Ryuichiro Nakato

This hypothesis provides a (potential) explanation to many paradoxes and confusions in the field of enhancer-promoter interactions. An absolute must read!!

Delighted to share a new preprint from the lab!

We identified zinc-finger associated domain (ZAD)-containing C2H2 zinc-finger proteins (ZAD-ZnFs) as insulator-binding proteins in Drosophila.
www.biorxiv.org/content/10.1...

Years ago, @arnausebe.bsky.social gave talk that prompted us to discuss on #3DGenomics and #Evolution. I offered we could help. Next, @ianakim.bsky.social came to the rescue 😁.

The results are out today at Nature, including support from @encent.bsky.social.

Iana explains what she did here 👇🏻🎉👏🏻 👏🏻👏🏻

Very happy to share the peer-reviewed version of our paper in which we study the formation and function of pair-wise and multi-way enhancer-promoter interactions in gene regulation (see thread below): www.nature.com/articles/s41...

In today's poster session #probgen25. To the pop gen folks, interesting observation: The influence of a nucleotide on reconstructing others, rather than its own reconstructability, is a better predictor of function. This metric makes DNA LMs beat conservation in several benchmarks.

Dr. Poonam Bheda, editor of Molecular Systems Biology and someone I met at the #EMBO meeting in February, visited our lab. She gave a seminar, and we had dinner together afterwards. It was a great time, we heard lots of interesting things about what an editor does and thinks. Thank you, Poonam!

Nice photo😁

Nice to catch up with Luca @lucagiorgetti.bsky.social in Tokyo!

日本のコミュニティはTwitterが好きだからね＞RP

ほんとか。自分の分野ではTwitter:Bluesky=100:1くらいに見える

Bye bye magical Kyoto, see you next time!

Tracing the Shared Foundations of Gene Expression and Chromatin Structure The three-dimensional organization of chromatin into topologically associating domains (TADs) may impact gene regulation by bringing distant genes into contact. However, many questions about TADs' fun...

Bio foundation models are great design and engg tools. But can they help decode the fundamental principles of life?

We harnessed a single-cell FM for decoding the long-debated relationship between genome arch. and gene coregulation. 1/

Preprint here: www.biorxiv.org/content/10.1...

Farewell party for Gima-san and Wilhelm!🎉

I had a wonderful time at Heidelberg! Huge thanks to the organizers from both EMBO and JST for making this all happen!!

Munich is a beautiful city.

I was truly moved by the warm welcome at the EMBO meeting! It was an incredible opportunity. Thank you #EMBO and #JST for hosting this wonderful event!

German feast in Freising!🍻 Had a great dinner with amazing company, including Eijy Nagai @en-coding.bsky.social, who's currently on sabbatical in Markus's lab. Cheers to great food and great people!

Thank you so much to Markus @itisalist.bsky.social and all the DaiSyBio members for inviting me to the seminar and the great dinner! I had a fantastic time and great discussions. Hope to see you all again soon! 🚀🍽️

This week, we had the honour to have visitors from Japan! 🇯🇵
@rnakato.bsky.social Lab of Computational Genomics, University of Tokyo gave the seminar talk "Deep learning-based approaches to elucidate unknown functional regions of the genome". Looking forward to further collaboration opportunities!

We are hosting the second joint meeting co-organized with the Japan Science and Technology Agency (JST). It is part of the EMBO Global Activities to strengthen the research dialogue and international interactions.
#LifeSciences #Conference 🧪

The #Japan Science and Technology Agency | EMBO Workshop brings together more than 100 participants to foster scientific exchanges and collaborations. We are delighted to welcome you in Heidelberg! 🧪

A comprehensive benchmark and guide for sequence-function interpretable deep learning models in genomics https://www.biorxiv.org/content/10.1101/2025.01.06.631405v1 🧬🖥️🧪 https://github.com/bioczsun/cisFinder

Atlas of the plasma proteome in health and disease in 53,026 adults

A real tour-de-force. Looking at total protein content in human plasma over 15 years: identifying potential disease causes and treatments based on existing drugs. #MedSky

www.cell.com/cell/fu...

Global insights in life sciences: bridging European and Japanese research EMBO and the Japan Science and Technology Agency (JST) cooperate to promote interactions between scientists in Europe and Japan. We have been co-organizing a series of meetings that not only showca…

Excited that I'll be giving an oral presentation at the upcoming EMBO conference in Heidelberg! I'll be discussing our work on epigenomic analysis using a BERT model. I'm looking forward to meeting and discussing with the community!
meetings.embo.org/event/embo-j...

Delighted to share new work from our lab:
MultiPerturb-seq 🎛️ ❌ ↕️

Over the last few years, we've been combining CRISPR screens with multimodal readouts of gene expression (RNA) and chromatin accessibility (DNA). In this study, we bring those together within the same cells.

Absolutely! Thanks again for doing most of the planning work.

Organized a symposium on large-scale epigenomics and the IHEC project with Guillaume @guilbourque.bsky.social at MBSJ2024. Couldn't be better! Had a nice lunch with the IHEC Japan team - such a great time! Let's do it again next year 😊!

Celebrated with the authors of the Springer book.

Okay first I'm going to upload a photo of a persimmon tree in my neighborhood. It was full of fruit and looked delicious. A seasonal scene in Japan.

I've noticed that many researchers on Twitter will be moving to Bluesky. Is it time to start tweeting here?