Johannes Stein
@jmstein.bsky.social
Group Leader at Max Planck Institute for Molecular Genetics
Studying genome organization with quantitative super-resolution microscopy
https://www.molgen.mpg.de/stein-lab
Studying genome organization with quantitative super-resolution microscopy
https://www.molgen.mpg.de/stein-lab
Pinned
Johannes Stein
@jmstein.bsky.social
· Aug 13
(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen!
Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵
Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵
Reposted by Johannes Stein
An ultra-rapid 3D immunostaining protocol can uniformly label organ-scale tissues go.nature.com/40wig8l
rdcu.be/eUK9R
rdcu.be/eUK9R
Uniform volumetric single-cell processing for organ-scale molecular phenotyping - Nature Biotechnology
An ultra-rapid 3D immunostaining protocol can uniformly label organ-scale tissues.
go.nature.com
December 30, 2025 at 4:36 AM
An ultra-rapid 3D immunostaining protocol can uniformly label organ-scale tissues go.nature.com/40wig8l
rdcu.be/eUK9R
rdcu.be/eUK9R
Reposted by Johannes Stein
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology
Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.
www.nature.com
December 22, 2025 at 11:45 AM
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Johannes Stein
🧬 Are you interested in synthetic biology, CRISPR-Cas9 genome editing and cutting-edge genomics? Apply by 07.01.2026 to join Stefan Mundlos’ lab @stemundi.bsky.social at the MPIMG. #IMPRS-BAC #gradschool! @nataliabenetti.bsky.social
👉 www.molgen.mpg.de/5124667/Mund...
👉 www.molgen.mpg.de/5124667/Mund...
December 11, 2025 at 2:07 PM
🧬 Are you interested in synthetic biology, CRISPR-Cas9 genome editing and cutting-edge genomics? Apply by 07.01.2026 to join Stefan Mundlos’ lab @stemundi.bsky.social at the MPIMG. #IMPRS-BAC #gradschool! @nataliabenetti.bsky.social
👉 www.molgen.mpg.de/5124667/Mund...
👉 www.molgen.mpg.de/5124667/Mund...
Reposted by Johannes Stein
Nuclear speckle associated RRM-containing proteins are block copolymers. They make size-limited, ordered microphases, tens of nm in size comprising tens of molecules. Speckles are likely clusters or emulsions of distinct microphases and not macrophases www.sciencedirect.com/science/arti...
Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases
Pre-mRNA processing components in nuclear speckles encompass one or more folded RNA recognition motifs (RRMs) and disordered regions with specific seq…
www.sciencedirect.com
December 19, 2025 at 7:14 PM
Nuclear speckle associated RRM-containing proteins are block copolymers. They make size-limited, ordered microphases, tens of nm in size comprising tens of molecules. Speckles are likely clusters or emulsions of distinct microphases and not macrophases www.sciencedirect.com/science/arti...
Very happy to share the published version of our study on the benefits of sodium sulfite + trolox (SST) as oxygen scavenger for #DNA-PAINT - now out in Small!
Thanks to the reviewers for helpful comments and again congrats, Becky, on your PhD's first paper!!
tinyurl.com/54m2pt9c
Thanks to the reviewers for helpful comments and again congrats, Becky, on your PhD's first paper!!
tinyurl.com/54m2pt9c
December 19, 2025 at 2:00 PM
Very happy to share the published version of our study on the benefits of sodium sulfite + trolox (SST) as oxygen scavenger for #DNA-PAINT - now out in Small!
Thanks to the reviewers for helpful comments and again congrats, Becky, on your PhD's first paper!!
tinyurl.com/54m2pt9c
Thanks to the reviewers for helpful comments and again congrats, Becky, on your PhD's first paper!!
tinyurl.com/54m2pt9c
Reposted by Johannes Stein
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
December 17, 2025 at 12:46 AM
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Reposted by Johannes Stein
New preprint from our lab: ‘Retroviral insertions contributed to the divergence of human and chimpanzee brains’. Very proud of this piece which took almost a decade to finish.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Retroviral insertions contributed to the divergence of human and chimpanzee brains
Over the past 5 to 7 million years, humans and chimpanzees have diverged in brain size, structural complexity, and cognitive abilities despite high conservation of protein-coding genes. Notably, the e...
www.biorxiv.org
December 14, 2025 at 8:16 PM
New preprint from our lab: ‘Retroviral insertions contributed to the divergence of human and chimpanzee brains’. Very proud of this piece which took almost a decade to finish.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Johannes Stein
Reposted by Johannes Stein
💥I am excited to present our first research paper from the lab about caveolae lipid trafficking 🎉 Led by my fantastic PhD candidate @estherocket.bsky.social
Here we looked into caveolae mediated dietary lipid uptake and how this process is mechanistically facilitated 👇 1/n
Here we looked into caveolae mediated dietary lipid uptake and how this process is mechanistically facilitated 👇 1/n
Lipid-induced Caveolin1-Lipid droplet trafficking is associated with lipid droplet growth https://www.biorxiv.org/content/10.64898/2025.12.10.693432v1
December 11, 2025 at 7:08 AM
💥I am excited to present our first research paper from the lab about caveolae lipid trafficking 🎉 Led by my fantastic PhD candidate @estherocket.bsky.social
Here we looked into caveolae mediated dietary lipid uptake and how this process is mechanistically facilitated 👇 1/n
Here we looked into caveolae mediated dietary lipid uptake and how this process is mechanistically facilitated 👇 1/n
Reposted by Johannes Stein
Here's another exciting doctoral project led by Research Group Leader Beatrice Ramm at the Friedrich Miescher Laboratory.
Check the list of other available projects on our website:
lnkd.in/gEMXNQY6
The application portal is open so apply now!
#PhD #IMPRS #graduateprogram #maxplanck
Check the list of other available projects on our website:
lnkd.in/gEMXNQY6
The application portal is open so apply now!
#PhD #IMPRS #graduateprogram #maxplanck
December 9, 2025 at 9:22 AM
Here's another exciting doctoral project led by Research Group Leader Beatrice Ramm at the Friedrich Miescher Laboratory.
Check the list of other available projects on our website:
lnkd.in/gEMXNQY6
The application portal is open so apply now!
#PhD #IMPRS #graduateprogram #maxplanck
Check the list of other available projects on our website:
lnkd.in/gEMXNQY6
The application portal is open so apply now!
#PhD #IMPRS #graduateprogram #maxplanck
Reposted by Johannes Stein
Janelia is hiring! "Invent new imaging methods, molecular tools, or protein chemistry approaches"
www.janelia.org/content/lead...
www.janelia.org/content/lead...
Lead a lab at Janelia
www.janelia.org
December 8, 2025 at 8:41 PM
Janelia is hiring! "Invent new imaging methods, molecular tools, or protein chemistry approaches"
www.janelia.org/content/lead...
www.janelia.org/content/lead...
Reposted by Johannes Stein
🔬 Call to create junior research groups at the Institut Pasteur
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research
The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...
research.pasteur.fr
December 8, 2025 at 8:53 AM
🔬 Call to create junior research groups at the Institut Pasteur
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Reposted by Johannes Stein
I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉!
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Cohesin guides homology search during DNA repair using loops and sister chromatid linkages
Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...
www.science.org
December 4, 2025 at 8:18 PM
I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉!
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵
Reposted by Johannes Stein
We developed a 'smart STED microscope' to detect rare objects/events in cells, and unraveled the 3D morphology of a nuclear membraneless organelle (paraspeckle). Amazing collaboration with Sjoerd Stallinga, Bernd Rieger (TU Delft) and @mixmue.bsky.social 🙏 (1/3) www.nature.com/articles/s41...
November 28, 2025 at 3:12 PM
We developed a 'smart STED microscope' to detect rare objects/events in cells, and unraveled the 3D morphology of a nuclear membraneless organelle (paraspeckle). Amazing collaboration with Sjoerd Stallinga, Bernd Rieger (TU Delft) and @mixmue.bsky.social 🙏 (1/3) www.nature.com/articles/s41...
Reposted by Johannes Stein
Bah, who needs cohesin if you're at the right place (near). Grover once taught us the difference between near and far (my favourite Sesame Street piece), and now amazing work from @elphegenoralab.bsky.social led by @karissalhansen.bsky.social shows us how: www.science.org/doi/10.1126/...
Synergy between regulatory elements can render cohesin dispensable for distal enhancer function
Enhancers are critical genetic elements controlling transcription from promoters, yet how they convey regulatory information across large genomic distances remains unclear. Here, we engineer pluripote...
www.science.org
November 27, 2025 at 7:10 PM
Bah, who needs cohesin if you're at the right place (near). Grover once taught us the difference between near and far (my favourite Sesame Street piece), and now amazing work from @elphegenoralab.bsky.social led by @karissalhansen.bsky.social shows us how: www.science.org/doi/10.1126/...
Reposted by Johannes Stein
Want to analyze the role of endogenous retroviruses in early human development or investigate their regulation in pluripotency and early development for your PhD?
Join the lab of @fueyoraquel.bsky.social via the IMPRS-BAC #gradschool!
👉 www.molgen.mpg.de/5094682/Fuey...
Join the lab of @fueyoraquel.bsky.social via the IMPRS-BAC #gradschool!
👉 www.molgen.mpg.de/5094682/Fuey...
November 27, 2025 at 2:06 PM
Want to analyze the role of endogenous retroviruses in early human development or investigate their regulation in pluripotency and early development for your PhD?
Join the lab of @fueyoraquel.bsky.social via the IMPRS-BAC #gradschool!
👉 www.molgen.mpg.de/5094682/Fuey...
Join the lab of @fueyoraquel.bsky.social via the IMPRS-BAC #gradschool!
👉 www.molgen.mpg.de/5094682/Fuey...
Reposted by Johannes Stein
🔬 Hot #PhD topic: Single-molecule fluorescence and super-resolution microscopy! Use quantitative nanoscale imaging to map nuclear organization. Apply by Jan 7 to join Johannes Stein’s Lab @jmstein.bsky.social & #IMPRS-BAC #gradschool!
👉 www.molgen.mpg.de/5098010/stei...
👉 www.molgen.mpg.de/5098010/stei...
November 25, 2025 at 2:18 PM
🔬 Hot #PhD topic: Single-molecule fluorescence and super-resolution microscopy! Use quantitative nanoscale imaging to map nuclear organization. Apply by Jan 7 to join Johannes Stein’s Lab @jmstein.bsky.social & #IMPRS-BAC #gradschool!
👉 www.molgen.mpg.de/5098010/stei...
👉 www.molgen.mpg.de/5098010/stei...
Reposted by Johannes Stein
A great opportunity to join our newly established imaging centre in Frankfurt as engineer/technician. If you love light microscopy, please apply!
Please share!
Please share!
November 19, 2025 at 5:20 PM
A great opportunity to join our newly established imaging centre in Frankfurt as engineer/technician. If you love light microscopy, please apply!
Please share!
Please share!
Reposted by Johannes Stein
IMPRS-BAC #gradschool: Our new groupleader @sedonamurphy.bsky.social has an open PhD project in her lab. Topic: Spatial feedback between epigenetic regulation and chromatin regulation. Apply by Jan 7, 2026!
👉 www.molgen.mpg.de/5091778/Murp...
👉 www.molgen.mpg.de/5091778/Murp...
November 18, 2025 at 4:05 PM
IMPRS-BAC #gradschool: Our new groupleader @sedonamurphy.bsky.social has an open PhD project in her lab. Topic: Spatial feedback between epigenetic regulation and chromatin regulation. Apply by Jan 7, 2026!
👉 www.molgen.mpg.de/5091778/Murp...
👉 www.molgen.mpg.de/5091778/Murp...
Reposted by Johannes Stein
🚨Curious how synthetic fluorophores simplify microscopy? Our review covers applications such as super-resolution microscopy and biosensing. 🎉👩🔬Congrats to my first PhD student, Agnese Nicoli, for the fearless deep dive! 🔬 ⚗️
D-CHAB @ethz.ch
www.nature.com/articles/s41...
D-CHAB @ethz.ch
www.nature.com/articles/s41...
Synthetic fluorophores for live-cell fluorescence microscopy and biosensing - Nature Chemical Biology
Performing live-cell microscopy experiments with high spatial and temporal resolution requires fluorophores with highly optimized properties. This Review examines the progress in developing synthetic ...
www.nature.com
November 5, 2025 at 9:29 PM
🚨Curious how synthetic fluorophores simplify microscopy? Our review covers applications such as super-resolution microscopy and biosensing. 🎉👩🔬Congrats to my first PhD student, Agnese Nicoli, for the fearless deep dive! 🔬 ⚗️
D-CHAB @ethz.ch
www.nature.com/articles/s41...
D-CHAB @ethz.ch
www.nature.com/articles/s41...
Reposted by Johannes Stein
Single-molecule friends!
The prelim. program of next year's sm- #Gordon conference in Switzerland is online: www.grc.org/single-molec...
It'll be 3x fantastic: science, people, place in the alps ⛰️. Kevin & I hope to see you all next June:
Have a look, tell your friends, and register!
The prelim. program of next year's sm- #Gordon conference in Switzerland is online: www.grc.org/single-molec...
It'll be 3x fantastic: science, people, place in the alps ⛰️. Kevin & I hope to see you all next June:
Have a look, tell your friends, and register!
2026 Single Molecule Approaches to Biology Conference GRC
The 2026 Gordon Research Conference on Single Molecule Approaches to Biology will be held in Les Diablerets, Vaud (fr) Switzerland. Apply today to reserve your spot.
www.grc.org
November 2, 2025 at 7:23 PM
Single-molecule friends!
The prelim. program of next year's sm- #Gordon conference in Switzerland is online: www.grc.org/single-molec...
It'll be 3x fantastic: science, people, place in the alps ⛰️. Kevin & I hope to see you all next June:
Have a look, tell your friends, and register!
The prelim. program of next year's sm- #Gordon conference in Switzerland is online: www.grc.org/single-molec...
It'll be 3x fantastic: science, people, place in the alps ⛰️. Kevin & I hope to see you all next June:
Have a look, tell your friends, and register!
Reposted by Johannes Stein
@lucianomartelotto, not on Bluesky, on a new Spatial RNA imaging method, PRISM. www.nature.com/articles/s41... Now added to #SingleCell #Spatial #Method bit.ly/scmethodstable
High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes - Nature Biotechnology
The 64-plex fluorescence imaging of RNA in tissues is achieved in one imaging cycle
www.nature.com
October 31, 2025 at 10:08 AM
@lucianomartelotto, not on Bluesky, on a new Spatial RNA imaging method, PRISM. www.nature.com/articles/s41... Now added to #SingleCell #Spatial #Method bit.ly/scmethodstable
Reposted by Johannes Stein
1/ Excited to share our new study with @brumbaugh-lab.bsky.social, out in @natbiotech.nature.com! P-bodies selectively sequester RNAs encoding cell fate regulators, often from the preceding developmental stage. Releasing these RNAs can drive changes in cell identity. 🧵 www.nature.com/articles/s41...
Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology
Stem cell differentiation is controlled by manipulating RNA condensates.
www.nature.com
October 28, 2025 at 4:02 PM
1/ Excited to share our new study with @brumbaugh-lab.bsky.social, out in @natbiotech.nature.com! P-bodies selectively sequester RNAs encoding cell fate regulators, often from the preceding developmental stage. Releasing these RNAs can drive changes in cell identity. 🧵 www.nature.com/articles/s41...
Reposted by Johannes Stein
Really excited to present the results of a fantastic collaboration with Jesse Veenvliet @jesseveenvliet.bsky.social @mpi-cbg.de @poldresden.bsky.social 🤩
We find a unique mechanism for body axis elongation in mammals, different from other vertebrate species
➡️ www.biorxiv.org/content/10.1...
We find a unique mechanism for body axis elongation in mammals, different from other vertebrate species
➡️ www.biorxiv.org/content/10.1...
October 28, 2025 at 8:25 AM
Really excited to present the results of a fantastic collaboration with Jesse Veenvliet @jesseveenvliet.bsky.social @mpi-cbg.de @poldresden.bsky.social 🤩
We find a unique mechanism for body axis elongation in mammals, different from other vertebrate species
➡️ www.biorxiv.org/content/10.1...
We find a unique mechanism for body axis elongation in mammals, different from other vertebrate species
➡️ www.biorxiv.org/content/10.1...
Reposted by Johannes Stein
Our photoswitchable HaloTag is out in Angewandte Chemie @angewandtechemie.bsky.social ! We now also show that this system can be used to control emitter density in SMLM. Congrats to Franzi, Bego, and our amazing collaborators. Check it out: onlinelibrary.wiley.com/doi/full/10....
A Photoswitchable HaloTag for Spatiotemporal Control of Fluorescence in Living Cells
Photoswitchable fluorophores are critical for advanced bioimaging. Here, we develop a photoswitchable self-labeling HaloTag that can reversibly modulate the emission of a bound fluorogenic dye via a ....
onlinelibrary.wiley.com
October 25, 2025 at 8:56 AM
Our photoswitchable HaloTag is out in Angewandte Chemie @angewandtechemie.bsky.social ! We now also show that this system can be used to control emitter density in SMLM. Congrats to Franzi, Bego, and our amazing collaborators. Check it out: onlinelibrary.wiley.com/doi/full/10....