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Ryuichiro Nakato

@rnakato.bsky.social
116 followers 128 following 38 posts

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.

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Reposted by Ryuichiro Nakato
Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13/05/2026
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 🧪 🧵👇
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Ryuichiro Nakato @rnakato.bsky.social · 27/04/2026
So happy that our lab student Jun received a Youth Innovation Award! Thank you, CSH Asia!
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Ryuichiro Nakato @rnakato.bsky.social · 21/04/2026
Great to meet Prof. Jian Zhou @zhou-jian.bsky.social at CSH Asia!
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Ryuichiro Nakato @rnakato.bsky.social · 20/04/2026
Came to Suzhou to attend CSH Asia AI and Biology
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Ryuichiro Nakato @rnakato.bsky.social · 17/04/2026
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!
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Ryuichiro Nakato @rnakato.bsky.social · 11/04/2026
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! 🙂
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Reposted by Ryuichiro Nakato
Naomichi Takemata @naomichitakemata.bsky.social · 09/04/2026
【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!
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Reposted by Ryuichiro Nakato
Itai Yanai @itaiyanai.bsky.social · 09/04/2026
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)
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Ryuichiro Nakato @rnakato.bsky.social · 07/04/2026
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
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Ryuichiro Nakato @rnakato.bsky.social · 14/03/2026
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.
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Reposted by Ryuichiro Nakato
Takashi Fukaya @fukayalab.bsky.social · 04/03/2026
Thanks Ibrahim for stimulating talk and discussion!!
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Fabian Theis @fabiantheis.bsky.social · 24/02/2026
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-...
cell-symposia.com
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
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Ryuichiro Nakato @rnakato.bsky.social · 16/02/2026
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!
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Reposted by Ryuichiro Nakato
Seychelle Vos @voslab.org · 09/02/2026
🧪🧬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...
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Ryuichiro Nakato @rnakato.bsky.social · 08/02/2026
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!
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Kaessmann Lab @kaessmannlab.bsky.social · 29/01/2026
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/...
science.org
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...
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Reposted by Ryuichiro Nakato
Žiga Avsec @avsecz.bsky.social · 28/01/2026
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
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Ryuichiro Nakato @rnakato.bsky.social · 28/01/2026
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.
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Markus List @itisalist.bsky.social · 24/01/2026
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
ls.tum.de
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.
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Ryuichiro Nakato @rnakato.bsky.social · 17/01/2026
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.
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Reposted by Ryuichiro Nakato
Sushmita Roy @sroyyors.bsky.social · 13/01/2026
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!
doi.org
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
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Ryuichiro Nakato @rnakato.bsky.social · 13/01/2026
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!
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Ryuichiro Nakato @rnakato.bsky.social · 05/01/2026
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...
ls.tum.de
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?”
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Ryuichiro Nakato @rnakato.bsky.social · 02/01/2026
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"!😀
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Ryuichiro Nakato @rnakato.bsky.social · 26/12/2025
Evening in Freising
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Jian Zhou @zhou-jian.bsky.social · 04/12/2025
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
csh-asia.org
WELCOME-Meetings-Cold Spring Harbor Asia
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Ryuichiro Nakato @rnakato.bsky.social · 21/12/2025
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!
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Naomichi Takemata @naomichitakemata.bsky.social · 11/12/2025
Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles! www.biorxiv.org/content/10.6...
biorxiv.org
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...
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Jacob Schreiber @jmschreiber91.bsky.social · 10/12/2025
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...
biorxiv.org
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...
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Ryuichiro Nakato @rnakato.bsky.social · 07/12/2025
I’m so glad I got to see Wilhelm again in Munich! He used to be a special student in our lab.
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Ryuichiro Nakato @rnakato.bsky.social · 05/12/2025
Snowing ❄
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Markus List @itisalist.bsky.social · 03/12/2025
Welcome Ryu, it's a pleasure having you in our @daisybio.de lab!
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Ryuichiro Nakato @rnakato.bsky.social · 01/12/2025
It was a great first day, and I've learned a lot already
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Richard Sever @richardsever.bsky.social · 27/11/2025
Hard choices for preprint servers. bioRxiv has always declined reviews/hypotheses b/c of concern about signal:noise and a wish to avoid subjective judgments. AI slop makes screening certain content similarly challenging so other servers are adopting new restrictions. Two thoughts... 1/3
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Anton Goloborodko @golobor.bsky.social · 27/11/2025
my experience with scientific coding was also relatively positive. I think autocompletion-style AI greatly speeds up data analyses when you know what you're doing; it also prevents typos. With modeling, it was worse - a draft of a 1D lattice simulation from Claude Code was bloated and inefficient
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Benoit Bruneau @benoitbruneau.bsky.social · 27/11/2025
Bah, who needs cohesin if you're at the right place (near). Grover once taught us the difference between near and far (my favourite Sesame Street piece), and now amazing work from @elphegenoralab.bsky.social led by @karissalhansen.bsky.social shows us how: www.science.org/doi/10.1126/...
science.org
Synergy between regulatory elements can render cohesin dispensable for distal enhancer function
Enhancers are critical genetic elements controlling transcription from promoters, yet how they convey regulatory information across large genomic distances remains unclear. Here, we engineer pluripote...
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Cees Dekker @ceesdekker.bsky.social · 27/11/2025
Atacama is a place of exceptional beauty 2/2
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Cees Dekker @ceesdekker.bsky.social · 27/11/2025
Spent a week in the Atacama desert in Chile last week - the driest place on earth 1/2
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Ryuichiro Nakato @rnakato.bsky.social · 25/11/2025
I’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!
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Anton Goloborodko @golobor.bsky.social · 25/09/2025
This hypothesis provides a (potential) explanation to many paradoxes and confusions in the field of enhancer-promoter interactions. An absolute must read!!
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Takashi Fukaya @fukayalab.bsky.social · 22/05/2025
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...
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Marc A. Marti-Renom @mamartirenom.bsky.social · 07/05/2025
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 👇🏻🎉👏🏻 👏🏻👏🏻
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Marieke Oudelaar @mariekeoudelaar.bsky.social · 13/05/2025
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...
nature.com
CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation - Nature Structural & Molecular Biology
Karpinska, Zhu and colleagues characterize the structure-function relationship of the genome during cellular differentiation and demonstrate a role for enhancer-promoter interactions in gene regulatio...
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Gagneur lab @gagneurlab.bsky.social · 07/03/2025
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.
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Ryuichiro Nakato @rnakato.bsky.social · 22/04/2025
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!
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Takashi Fukaya @fukayalab.bsky.social · 13/04/2025
Nice to catch up with Luca @lucagiorgetti.bsky.social in Tokyo!
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Ryuichiro Nakato @rnakato.bsky.social · 13/04/2025
日本のコミュニティはTwitterが好きだからね>RP
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Haruhiko Okumura @okumura.bsky.social · 13/04/2025
ほんとか。自分の分野ではTwitter:Bluesky=100:1くらいに見える
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Guillaume Bourque @guilbourque.bsky.social · 10/04/2025
Bye bye magical Kyoto, see you next time!
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Rohit Singh @rohitsingh8080.bsky.social · 05/04/2025
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...
biorxiv.org
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...
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