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
Ryuichiro Nakato
@rnakato.bsky.social
· Jan 5
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?”
www.ls.tum.de
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...
www.ls.tum.de/en/ls/public...
Reposted by Ryuichiro Nakato
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/...
January 29, 2026 at 7:23 PM
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/...
Reposted by Ryuichiro Nakato
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
📄 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
January 28, 2026 at 9:02 PM
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
📄 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.
In my two months, I've received so much from them in many ways. I’m glad I had the chance to visit.
January 28, 2026 at 3:26 PM
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.
In my two months, I've received so much from them in many ways. I’m glad I had the chance to visit.
Reposted by Ryuichiro Nakato
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.
www.ls.tum.de
January 24, 2026 at 7:13 PM
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
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.
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!
January 17, 2026 at 9:06 AM
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.
Reposted by Ryuichiro Nakato
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
January 13, 2026 at 4:49 AM
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!
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!
January 13, 2026 at 10:51 AM
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...
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?”
www.ls.tum.de
January 5, 2026 at 11:26 AM
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...
www.ls.tum.de/en/ls/public...
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"!😀
January 2, 2026 at 10:09 AM
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"!😀
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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/1
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
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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!!