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.
Pinned
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!
Evening in Freising
December 26, 2025 at 4:16 PM
Evening in Freising
Reposted by Ryuichiro Nakato
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
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
www.csh-asia.org
December 4, 2025 at 5:50 AM
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
We invite abstract submissions from all intersecting fields (deadline Feb 13).
Please help spread the word!
www.csh-asia.org?content/3008
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!
December 21, 2025 at 7:01 PM
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!
Reposted by Ryuichiro Nakato
Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles!
www.biorxiv.org/content/10.6...
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...
www.biorxiv.org
December 11, 2025 at 6:40 AM
Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Ryuichiro Nakato
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...
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...
www.biorxiv.org
December 10, 2025 at 3:18 PM
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...
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...
I’m so glad I got to see Wilhelm again in Munich! He used to be a special student in our lab.
December 7, 2025 at 7:17 PM
I’m so glad I got to see Wilhelm again in Munich! He used to be a special student in our lab.
Reposted by Ryuichiro Nakato
Welcome Ryu, it's a pleasure having you in our @daisybio.de lab!
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!
December 3, 2025 at 1:36 PM
Welcome Ryu, it's a pleasure having you in our @daisybio.de lab!
It was a great first day, and I've learned a lot already
December 1, 2025 at 6:25 PM
It was a great first day, and I've learned a lot already
Reposted by Ryuichiro Nakato
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
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
In light of record submission rates and a large volume of AI-generated slop, SocArXiv recently implemented a policy requiring ORCIDs linked in the OSF profile of submitting authors, and narrowing our focus to social science subjects. Today we are taking two more steps:
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November 27, 2025 at 5:46 PM
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
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
Reposted by Ryuichiro Nakato
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
With modeling, it was worse - a draft of a 1D lattice simulation from Claude Code was bloated and inefficient
At the risk of starting the flame war to end all flame wars...
Modern LLMs (GPT-5.1, Claude 4.5, Gemini 3) produce excellent code and can be a significant productivity boost to software engineers who take the time to learn how to effectively apply them - especially if used with coding agent tools
Modern LLMs (GPT-5.1, Claude 4.5, Gemini 3) produce excellent code and can be a significant productivity boost to software engineers who take the time to learn how to effectively apply them - especially if used with coding agent tools
November 27, 2025 at 9:06 PM
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
With modeling, it was worse - a draft of a 1D lattice simulation from Claude Code was bloated and inefficient
Reposted by Ryuichiro Nakato
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/...
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...
www.science.org
November 27, 2025 at 7:10 PM
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/...
Reposted by Ryuichiro Nakato
Atacama is a place of exceptional beauty
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November 27, 2025 at 1:13 AM
Atacama is a place of exceptional beauty
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Reposted by Ryuichiro Nakato
Spent a week in the Atacama desert in Chile last week - the driest place on earth
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1/2
November 27, 2025 at 1:12 AM
Spent a week in the Atacama desert in Chile last week - the driest place on earth
1/2
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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!
November 25, 2025 at 8:05 AM
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!
Reposted by Ryuichiro Nakato
This hypothesis provides a (potential) explanation to many paradoxes and confusions in the field of enhancer-promoter interactions. An absolute must read!!
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🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
September 25, 2025 at 6:39 AM
This hypothesis provides a (potential) explanation to many paradoxes and confusions in the field of enhancer-promoter interactions. An absolute must read!!
Reposted by Ryuichiro Nakato
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...
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...
May 22, 2025 at 12:30 AM
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...
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...
Reposted by Ryuichiro Nakato
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 👇🏻🎉👏🏻 👏🏻👏🏻
The results are out today at Nature, including support from @encent.bsky.social.
Iana explains what she did here 👇🏻🎉👏🏻 👏🏻👏🏻
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature
The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...
www.nature.com
May 7, 2025 at 4:16 PM
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 👇🏻🎉👏🏻 👏🏻👏🏻
The results are out today at Nature, including support from @encent.bsky.social.
Iana explains what she did here 👇🏻🎉👏🏻 👏🏻👏🏻
Reposted by Ryuichiro Nakato
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...
May 13, 2025 at 9:41 AM
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...
Reposted by Ryuichiro Nakato
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.
March 7, 2025 at 6:57 PM
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!
April 22, 2025 at 9:00 AM
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!
Reposted by Ryuichiro Nakato
Nice to catch up with Luca @lucagiorgetti.bsky.social in Tokyo!
April 13, 2025 at 12:44 PM
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
April 13, 2025 at 10:34 PM
日本のコミュニティはTwitterが好きだからね＞RP
Reposted by Ryuichiro Nakato
ほんとか。自分の分野ではTwitter:Bluesky=100:1くらいに見える
Twitter上のアカデミック・リサーチは「死んだ」。
研究者らはXを離れブルースカイへの移行を早めており、新しい研究内容についての情報は、3月はついにブルースカイ上のポスト数が、Xのそれを上回ったそう。記事リンク↓
www.timeshighereducation.com/news/xs-domi...
研究者らはXを離れブルースカイへの移行を早めており、新しい研究内容についての情報は、3月はついにブルースカイ上のポスト数が、Xのそれを上回ったそう。記事リンク↓
www.timeshighereducation.com/news/xs-domi...
April 13, 2025 at 12:21 PM
ほんとか。自分の分野ではTwitter:Bluesky=100:1くらいに見える
Reposted by Ryuichiro Nakato
Bye bye magical Kyoto, see you next time!
April 10, 2025 at 7:04 AM
Bye bye magical Kyoto, see you next time!