want to especially thank my supervisor Martin @becklab.bsky.social and our amazing collaborators @maziarheidari.bsky.social from @hummerlab.bsky.social, Vojtech Zila from the Kräusslich lab and many others.
In a great collaboration with @hummerlab.bsky.social and the Kräusslich lab: HIV capsid doesn't break at the NPC; instead, it cracks open the NPC itself! Details in Cell: authors.elsevier.com/sd/article/S... @mpibp.bsky.social @uniheidelberg.bsky.social A thread below:
January 17, 2025 at 6:53 PM
So happy that my main PhD project on HIV-1 nuclear entry is now out in Cell. I want to especially thank my supervisor Martin @becklab.bsky.social and our amazing collaborators @maziarheidari.bsky.social from @hummerlab.bsky.social, Vojtech Zila from the Kräusslich lab and many others.
Reposted by Jan Philipp Kreysing
cryoTIGER: Deep-Learning Based Tilt Interpolation Generator for Enhanced Reconstruction in Cryo Electron Tomography https://www.biorxiv.org/content/10.1101/2024.12.17.628939v1
December 21, 2024 at 1:19 PM
cryoTIGER: Deep-Learning Based Tilt Interpolation Generator for Enhanced Reconstruction in Cryo Electron Tomography https://www.biorxiv.org/content/10.1101/2024.12.17.628939v1
Exciting times in HIV research and prevention! HIV capsid is a great drug target because it's not just a protective shell for the viral genome but also a key facilitator for HIV entering the nucleus via the nuclear pore (NPC).
Science’s 2024 Breakthrough of the Year is lenacapavir, an injectable drug that demonstrated remarkable success at preventing HIV infection with one shot every 6 months.
Learn more about this year's #BOTY and other big advances in science: scim.ag/3BrCtUn
Learn more about this year's #BOTY and other big advances in science: scim.ag/3BrCtUn
December 13, 2024 at 12:44 PM
Exciting times in HIV research and prevention! HIV capsid is a great drug target because it's not just a protective shell for the viral genome but also a key facilitator for HIV entering the nucleus via the nuclear pore (NPC).
Reposted by Jan Philipp Kreysing
Celebrating Dr. Huaipeng Xing from #molecularsociology on successfully defending his #PhD! 👏🥳 He studied the visualization of protein synthesis and folding inside human cells by #cryoET #teamTOMO. Congrats, Huaipeng, and best wishes for your future! 🤩
December 12, 2024 at 6:20 PM
Celebrating Dr. Huaipeng Xing from #molecularsociology on successfully defending his #PhD! 👏🥳 He studied the visualization of protein synthesis and folding inside human cells by #cryoET #teamTOMO. Congrats, Huaipeng, and best wishes for your future! 🤩