Ryuichiro Nakato
@rnakato.bsky.social
Associate Professor, Lab of Comput. Genomics, University of Tokyo, Japan. Dad of 3 kids🧒🧒👧Data-driven analysis, Epigenomics, 3D genome, Single cell, Cohesin and CTCF.
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 🧪 🧵👇
So happy that our lab student Jun received a Youth Innovation Award! Thank you, CSH Asia!
We were delighted to host the UTokyo-NTU Symposium 2026 and welcome the NTU professors to IQB! Thank all participants for their attendance and engagement!
Ryuichiro Nakato@rnakato.bsky.social · 5mo agoWe have been invited to the symposium at National Taiwan University every year, but this year the IQB will host it and welcome professors from NTU. We are preparing to make it a great event, which will be held next week! ut-ntu-2026.iqb.u-tokyo.ac.jp
Lab group photo for 2026. With two interns joining in February and five students joining in April, our lab has grown into quite a large group! 🙂
【拡散希望】私も運営に携わらせてもらっているEMBO–MBSJ Laboratory Leadership Forumが6月27日に東京で開催されます！ラボ運営に必要なスキルについて学べる貴重な機会だと思いますので、みなさん是非ご参加ください！
The Molecular Biology Society of Japan (MBSJ)@mbsj-official.bsky.social · 5mo ago【NEWS】EMBO–MBSJ Laboratory Leadership Forum 2026 in Tokyo Institute of Science Tokyo Yushima Campus, M&D Tower (formerly Tokyo Medical and Dental University) Saturday, June 27, 2026 sites.google.com/view/embo-mb...
Doing science requires us to speak 2 different languages: (1) Day science language is a highly precise language for designing & executing experiments; while (2) Night science language uses analogies & anthropomorphizes to give us intuitions about the unknowns we explore. (Night Science recap, Day 4)
We have been invited to the symposium at National Taiwan University every year, but this year the IQB will host it and welcome professors from NTU. We are preparing to make it a great event, which will be held next week! ut-ntu-2026.iqb.u-tokyo.ac.jp
Recently AI-driven automation has been especially celebrated, but I have come to feel even greater pride in reading papers, reviewing them carefully, and writing and submitting my comments in my own words.
Join us at Cell Symposia: Single-Cell Biology in the Era of AI (Dec 2–4, 2026, Munich) 🇩🇪 From multi-omics to AI-driven models of cellular dynamics — an exciting lineup across experimental & computational biology. Hope to see you there! 🔗 www.cell-symposia.com/single-cell-...
Home – Cell Symposia: Decoding Cellular Complexity: Single Cell Biology in the Era of AI
Cell Symposia: Decoding Cellular Complexity: Single Cell Biology in the Era of AI
cell-symposia.com
To celebrate my return from Germany, I served Glühwein in the lab🍷 The three wine mugs I bought at the Christmas market came in handy!
🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...
After staying for two months in Munich, I returned to Japan. I met many excellent professors and students, had great discussions, and gained invaluable experience that would be difficult to obtain in a short visit. I want to thank Markus @itisalist.bsky.social for hosting me!
Ryuichiro Nakato@rnakato.bsky.social · 10mo agoI’m happy to announce that I'll be joining Prof. Markus List's lab @itisalist.bsky.social at @tum.de for two months, starting in December. I’m looking forward to establishing new collaborations on deep learning and network analysis. I’m grateful to the @embo.org grant for supporting this stay!
We are thrilled that our study on the evolution of gene regulation in mammalian cerebellum development – led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social – is now out in @ScienceMagazine! www.science.org/doi/10.1126/...
The evolution of gene regulation in mammalian cerebellum development
Gene regulatory changes are considered major drivers of evolutionary innovations, including the cerebellum’s expansion during human evolution, yet they remain largely unexplored. In this study, we com...
science.org
Kaessmann Lab@kaessmannlab.bsky.social · last yr.How does gene regulation shape brain evolution? Our new preprint dives into this question in the context of mammalian cerebellum development! rb.gy/dbcxjz Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
AlphaGenome is out in @nature.com today along with model weights! 🧬 📄 Paper: www.nature.com/articles/s41... 💻 Weights: github.com/google-deepm... Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc
Yesterday was my last day with the Markus lab members. They surprised me with a gift to thank me for my two months. I’m moved and very happy. In my two months, I've received so much from them in many ways. I’m glad I had the chance to visit.
On Wednesday, @rnakato.bsky.social gave an excellent talk in our new @tum.de Life Science Talks series: www.ls.tum.de/en/ls/public.... It was nice to see so many people join to hear about the role of multi-omics data in elucidating gene-regulatory mechanisms. Well done @rnakato.bsky.social
New lecture series: TUM Life Science Talks foster interdisciplinary discourse
New lecture series: TUM Life Science Talks in Freising-Weihenstephan promote exchange with renowned scientists.
ls.tum.de
Our research exchange seminar between the Nakato and Markus labs has finally taken place! It was a great opportunity to share our work and to learn from many excellent presentations by their students. We are grateful to them for making a full-day seminar possible despite their very busy schedules.
Ryuichiro Nakato@rnakato.bsky.social · 8mo agoHappy to welcome our lab members to @tum.de for a research exchange with Markus’s lab @daisybio.de. Looking forward to the research presentations on the 15th!
Very happy to see this published: doi.org/10.1093/nar/...: a GRN-based approach to predict regulatory subnetworks for developmental and pathogenic processes in Aspergillus fumigatus and GRAsp: a network viz tool: grasp.wid.wisc.edu with @jeanmichelane.bsky.social and Nancy Keller labs!
A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen
Abstract. Aspergillus fumigatus is a notorious pathogenic fungus responsible for various harmful, sometimes lethal, diseases known as aspergilloses. Unders
doi.org
Happy to welcome our lab members to @tum.de for a research exchange with Markus’s lab @daisybio.de. Looking forward to the research presentations on the 15th!
I’m honored to give a seminar at the TUM School of Life Sciences in January. I’ll be presenting our work on multi-omics analysis. I look forward to the discussion! www.ls.tum.de/en/ls/public...
TUM Life Science Talks: Prof. Ryuichiro Nakato (University of Tokyo)
TUM Life Science Talks start with Prof. Ryuichiro Nakato: “Can multi-omics analysis elucidate genome regulatory mechanisms?”
ls.tum.de
My hotel room is a bit too dark to work in, so I came to the TUM library today. I'm glad that visitors like me are allowed in. I also found the famous "Parabola Slide"!😀
Join us for the AI & Biology conference in beautiful Suzhou, China, Apr 20–23, 2026! A place to spark dialogue about the future of AI × biology. We invite abstract submissions from all intersecting fields (deadline Feb 13). Please help spread the word! www.csh-asia.org?content/3008
WELCOME-Meetings-Cold Spring Harbor Asia
csh-asia.org
My first month at TUM has been wonderful. I arrived with high expectations, and I have already learned much more than I anticipated. I'm looking forward to spending another month doing research here. Thank you, Markus @itisalist.bsky.social @daisybio.de for hosting me!
Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles! www.biorxiv.org/content/10.6...
Reverse gyrase and 3D genome architecture suppress hyperthermophile genome instability arising from horizontal gene transfer
Reverse gyrase (Rgy), a distinctive topoisomerase conserved in all hyperthermophiles, has the unique ability to introduce positive DNA supercoils. It has long been hypothesized that Rgy overwinds geno...
biorxiv.org
After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out! In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells. www.biorxiv.org/content/10.1...
Programmatic design and editing of cis-regulatory elements
The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...
biorxiv.org
I’m so glad I got to see Wilhelm again in Munich! He used to be a special student in our lab.
