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
"RNAPII clusters reflect local accumulations of transcriptionally engaged polymerases and do not form through higher-order mechanisms such as phase separation"
😬
www.biorxiv.org/content/10.1...
by the @mirlab.bsky.social
😬
www.biorxiv.org/content/10.1...
by the @mirlab.bsky.social
A single cluster of RNA Polymerase II molecules is stably associated with active genes
In eukaryotic nuclei, transcription is associated with the clustering of RNA Polymerase II (RNAPII) molecules. The mechanisms underlying cluster formation, their interactions with genes, and their imp...
www.biorxiv.org
January 15, 2026 at 9:50 AM
"RNAPII clusters reflect local accumulations of transcriptionally engaged polymerases and do not form through higher-order mechanisms such as phase separation"
😬
www.biorxiv.org/content/10.1...
by the @mirlab.bsky.social
😬
www.biorxiv.org/content/10.1...
by the @mirlab.bsky.social
Reposted by Timothée Lionnet
The appropriations bill that includes NIH is being finalized.
The Senate bill includes a bipartisan amendment from Senators Capito (WV) and Baldwin (WI) limiting multi-year funding of grants.
The House version does not and OMB has issued a veto threat if the House includes such language.
1/3
The Senate bill includes a bipartisan amendment from Senators Capito (WV) and Baldwin (WI) limiting multi-year funding of grants.
The House version does not and OMB has issued a veto threat if the House includes such language.
1/3
a close up of a brown surface with a few spots
ALT: a close up of a brown surface with a few spots
media.tenor.com
January 14, 2026 at 1:33 PM
The appropriations bill that includes NIH is being finalized.
The Senate bill includes a bipartisan amendment from Senators Capito (WV) and Baldwin (WI) limiting multi-year funding of grants.
The House version does not and OMB has issued a veto threat if the House includes such language.
1/3
The Senate bill includes a bipartisan amendment from Senators Capito (WV) and Baldwin (WI) limiting multi-year funding of grants.
The House version does not and OMB has issued a veto threat if the House includes such language.
1/3
entering the academic/medical centers are real estate companies in a trench coat era
The California College of the Arts is closing in 2027 and selling its physical campus to Vanderbilt, which will then have its third outpost beyond Tennessee. It's another example of college acquisitions being more about real estate than anything else.
Calif. College of Arts to Close, Sell Campus to Vanderbilt
California College of the Arts will close by the end of the 2026–27 academic year amid enrollment declines that have rendered its business model unsustainable, officials announced.
www.insidehighered.com
January 14, 2026 at 1:04 PM
entering the academic/medical centers are real estate companies in a trench coat era
Reposted by Timothée Lionnet
The @zeitlingerlab.bsky.social is pleased to announce @sergio-gma91.bsky.social’s preprint “High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo” (www.biorxiv.org/content/10.6...).
TLDR; TFIID behaves differently depending on promoter type. More below:
TLDR; TFIID behaves differently depending on promoter type. More below:
High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo
TFIID is instrumental in recognizing promoter sequences and initiating transcription, yet a cohesive understanding of how this complex interacts with and functions at different promoter types in vivo ...
www.biorxiv.org
January 9, 2026 at 6:30 PM
The @zeitlingerlab.bsky.social is pleased to announce @sergio-gma91.bsky.social’s preprint “High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo” (www.biorxiv.org/content/10.6...).
TLDR; TFIID behaves differently depending on promoter type. More below:
TLDR; TFIID behaves differently depending on promoter type. More below:
Reposted by Timothée Lionnet
This went under the radar but answers a fundamental question in Epigenetics...
From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How?
Outstanding work from Mathieu Boulard and colleagues
www.biorxiv.org/content/10.6...
From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How?
Outstanding work from Mathieu Boulard and colleagues
www.biorxiv.org/content/10.6...
The transcription of a single olfactory receptor per neuron is enforced by epigenetic silencing of their enhancers
The ability to discriminate thousands of odors in our environment requires each olfactory neuron to express a single olfactory receptor from hundreds of available genes. The biochemical mechanism enfo...
www.biorxiv.org
January 5, 2026 at 12:51 PM
This went under the radar but answers a fundamental question in Epigenetics...
From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How?
Outstanding work from Mathieu Boulard and colleagues
www.biorxiv.org/content/10.6...
From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How?
Outstanding work from Mathieu Boulard and colleagues
www.biorxiv.org/content/10.6...
Reposted by Timothée Lionnet
Really encouraging to see siRNA therapies enter the mainstream. A sobering reminder of how long this stuff takes to get to the clinic, though - here's me writing about their promise (and what you'd need to deliver them) in 2005
softmachines.org?p=143
softmachines.org?p=143
Delivering interfering RNA – Soft Machines, by Richard Jones
softmachines.org
December 28, 2025 at 9:31 PM
Really encouraging to see siRNA therapies enter the mainstream. A sobering reminder of how long this stuff takes to get to the clinic, though - here's me writing about their promise (and what you'd need to deliver them) in 2005
softmachines.org?p=143
softmachines.org?p=143
Reposted by Timothée Lionnet
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 Timothée Lionnet
1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.
December 24, 2025 at 10:44 PM
1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.
Reposted by Timothée Lionnet
As the year ends, let me thank public school teachers who, under difficult circumstances, are doing their best to educate our kids.
If this country is to flourish, we need the best education system in the world. Let’s fight for a nation where teachers are well-paid & respected.
If this country is to flourish, we need the best education system in the world. Let’s fight for a nation where teachers are well-paid & respected.
December 24, 2025 at 6:23 PM
As the year ends, let me thank public school teachers who, under difficult circumstances, are doing their best to educate our kids.
If this country is to flourish, we need the best education system in the world. Let’s fight for a nation where teachers are well-paid & respected.
If this country is to flourish, we need the best education system in the world. Let’s fight for a nation where teachers are well-paid & respected.
Reposted by Timothée Lionnet
Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social
December 24, 2025 at 3:51 PM
Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social
Reposted by Timothée Lionnet
Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)
Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo
Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...
www.biorxiv.org
December 24, 2025 at 3:06 PM
Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)
Reposted by Timothée Lionnet
Read our new preprint where we uncover a hierarchy in human PIC assembly and establish a quantitative framework that connects factor exchange kinetics to the regulation of Pol II activity in living human cells. doi: doi.org/10.64898/202...
By A. Oravecz and our collaborators @molinalab.bsky.social
By A. Oravecz and our collaborators @molinalab.bsky.social
RNA polymerase II initiation factors show different dynamic behaviour upon induced transcription in live cells
Transcription by RNA polymerase II (Pol II) requires the ordered action of general transcription factors (GTFs) forming the pre-initiation complex (PIC). How these events unfold kinetically remains un...
doi.org
December 24, 2025 at 1:35 PM
Read our new preprint where we uncover a hierarchy in human PIC assembly and establish a quantitative framework that connects factor exchange kinetics to the regulation of Pol II activity in living human cells. doi: doi.org/10.64898/202...
By A. Oravecz and our collaborators @molinalab.bsky.social
By A. Oravecz and our collaborators @molinalab.bsky.social
Reposted by Timothée Lionnet
“2025 will be known as the year of the peak bubble, and also the moment at which Wall Street began to lose confidence in generative AI... the Oracle craze early in September and what has happened since will in hindsight be seen as the beginning of the end.” garymarcus.substack.com/p/six-or-sev...
Six (or seven) predictions for AI 2026 from a Generative AI realist
2025 turned out pretty much as I anticipated. What comes next?
garymarcus.substack.com
December 20, 2025 at 5:38 PM
“2025 will be known as the year of the peak bubble, and also the moment at which Wall Street began to lose confidence in generative AI... the Oracle craze early in September and what has happened since will in hindsight be seen as the beginning of the end.” garymarcus.substack.com/p/six-or-sev...
Reposted by Timothée Lionnet
I'm working on a new water-dipping objective targeting expansion imaging. Targeting the following specs:
5mm WD
NA 1.0
1.2mm FOV, plan-corrected
8mm EFL ("25x") but this is flexible
well-corrected in visible
minimum mechanical profile
Optics question: is there any reason to make it telecentric?
5mm WD
NA 1.0
1.2mm FOV, plan-corrected
8mm EFL ("25x") but this is flexible
well-corrected in visible
minimum mechanical profile
Optics question: is there any reason to make it telecentric?
December 18, 2025 at 7:54 PM
I'm working on a new water-dipping objective targeting expansion imaging. Targeting the following specs:
5mm WD
NA 1.0
1.2mm FOV, plan-corrected
8mm EFL ("25x") but this is flexible
well-corrected in visible
minimum mechanical profile
Optics question: is there any reason to make it telecentric?
5mm WD
NA 1.0
1.2mm FOV, plan-corrected
8mm EFL ("25x") but this is flexible
well-corrected in visible
minimum mechanical profile
Optics question: is there any reason to make it telecentric?
Reposted by Timothée Lionnet
“A process which led from the amoeba to man appeared to the philosophers to be obviously a progress - though whether the amoeba would agree with this opinion is not known"
- Bertrand Russell, 1976.
Time-lapse video of Vampyrella lateritia eating Spirogyra algae from Science Source/Oliver Skibbe. 🦠
- Bertrand Russell, 1976.
Time-lapse video of Vampyrella lateritia eating Spirogyra algae from Science Source/Oliver Skibbe. 🦠
December 17, 2025 at 4:53 PM
“A process which led from the amoeba to man appeared to the philosophers to be obviously a progress - though whether the amoeba would agree with this opinion is not known"
- Bertrand Russell, 1976.
Time-lapse video of Vampyrella lateritia eating Spirogyra algae from Science Source/Oliver Skibbe. 🦠
- Bertrand Russell, 1976.
Time-lapse video of Vampyrella lateritia eating Spirogyra algae from Science Source/Oliver Skibbe. 🦠
Reposted by Timothée Lionnet
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An integrated view of the structure and function of the human 4D nucleome - Nature
The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...
www.nature.com
December 17, 2025 at 8:59 PM
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Timothée Lionnet
Our study with @stadtfeldlab.bsky.social on the dual mechanism by which EHMT2 is repressing totipotency-associated vs lineage-specific loci is now out @emboreports.org. See thread by @cmuyehara.bsky.social who led the study with K Chatterjee. Full article here link.springer.com/article/10.1...
December 14, 2025 at 8:15 PM
Our study with @stadtfeldlab.bsky.social on the dual mechanism by which EHMT2 is repressing totipotency-associated vs lineage-specific loci is now out @emboreports.org. See thread by @cmuyehara.bsky.social who led the study with K Chatterjee. Full article here link.springer.com/article/10.1...
Reposted by Timothée Lionnet
Now published here!
doi.org/10.1038/s443...
@efapostolou29.bsky.social @stadtfeldlab.bsky.social @kritikakasliwal.bsky.social
doi.org/10.1038/s443...
@efapostolou29.bsky.social @stadtfeldlab.bsky.social @kritikakasliwal.bsky.social
December 12, 2025 at 11:13 PM
Reposted by Timothée Lionnet
(1/10) How do diverse leukemia mutations converge on the same molecular program? In #RibackLab first manuscript @cp-cell.bsky.social, collaboration with @goodell-lab.bsky.social shows that disparate mutations rewire shared protein networks to form nuclear condensates called C-bodies.
November 4, 2025 at 5:58 PM
(1/10) How do diverse leukemia mutations converge on the same molecular program? In #RibackLab first manuscript @cp-cell.bsky.social, collaboration with @goodell-lab.bsky.social shows that disparate mutations rewire shared protein networks to form nuclear condensates called C-bodies.
Reposted by Timothée Lionnet
Really important that this is out for those waiting for it
I think some folks might be happy to see this. NIGMS MIRA R35 for EI/NI has been published. PAR-26-121 files.simpler.grants.gov/opportunitie...
PAR-26-121: Maximizing Investigators' Research Award (MIRA) (R35 - Clinical Trial Optional)
files.simpler.grants.gov
December 11, 2025 at 7:50 PM
Really important that this is out for those waiting for it
Reposted by Timothée Lionnet
CellSAM
A foundation model for Cell Segmentation
Segment Anything Model - Vision Transformer
cellsam.deepcell.org
Outperforming CellPose
Similar to Human
Single-cell spatial transcriptomics
Live-cell tracking
3D cell segmentation
@natmethods.nature.com 2025
www.nature.com/articles/s41...
A foundation model for Cell Segmentation
Segment Anything Model - Vision Transformer
cellsam.deepcell.org
Outperforming CellPose
Similar to Human
Single-cell spatial transcriptomics
Live-cell tracking
3D cell segmentation
@natmethods.nature.com 2025
www.nature.com/articles/s41...
December 11, 2025 at 12:36 PM
CellSAM
A foundation model for Cell Segmentation
Segment Anything Model - Vision Transformer
cellsam.deepcell.org
Outperforming CellPose
Similar to Human
Single-cell spatial transcriptomics
Live-cell tracking
3D cell segmentation
@natmethods.nature.com 2025
www.nature.com/articles/s41...
A foundation model for Cell Segmentation
Segment Anything Model - Vision Transformer
cellsam.deepcell.org
Outperforming CellPose
Similar to Human
Single-cell spatial transcriptomics
Live-cell tracking
3D cell segmentation
@natmethods.nature.com 2025
www.nature.com/articles/s41...
Reposted by Timothée Lionnet
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
SET1/MLL complexes control transcription independently of H3K4me3
Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...
www.biorxiv.org
December 11, 2025 at 6:09 AM
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Timothée Lionnet
Very happy to share our 'Evoscape' paper, now published in PNAS ! www.pnas.org/doi/10.1073/...
Generative epigenetic landscapes map the topology and topography of cell fates | PNAS
Epigenetic landscapes were proposed by Waddington as the central concept to describe
cell fate dynamics in a locally low-dimensional space. In mode...
www.pnas.org
December 10, 2025 at 1:27 PM
Very happy to share our 'Evoscape' paper, now published in PNAS ! www.pnas.org/doi/10.1073/...
Reposted by Timothée Lionnet
Here is the new meditative film about zooplankton and other cute animals from Okinawa. If you feel a need to calm down - just start watching it: youtu.be/JtwwoEzW3vU?...
Meditative plankton from Okinawa
YouTube video by Igor Adameyko
youtu.be
December 8, 2025 at 11:31 PM
Here is the new meditative film about zooplankton and other cute animals from Okinawa. If you feel a need to calm down - just start watching it: youtu.be/JtwwoEzW3vU?...
Reposted by Timothée Lionnet
Missed #FluorescenceFriday, but let's go for #GlowingSaturday!
freshly out of the prep JF549 derivative for a colleague
freshly out of the prep JF549 derivative for a colleague
December 6, 2025 at 9:43 AM
Missed #FluorescenceFriday, but let's go for #GlowingSaturday!
freshly out of the prep JF549 derivative for a colleague
freshly out of the prep JF549 derivative for a colleague