We would like to add one or two postdocs to our lab in the next couple of years. If you are close to finishing your PhD and interested in the science we do, feel free to reach out to discuss opportunities.
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
How do nuclear compartments form inside cell nuclei? We show RNA glues certain loci together to form a nuclear compartment. This involves special GC-rich regions of highly expressed genes that also associate with nuclear speckles, but interactions between these loci are independent of speckles!
bioRxiv Genomics@biorxiv-genomic.bsky.social · 5d agoFormation of an RNA-mediated nuclear compartment https://www.biorxiv.org/content/10.64898/2026.08.20.746005v1
Formation of an RNA-mediated nuclear compartment https://www.biorxiv.org/content/10.64898/2026.08.20.746005v1
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
nature.com
Erik van Nimwegen@erikvannimwegen.bsky.social · last yr.Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...
In 2023, @nature.com published 'Papers and patents are becoming less disruptive over time', receiving world-wide media attention. Our Matters Arising, published after a 32 month delay (more on that soon), shows that the reported decline can largely be attributed to dataset artefacts. 🧵
Excited to share our newest work! We asked whether RNA molecules need to be in a specific place in the cell to do their job. We found that a single RNA must reach the midbody, the structure that pinches two dividing cells apart, for cell division to finish efficiently. 🧵⬇️
(1/4) We are very excited to share our latest preprint from @sauer-lab.bsky.social: Mega Expansion Microscopy (Mega-ExM)! We combine iterative hydrogel expansion with whole-proteome NHS labeling and post-expansion immunostaining, reaching tunable expansion factors up to ~1500× in whole cells 🤯
bioRxiv Biophysics@biorxiv-biophys.bsky.social · 3w agoStructural cell biology by mega-expansion microscopy https://www.biorxiv.org/content/10.64898/2026.08.05.743040v1
🔬🧫 Biology friends. Who do you outsource cell line CRISPR editing to? We could do in my lab, but given people and time constraints I want to explore commercial $ to edit standard hES cell line - KO/cKO. Bonus if work is done in USA and not shipped to international facility.
SML Chef Pee Pee: The Crisper, The Better
Alt: SML Chef Pee Pee: The Crisper, The Better
static.klipy.com
One thing strikes me : while LLMs now seem to excel in maths, they have yet to produce any great book (despite having been trained on virtually everything available that was ever written, and having been used to produce text for several years now).
Benjamin Riley@benjaminjriley.bsky.social · 4w agoClearly AI is proving useful in advanced mathematics. But to what degree and of what import remains hazy to me. This article provides a nice entry point into the latest developments.
New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...
RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...
Analog intrinsic recoding measures RNA dynamics without chemical conversion
Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...
biorxiv.org
Thank you @natgenet.nature.com for this nice Research Briefing www.nature.com/articles/s41... on our recent paper reporting live-cell measurements of Sox2 promoter bursting kinetics when varying its genomic distance from the SCR enhancer 👉 www.nature.com/articles/s41...
The genomic position of an enhancer modulates bursting dynamics of the cognate promoter - Nature Genetics
We show that, in a genomic locus with minimal complexity, the distance between promoter and enhancer modulates the frequency of clustered transcriptional bursts. Thus, besides the nucleotide sequence,...
nature.com
Our latest is now out in @nataging.nature.com giving reason to celebrate! Led by talented Spiros Palikyras, it improves our preprint (posted 2 years ago!) dissecting the mechanism and functional consequences of CTCF clustering upon senescence commitment of human cells. www.nature.com/articles/s43...
Senescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program - Nature Aging
Palikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...
nature.com
I have always wanted to be able to view the genome, protein, and protein structure at the same time. Last week I built this utility with Claude Science. Click protein domain to zoom to structure and genomic region. I hope you find it as revealing and useful as I do. github.com/DavidSternLa...
Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:
Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics
Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...
doi.org
Luca Giorgetti lab @FMI@lucagiorgetti.bsky.social · last yr.Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth
New paper 🧵 What if the "landscape" that guides cell differentiation isn't fixed, but is sculpted, in real time, by the very cells moving through it? We call this a 'sandscape' : grains of sand that carve dunes as they move, while the dunes' shape simultaneously steers where the grains go next.
So nice to see Pierre's @pierrecaron.bsky.social highlight of our preprint (led by @lillianwu.bsky.social ) was selected by @jcellsci.bsky.social to include in their latest issue. Also, what a great initiative - ended up reading them all! prelights.biologists.com/highlights/c...
CENP-B binds hairpin motifs in chromosome arms influencing gene expression - preLights
CENP-B escapes the centromere and plays a surprising role in gene regulation
prelights.biologists.com
AF-CALVADOS is now published doi.org/10.1002/pro.... We combine AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale: — Ensembles of >12000 full-length human proteins — Comparison of IDRs alone and I n context for >1500 TFs @sobuelow.bsky.social @kejohansson.bsky.social
New review in Nature Reviews Cancer: "Imaging the hallmarks of cancer." A collaborative effort to map non-invasive clinically relevant in vivo imaging onto every cancer hallmark, separating what can be seen directly from what is only accessible via surrogates. 🧵 doi.org/10.1038/s415...
Imaging the hallmarks of cancer - Nature Reviews Cancer
In this Review, Grimm et al. describe the range of non-invasive diagnostic imaging approaches to monitor the various hallmarks of cancer and how their implementation is shaping clinical practice.
doi.org
Are tapes a good option for long-term cold storage of microscopy data? I'm looking at storing ~200 TB with no recurring fee (no cloud) and with as little esoteric server/command line fuss as possible www.ibm.com/fr-fr/produc...
1/ 🧬🔬 How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇 www.kaggle.com/competitions... @biohub.org
1/🧵 Can transcription factor condensate formation be explained without phase separation? Our new preprint introduces SPARK, a simulation tool that reproduces condensate behavior (clustering, fusion, FRAP) from diffusion & binding kinetics alone. Movie: 60 sec FRAP sim www.biorxiv.org/content/10.6...
Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...
Help please! We need to do some large(ish) cell culture inhibiting E-cadherin with a monoclonal antibody. Does anyone have the DECMA-1 hybridoma cell line so we could purify our own antibody? or a similar monoclonal that would do the job. Any help greatly appreciated, just DM me. Please repost!
If you don’t know how ridiculously cool dinoflagellates are, this is your chance to find out!
Liz Cooney@protistwtmostest.bsky.social · 3mo agoWe are looking for candidates to fill a PhD position in Grenoble, France. Please share with anyone interested in microbial symbioses! #dinoflagellate #symbiosis www.linkedin.com/posts/johan-...
For 40 years the 8-nt ‘Kozak Sequence’ was thought to mark sites of translation initiation. In a new study, we revise this model by identifying an ~80-nt sequence—the extended Translation Initiation Sequence (eTIS)— that guides ribosomes to correct start sites. 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...
biorxiv.org
Cells are not just bags of molecules. Function depends on spatial interactions: RNAs and/or proteins come together with interaction partners to drive regulation and function. In our new preprint, we introduce ProPER, a novel method for in situ proximity detection. Preprint: tinyurl.com/muju86s6
Jorge Trojanowski@jorgetrojanowski.bsky.social · 4mo ago1/ ProPER - Our novel ligation-free proximity detection method for efficient multiplexed imaging of molecular interactions in situ. Among other things we use it to image the life cycle of RNA molecules and resolve differential kinetics of gene expression steps. New preprint: doi.org/10.64898/202...
Did you know that Pierre Chambon's laboratory was the first to use the term "nucleosome" in 1975 ? www.cell.com/cell/fulltex...
