iiinova — where your digital self keeps evolving

Reposted by Yohsuke T. Fukai

Christophe 🔬 Leterrier @christlet.bsky.social · 02/09/2026

Really cool! Smaller than GFP and reversibly binding last-generation rhodamine dyes. De novo pan-rhodamine binders for fluorescence microscopy from mammalian cells to extremophiles www.cell.com/cell/fulltex... Congrats @bohuang.bsky.social @rhodamine110.bsky.social @mullinslab.bsky.social et al

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Yohsuke T. Fukai @fukaity.bsky.social · 03/09/2026

Thank you, Juan! 🤩 And thanks for catching my out-of-date bio; I fixed it, and I'm gradually learning that "lofty" might mean "filling out more forms." Anyway, I'm excited to be here, and I hope to involve more people in OSS projects while balancing it with physics education. See you soon!☺️

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Yohsuke T. Fukai @fukaity.bsky.social · 02/09/2026

Hi Susie, thank you for your message! We’ve finally moved to Fukuoka instead of Wako. We hope you’re doing well and looking forward to seeing you again soon!

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Yohsuke T. Fukai @fukaity.bsky.social · 02/09/2026

The move have drove me too busy for a while, but surely I’ll restart the dev soonish! I also hope to involve those interested in image analysis in the university. Looking forward to seeing you soon!

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Yohsuke T. Fukai @fukaity.bsky.social · 02/09/2026

Hi thank you for your warm message Tim! Kyushu is a wonderful place and Fukuoka and Itoshima cities around the campus are full of natural and historical sights. It’s a bit far from the city center as the price of them, but I’m looking forward to an opportunity to host events here!

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Yohsuke T. Fukai @fukaity.bsky.social · 02/09/2026

Delighted to share that I've joined Kyushu University as an Associate Professor in the Department of Physics! I'm looking forward to working on nonequilibrium physics and biophysics with students here. Feel free to reach out about JSPS postdoc opportunities or collaborations!

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Reposted by Yohsuke T. Fukai

RIKEN Center for Biosystems Dynamics Research (BDR) @riken-bdr.bsky.social · 28/11/2025

Yohsuke T. Fukai, Kyogo Kawaguchi, et al. reconstituted gene-scale #chromatin arrays with controlled #histone modification patterns in vitro and showed that heterogeneous #acetylation alone can drive pattern-dependent changes in chromatin architecture and dynamics. doi.org/10.1126/scia...

doi.org

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.

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Reposted by Yohsuke T. Fukai

Jean-Yves Tinevez @jytinevez.bsky.social · 20/11/2025

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:

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Reposted by Yohsuke T. Fukai

Kyogo Kawaguchi @kyogok.bsky.social · 20/11/2025

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/...

science.org

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.

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Yohsuke T. Fukai @fukaity.bsky.social · 31/10/2025

I truly appreciate the organizers, core contributors, and all attendees for this wonderful opportunity! I enjoyed learning and working on napari in a welcoming environment. Those interested in talking about and contributing to napari, let’s join the regular community meeting together!

napari.org

Community

There are several different ways to be a part of the napari community. From being a code or documentation contributor, to creating educational content or examples, you are welcome to help develop and ...

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Reposted by Yohsuke T. Fukai

napari @napari.org · 30/10/2025

Longer wrap-up to come, but in the meantime: we had a fantastic and productive time at the napari hackathon at @globias.bsky.social 2025 conference! Thanks to all the participants and to the GloBIAS team for hosting us!

napari core team members coding with community members at the GloBIAS 2025 hackathon at RIKEN BDR in Kobe, Japan.

napari core team members and community members in a discussion at the GloBIAS 2025 hackathon at RIKEN BDR in Kobe, Japan.

napari core team members and community members posing together for a group photo on a staircase at the GloBIAS 2025 hackathon at RIKEN BDR in Kobe, Japan.

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Reposted by Yohsuke T. Fukai

Ulrike Endesfelder @uendesfelder.bsky.social · 22/10/2025

Last call for Les Houches! Apply now or never! ;) (ok, in 2 years again then) and share with your friends.

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Reposted by Yohsuke T. Fukai

Kyogo Kawaguchi @kyogok.bsky.social · 23/05/2025

Call for RIKEN ECL Team / Unit Leaders. In my (biased) opinion, this is probably the best option if you are seeking an independent position in Japan. I will be happy to chat/answer questions via email. www.riken.jp/en/careers/p...

riken.jp

FY 2025 Call for RIKEN ECL Team / Unit Leaders

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Reposted by Yohsuke T. Fukai

Sergio Cruz-León @sergiocruzleon.bsky.social · 11/04/2025

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social, @marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social 🔗 Preprint here tinyurl.com/3a74uanv

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Reposted by Yohsuke T. Fukai

Kyogo Kawaguchi @kyogok.bsky.social · 13/03/2025

Congratulations to Zihui, Sano-san, and the team on this interesting work! They found that +1 topological defects attract neural progenitors—an observation that seems at odds with expectations for an extensile active nematic. www.nature.com/articles/s41...

nature.com

Integer topological defects offer a methodology to quantify and classify active cell monolayers - Nature Communications

The orientation of elongated cells often rotates once around the center in tissue. Such structures are called +1 topological defects and play some roles in biological development. By inducing various ...

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Reposted by Yohsuke T. Fukai

Kyogo Kawaguchi @kyogok.bsky.social · 14/02/2025

I feel like this post is becoming even more relevant for our early-career researcher friends in the US—unless it’s already too late. It doesn’t have to be our lab or RIKEN; if you’re interested in coming to Japan, I’m always happy to chat!

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Reposted by Yohsuke T. Fukai

Kyogo Kawaguchi @kyogok.bsky.social · 04/02/2025

Starting in April 2025, our RIKEN Hakubi Lab will transition to a Chief Scientist Lab, and we plan to move to Wako in 2026. My affiliation with the IPI, Department of Physics at The University of Tokyo, will continue as before.

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Yohsuke T. Fukai @fukaity.bsky.social · 05/01/2025

Re-posting from my twitter: LapTrack ( github.com/yfukai/laptr... ) provides you the linear-assignment based robust tracking algorithm, aware of splitting and merging particles, in a simple, Pythonic and flexible API. Installable with “pip install laptrack”.

github.com

GitHub - yfukai/laptrack: Particle tracking by solving linear assignment problem.

Particle tracking by solving linear assignment problem. - yfukai/laptrack

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Yohsuke T. Fukai @fukaity.bsky.social · 05/01/2025

We’re entering an exciting era of gene-scale chromatin reconstitution with precise modification patterns🚀 We hope this work will stimulate further studies to understand how different histone modifications and solution environment control chromatin architecture and function. 5/5

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Yohsuke T. Fukai @fukaity.bsky.social · 05/01/2025

We developed an in vitro Hi-C method to map nucleosome interactions and found how the acetylation reduces the nucleosome interaction frequency. For the ligated arrays (12-96-mer mixture), we found that the acetylation patterns directly control the long-range contact patterns. 4/5

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Yohsuke T. Fukai @fukaity.bsky.social · 05/01/2025

We observed arrays with different H4 hyperacetylation patterns, and found that higher acetylation density makes the array larger. There's an interesting relationship between the size and fluctuation timescales which agrees with the prediction of a simple polymer model. 3/5

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Yohsuke T. Fukai @fukaity.bsky.social · 05/01/2025

How do histone modifications affect large-scale chromatin structure? We tackled this question in vitro by reconstituting gene-scale chromatin arrays with precise histone modification patterns and analyzing them using single-molecule fluorescence imaging and in vitro Hi-C. 2/5

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Yohsuke T. Fukai @fukaity.bsky.social · 05/01/2025

Thrilled to share our latest preprint on bioRxiv! 🎉 This collaboration with @kyogok.bsky.social and lab members, Kurumizaka lab(Kujirai-san in particular!) and Umehara lab sheds new light on how histone modification shapes chromatin architecture. 1/5 biorxiv.org/content/10.1...

biorxiv.org

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture

Chromatin organization plays a crucial role in gene regulation [[1][1], [2][2], [3][3]], but disentangling the contributions of various epigenetic components to gene-scale chromatin structure remains ...

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Reposted by Yohsuke T. Fukai

Kyogo Kawaguchi @kyogok.bsky.social · 27/11/2024

And our new preprint! "Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture", biorxiv (2024). Led by Yohsuke T Fukai, in collaboration with Kurumizaka lab (U Tokyo) and Umehara lab (RIKEN BDR). www.biorxiv.org/content/10.1...

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