Timothée Lionnet
@successprocess.bsky.social
faculty at NYU School of Medicine. We use advanced microscopy techniques to understand gene expression. Opinions my own. timotheelionnet.net
Reposted by Timothée Lionnet
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
November 27, 2025 at 1:17 PM
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
Reposted by Timothée Lionnet
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 Timothée Lionnet
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
November 27, 2025 at 9:59 PM
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Reposted by Timothée Lionnet
Transcribing Pol2
With elongation factors
Kinetic control
#ChromatinHaiku #SingleMolecule
www.nature.com/articles/s41...
With elongation factors
Kinetic control
#ChromatinHaiku #SingleMolecule
www.nature.com/articles/s41...
November 27, 2025 at 12:57 PM
Transcribing Pol2
With elongation factors
Kinetic control
#ChromatinHaiku #SingleMolecule
www.nature.com/articles/s41...
With elongation factors
Kinetic control
#ChromatinHaiku #SingleMolecule
www.nature.com/articles/s41...
Reposted by Timothée Lionnet
Today is the International day for the elimination of violence against women. In 2024, an estimated 50,000 women and girls were killed by intimate partners or family members worldwide. That is 137 women and girls every day. One every ten minutes. www.un.org/en/observanc...
International Day for the Elimination of Violence against Women | United Nations
The International Day for the Elimination of Violence against Women aims to create awareness of the fact that violence against women is a human rights violation that impedes progress in many areas, in...
www.un.org
November 25, 2025 at 4:28 PM
Today is the International day for the elimination of violence against women. In 2024, an estimated 50,000 women and girls were killed by intimate partners or family members worldwide. That is 137 women and girls every day. One every ten minutes. www.un.org/en/observanc...
NY folks, please support this initiative!
📢 SIGN & SHARE THE PETITION! 📢
New York needs an Empire Biomedical Research Institute to create new statewide funding opportunities for scientists & physician-scientists so that patients and their families get the life-saving and life-changing new therapeutics they're hoping for ✏️ c.org/TDMy2H9JTW
New York needs an Empire Biomedical Research Institute to create new statewide funding opportunities for scientists & physician-scientists so that patients and their families get the life-saving and life-changing new therapeutics they're hoping for ✏️ c.org/TDMy2H9JTW
Sign the Petition
Support a New York State Biomedical Institute for a Healthier, More Affordable Future
c.org
November 25, 2025 at 2:11 PM
NY folks, please support this initiative!
Reposted by Timothée Lionnet
A new and fascinating story from @bencarty.bsky.social and the group, with crucial help from the teams of @naltemose.bsky.social, Simona Giunta, and @dfachinetti.bsky.social. Many thanks to all for a fantastic collaboration.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 25, 2025 at 12:16 PM
A new and fascinating story from @bencarty.bsky.social and the group, with crucial help from the teams of @naltemose.bsky.social, Simona Giunta, and @dfachinetti.bsky.social. Many thanks to all for a fantastic collaboration.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Timothée Lionnet
I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories!
link.springer.com/collections/...
link.springer.com/collections/...
Enhancer-promoter interactions
Genome Biology is calling for submissions to our Collection on enhancer-promoter interactions.
Enhancer–promoter interactions are central to the regulation ...
link.springer.com
November 25, 2025 at 10:55 AM
I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories!
link.springer.com/collections/...
link.springer.com/collections/...
Reposted by Timothée Lionnet
We are kicking off a blog series with @focalplane.bsky.social to provide insight into life at the AIC, microscopy careers, image analysis, and more! Read our intro post here: focalplane.biologists.com/2025/11/20/a...
AIC at HHMI Janelia
Introduction to the AIC at HHMI Janelia blog on FocalPlane
focalplane.biologists.com
November 24, 2025 at 5:25 PM
We are kicking off a blog series with @focalplane.bsky.social to provide insight into life at the AIC, microscopy careers, image analysis, and more! Read our intro post here: focalplane.biologists.com/2025/11/20/a...
Reposted by Timothée Lionnet
Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.
November 23, 2025 at 11:18 PM
Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.
Reposted by Timothée Lionnet
This is an amazing sentence: "The Peekskill Meteorite Car ("PMC"), a 1980 red Chevy Malibu, is one of the two most famous objects struck by a meteorite (the other, Ms. Ann Hodges, died in 1972). "
meteoritecar.com
meteoritecar.com
The Peekskill Meteorite Car Official Website
The official website of the Peekskill Meteorite Car, the most famous object to ever be struck by a meteorite.
meteoritecar.com
November 22, 2025 at 2:39 PM
This is an amazing sentence: "The Peekskill Meteorite Car ("PMC"), a 1980 red Chevy Malibu, is one of the two most famous objects struck by a meteorite (the other, Ms. Ann Hodges, died in 1972). "
meteoritecar.com
meteoritecar.com
Reposted by Timothée Lionnet
We wrote a review on the "Physics of droplet regulation in biological cells": arxiv.org/abs/2501.13639 Beside the basic #physics of phase separation, we discuss three aspects that separate cellular from traditional droplets:
January 24, 2025 at 7:55 AM
We wrote a review on the "Physics of droplet regulation in biological cells": arxiv.org/abs/2501.13639 Beside the basic #physics of phase separation, we discuss three aspects that separate cellular from traditional droplets:
Reposted by Timothée Lionnet
Hypothesis-based research: not dead yet
Science will often take you to unexpected and delightful places. In this study, researchers hypothesized that riders in a crowded subway car would be more likely to offer their seat to a pregnant person if there were someone in the subway car dressed as Batman 🧪🦇
www.nature.com/articles/s44...
www.nature.com/articles/s44...
November 21, 2025 at 11:16 PM
Hypothesis-based research: not dead yet
Reposted by Timothée Lionnet
Check out our paper on transcriptional control of an artificial condensate, including engineering a feedback loop that includes phase separation. Led by the amazing @samwilken.bsky.social
We’re excited to share our new work in Soft Matter: doi.org/10.1039/D5SM...
We demonstrate how in vitro transcription can drive biomolecular phase separation — and how that phase separation in turn regulates transcription.
We demonstrate how in vitro transcription can drive biomolecular phase separation — and how that phase separation in turn regulates transcription.
Condensation and activator/repressor control of a transcription-regulated biomolecular liquid
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by util...
doi.org
November 21, 2025 at 1:38 PM
Check out our paper on transcriptional control of an artificial condensate, including engineering a feedback loop that includes phase separation. Led by the amazing @samwilken.bsky.social
Reposted by Timothée Lionnet
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...
forum.image.sc
November 21, 2025 at 9:29 AM
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
Reposted by Timothée Lionnet
To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...
Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture
Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.
www.science.org
November 20, 2025 at 7:46 AM
To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...
Reposted by Timothée Lionnet
Radiolaria are microscopic unicellular sea creatures that create skeletons from silica. Their skeletons are among the most beautiful and complex natural microstructures, resembling elaborate filigree. blog post: n-e-r-v-o-u-s.com/blog/?p=9861
November 20, 2025 at 5:16 PM
Radiolaria are microscopic unicellular sea creatures that create skeletons from silica. Their skeletons are among the most beautiful and complex natural microstructures, resembling elaborate filigree. blog post: n-e-r-v-o-u-s.com/blog/?p=9861
Reposted by Timothée Lionnet
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
Reposted by Timothée Lionnet
Very excited to present OpenCGChromatin🔥🔥🔥
A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation
Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups
A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation
Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups
November 18, 2025 at 3:07 PM
Very excited to present OpenCGChromatin🔥🔥🔥
A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation
Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups
A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation
Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups
Reposted by Timothée Lionnet
Wonderful to see the beautiful preprint from Sabate et al now published - TADs are also dynamic structures in human cells, with remarkably similar parameters between mESCs and HCT116 cells
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 15, 2025 at 5:24 PM
Wonderful to see the beautiful preprint from Sabate et al now published - TADs are also dynamic structures in human cells, with remarkably similar parameters between mESCs and HCT116 cells
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Timothée Lionnet
Re-upping this with a Bluetorial in a shameless act of self-promotion. 1/n
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors
Wei Wang, @lionlchristiaen.bsky.social and colleagues
www.embopress.org/doi/full/10....
Wei Wang, @lionlchristiaen.bsky.social and colleagues
www.embopress.org/doi/full/10....
November 15, 2025 at 8:15 AM
Re-upping this with a Bluetorial in a shameless act of self-promotion. 1/n
Reposted by Timothée Lionnet
Part 10 of 200 in historically interesting things to inspire your ttrpg
Guillotine Earrings From France’s Reign of Terror
Guillotine Earrings From France’s Reign of Terror
November 13, 2025 at 1:16 PM
Part 10 of 200 in historically interesting things to inspire your ttrpg
Guillotine Earrings From France’s Reign of Terror
Guillotine Earrings From France’s Reign of Terror
Reposted by Timothée Lionnet
This is lunacy. The Chinese scholars I know are among the hardest working, most selfless people I've ever encountered. They want to contribute to our intellectual endeavors, and they make our research teams better.
U.S. Congress considers sweeping ban on Chinese collaborations
Researchers speak out against proposal that would bar funding for U.S. scientists working with Chinese partners or training Chinese students
www.science.org
November 14, 2025 at 1:04 PM
This is lunacy. The Chinese scholars I know are among the hardest working, most selfless people I've ever encountered. They want to contribute to our intellectual endeavors, and they make our research teams better.
Reposted by Timothée Lionnet
I'd guess that 85-90% of American scientists would be ineligible for future funding under this law, maybe close to 100% in the R1 universities. So much for funding proposals based on scientific merit.
Apart from being sinophobes, the people pushing this have no clue how science or higher ed works.
Apart from being sinophobes, the people pushing this have no clue how science or higher ed works.
“The prohibited activities would include joint research, co-authorship on papers, and advising a foreign graduate student or postdoctoral fellow. The language is retroactive, meaning any interactions during the previous 5 years could make a scientist ineligible for future federal funding.”
U.S. Congress considers sweeping ban on Chinese collaborations
Researchers speak out against proposal that would bar funding for U.S. scientists working with Chinese partners or training Chinese students
www.science.org
November 14, 2025 at 11:31 AM
I'd guess that 85-90% of American scientists would be ineligible for future funding under this law, maybe close to 100% in the R1 universities. So much for funding proposals based on scientific merit.
Apart from being sinophobes, the people pushing this have no clue how science or higher ed works.
Apart from being sinophobes, the people pushing this have no clue how science or higher ed works.