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
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.
Reposted by Timothée Lionnet
New preprint 🥳! We made photoclickable HaloTag ligands to precisely control protein labeling on living cells. With it, we can do some cool multicolor stuff. Huge congrats to Franzi and all co-authors! Check it out 👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 13, 2025 at 4:20 PM
New preprint 🥳! We made photoclickable HaloTag ligands to precisely control protein labeling on living cells. With it, we can do some cool multicolor stuff. Huge congrats to Franzi and all co-authors! Check it out 👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Timothée Lionnet
With sequencing of Hitler's DNA making headlines, time for a reminder: analysing a polygenic score from a dead historically-significant figure won't give new insights into that person's behaviour. In a brief paper last year, we used Beethoven's genome to directly illustrate the fallacies involved.🧪👇
Notes from Beethoven’s genome
Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven
with population-based datasets used to quantify musical achievement.
www.cell.com
November 13, 2025 at 11:26 AM
With sequencing of Hitler's DNA making headlines, time for a reminder: analysing a polygenic score from a dead historically-significant figure won't give new insights into that person's behaviour. In a brief paper last year, we used Beethoven's genome to directly illustrate the fallacies involved.🧪👇
Reposted by Timothée Lionnet
What if instead of Cyber Monday (aka Daddy Bezos Day), we did a Support Indie Media Monday?
What are your favorite indie publications? Who are some of your favorite freelance and indie reporters and commentators?
Can we make this a thing?
What are your favorite indie publications? Who are some of your favorite freelance and indie reporters and commentators?
Can we make this a thing?
November 12, 2025 at 5:33 PM
What if instead of Cyber Monday (aka Daddy Bezos Day), we did a Support Indie Media Monday?
What are your favorite indie publications? Who are some of your favorite freelance and indie reporters and commentators?
Can we make this a thing?
What are your favorite indie publications? Who are some of your favorite freelance and indie reporters and commentators?
Can we make this a thing?
Reposted by Timothée Lionnet
Diving into the literature… I think it's the first time I see correlative live-cell/EM data after photobleaching - it shows how intense light can actually destroy microtubules rather than just bleach fluorescent tubulin along a neurite (from onlinelibrary.wiley.com/doi/10.1002/...)
November 10, 2025 at 10:26 AM
Diving into the literature… I think it's the first time I see correlative live-cell/EM data after photobleaching - it shows how intense light can actually destroy microtubules rather than just bleach fluorescent tubulin along a neurite (from onlinelibrary.wiley.com/doi/10.1002/...)
Reposted by Timothée Lionnet
Reposted by Timothée Lionnet
This is a most excellent read. Reducing Rosalind Franklin to simply a victim in the discovery of the DNA double helix inadvertently strips her of her very real contributions.
If you believe either that Franklin discovered the double helix, and / or Watson and Crick stole her data, ask yourself how you know this. Then take a read of this article.
If I see one more stupid Rosalind Franklin take I'm going to lose my mind. Thank god for @matthewcobb.bsky.social and @nccomfort.bsky.social. www.nature.com/articles/d41...
November 8, 2025 at 11:06 AM
This is a most excellent read. Reducing Rosalind Franklin to simply a victim in the discovery of the DNA double helix inadvertently strips her of her very real contributions.
Reposted by Timothée Lionnet
We’ve been heads down @ArcadiaScience for a bit but the @arenabioworks news this week caused me to dump thoughts. hard things are hard; don’t be such a fucking hater. Reflections on parallels w our own institutional experiment here seemay.substack.com/p/big-experi...
Big experiments are only big if they can fail
Some reflections on Arena Bioworks' unexpected wind down as a fellow institutional experimentalist
seemay.substack.com
November 6, 2025 at 4:20 PM
We’ve been heads down @ArcadiaScience for a bit but the @arenabioworks news this week caused me to dump thoughts. hard things are hard; don’t be such a fucking hater. Reflections on parallels w our own institutional experiment here seemay.substack.com/p/big-experi...
Reposted by Timothée Lionnet
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Timothée Lionnet
Janelia is hosting a course on DL for bioimage analysis www.janelia.org/you-janelia/...
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
www.janelia.org
November 6, 2025 at 5:02 PM
Janelia is hosting a course on DL for bioimage analysis www.janelia.org/you-janelia/...
Reposted by Timothée Lionnet
Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice - Nature Communications
KRAB-zinc finger proteins repress retrotransposons and rapidly evolve in mammals. Here, the authors show that ERV insertions drive the emergence and diversification of new KZFP genes in mice, revealin...
www.nature.com
November 6, 2025 at 9:40 AM
Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Reposted by Timothée Lionnet
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
November 5, 2025 at 5:20 PM
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
Reposted by Timothée Lionnet
Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching
November 3, 2025 at 10:04 AM
Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching
neither did I! this seems like a super important result
November 1, 2025 at 2:33 PM
neither did I! this seems like a super important result
Reposted by Timothée Lionnet
This is such an interesting paper. Why? Because the binding of transcription factor (TF) proteins to DNA governs how our genes are turned on/off/up/down, & so is the primary issue for how our genes work in development and how our cells respond to just about anything.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multiple overlapping binding sites determine transcription factor occupancy - Nature
A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...
www.nature.com
October 30, 2025 at 11:04 PM
This is such an interesting paper. Why? Because the binding of transcription factor (TF) proteins to DNA governs how our genes are turned on/off/up/down, & so is the primary issue for how our genes work in development and how our cells respond to just about anything.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Timothée Lionnet
@jhigginswriter.bsky.social wrote an article about my lab and our frog 🐸 at the Hutch! Thank you!
Dr. @yarimura.bsky.social brings frogs back to Fred Hutch after a long absence to study the structure of DNA-linked molecular complexes that change during the cell cycle and malfunction in cancer and other diseases. bit.ly/3J8S5Ae
Frogs help Fred Hutch find the shape of small things
Frogs have made significant contributions to Fred Hutch science over the years as a model organism that shares much of our biology, but they've been absent from the menagerie for about two decades. Dr...
bit.ly
October 29, 2025 at 6:29 AM
@jhigginswriter.bsky.social wrote an article about my lab and our frog 🐸 at the Hutch! Thank you!
Reposted by Timothée Lionnet
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....
Reposted by Timothée Lionnet
Fed employee mood this weekend:
a man and a woman are standing next to each other in a living room and talking .
ALT: a man and a woman are standing next to each other in a living room and talking .
media.tenor.com
October 25, 2025 at 1:17 PM
Fed employee mood this weekend:
Reposted by Timothée Lionnet
For your enjoyment (by @jagarikin)
October 25, 2025 at 11:58 AM
For your enjoyment (by @jagarikin)
Reposted by Timothée Lionnet
How can we see the cells that make up a living organism? Membrane-localising tags can drive fluorescent proteins to the cell's outer membrane, making their outlines visible. But the tags don't work well in all organisms. How do you find one for your species of interest? 🧵
Check our latest preprint
Check our latest preprint
A toolkit for testing membrane-localising tags across species
Transgenic markers and tools have revolutionised how we study cells and developing organisms. Some of the elements needed to construct those tools are universally applicable (e.g. fluorescent proteins...
www.biorxiv.org
October 23, 2025 at 8:16 AM
How can we see the cells that make up a living organism? Membrane-localising tags can drive fluorescent proteins to the cell's outer membrane, making their outlines visible. But the tags don't work well in all organisms. How do you find one for your species of interest? 🧵
Check our latest preprint
Check our latest preprint