Stephen Methot

And the next one: dx.doi.org/10.1038/s44318-025-00585-z . Super-fun collaboration with @partchlab.bsky.social & @gotworms.bsky.social to find similarities between developmental and circadian clocks – supported by @fmiscience.bsky.social Facilities and, financially, @snsf.ch and @erc.europa.eu . 1/n

Shared mechanisms across distinct biological clocks:
Jordan Ward @gotworms.bsky.social , Helge Grosshans @labgrosshans.bsky.social & collaborators find the nematode homologs of mammalian circadian clock proteins PERIOD & CK1 to control developmental timing in worms
www.embopress.org/doi/full/10....

Template Learning: Deep learning with domain randomization for particle picking in cryo-electron tomography - Nature Communications Particle picking is a key bottleneck in bridging structural and cell biology with cryo-electron tomography. Here, authors develop Template Learning, using domain-randomized simulations to train deep l...

Generate synthetic cryo-ET data and train your model for particle picking in real data.
Impressive work by Mohamad Harastani:
www.nature.com/articles/s41...

YouTube video by The Friedrich Miescher Institute for Biomedical Research DNA rhythms orchestrate gene activity across development

🎥 FMI scientists discovered that thousands of C. elegans genes switch on and off in rhythmic patterns controlled by chromatin, revealing how gene timing shapes development & offering clues to human biological clocks. @labgrosshans.bsky.social www.youtube.com/watch?v=Dibw...

Model organisms as platforms for training scientific minds

www.nature.com/articles/s41...

a man in a blue sweater stands in front of a swr3 sign ALT: a man in a blue sweater stands in front of a swr3 sign

This was a very nice project to be a part of! The modeling had me completely out of my comfort zone (thanks to Dimos Gaidatzis for partiently explaining it to me). I have new appreciation for how powerful it can be to integrate modeling approaches into biological studies.

Paper alert! doi.org/10.1038/s443... - "A scheduler for rhythmic gene expression". We show how 9 txn factors suffice for rhythmic gene expression of thousands of genes with any phase or amplitude in #Celegans larvae (and also look at the tissues where oscillations happen) 1/n

Preprint by the Grosshans lab w/ co-1st authors Dimos Gaidatzis, Maike Graf-Landua & Stephen P. Methot "A scheduler for rhythmic gene expression" @biorxivpreprint.bsky.social
doi.org/10.1101/2025...
@labgrosshans.bsky.social
@smethot.bsky.social
@fmiscience.bsky.social

ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment Short interspersed nuclear elements (SINEs) are abundant non-autonomous transposable elements derived from RNA polymerase III (POL III)-transcribed short non-coding RNAs. SINEs retain sequence feature...

📖 Happy to share our recent preprint! www.biorxiv.org/content/10.1... We discovered how SINEs are kept silent: the ChAHP protein complex acts as a molecular brake on POL III transcription retrotransposons. A 🧵:

We’re excited to host the next TriRhena Gene Regulation Club on November 5!

Attendance is free, but registration (by October 20) is mandatory 👇🏽

Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇

I am excited to announce that we are looking for a Lab Manager @fmiscience.bsky.social in Basel. If you want to be part of a growing team investigating development and tissue formation, and are enthusiastic about helping set up a new lab, please check out the role:

www.fmi.ch/education-ca...

a bunch of clocks are hanging on a wall including one that says ' 3:00 ' on it ALT: a bunch of clocks are hanging on a wall including one that says ' 3:00 ' on it

New preprint!

How are developmental cycles coordinated across cell types?

It turns out that, like Geppetto's cuckoo clocks in the GIF below, individual cell types are each performing their own little crazy routine, but all in sync with each other.

🚨 We're hiring, please share! The FMI seeks a tenure-track Group Leader (Assistant Prof) in Structural Biology 🔬
Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...

Is euchromatin really “open”? Our new study @bioRxiv suggests otherwise. Using super-resolution imaging @shiori-iida.bsky.social‬ @masaashimazoe.bsky.social reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing.
www.biorxiv.org/cgi/content/...

I am excited to share that I will join the Friedrich Miescher Institute @fmiscience.bsky.social in Basel as a group leader, starting my lab in March 2026 🎉

We will explore cell fate regulation during organogenesis, with a focus on how cell elimination underlies the emergence of functional tissues.

A novel deep learning-based framework reveals a continuum of chromatin sensitivities across transcription factors The genome-wide binding of many transcription factors (TFs) depends not only on the presence of their recognition motifs, but also on the surrounding chromatin context. This raises the question of how...

Excited to share our latest preprint. www.biorxiv.org/content/10.1.... Lead by Lukas, we investigated multiple ways of assessing a TF's sensitivity to chromatin based on genome-wide binding profiles. The developed methods allowed us to quantify chromatin sensitivity across tested TFs.

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

After 10 years of work, a complete telomere-to-telomere gap-free genome for C. elegans finally exists: it has 106 Mb rather than the textbook 100.3 Mb, and up to 366 additional genes.
genome.cshlp.org/content/35/8...

📢Master thesis project opportunity

‼️We are looking for a motivated Master student to join the lab working on semi-automated analysis pipelines for organoid microscopy images.

Please spread the word and check out our website for more information: www.annikahausmannlab.com

Very excited to share the first preprint of the lab! We show that the nuclear pore protein TPR forms biomolecular condensates which keep heterochromatin away from the nuclear pore complexes and maintains global chromatin organization. Check it out, share it, tell us what you think!!

Job opening in my research group!! Please share.

I'm looking for a lab technician to join my small team investigating how chromatin structure regulates gene expression in C. elegans.

www.fmi.ch/education-ca...