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.
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!
Reposted by Ryuichiro Nakato
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...
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...
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...
www.biorxiv.org
April 5, 2025 at 3:31 PM
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...
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!🎉
March 18, 2025 at 7:53 AM
Farewell party for Gima-san and Wilhelm!🎉
Reposted by Ryuichiro Nakato
I had a wonderful time at Heidelberg! Huge thanks to the organizers from both EMBO and JST for making this all happen!!
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 🧪
#LifeSciences #Conference 🧪
March 3, 2025 at 4:59 AM
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.
March 3, 2025 at 12:37 PM
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!
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 🧪
#LifeSciences #Conference 🧪
March 3, 2025 at 5:09 AM
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!
March 3, 2025 at 4:25 AM
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!
@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!
March 3, 2025 at 4:11 AM
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! 🚀🍽️
Reposted by Ryuichiro Nakato
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!
@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!
February 27, 2025 at 12:50 PM
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!
@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!
Reposted by Ryuichiro Nakato
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 🧪
#LifeSciences #Conference 🧪
February 28, 2025 at 11:49 AM
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 🧪
#LifeSciences #Conference 🧪
Reposted by Ryuichiro Nakato
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! 🧪
February 28, 2025 at 1:29 AM
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! 🧪
Reposted by Ryuichiro Nakato
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
January 10, 2025 at 9:00 PM
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
Reposted by Ryuichiro Nakato
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...
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...
Atlas of the plasma proteome in health and disease in 53,026 adults
A large-scale proteomics study involving 53,026 individuals maps 2,920 plasma proteins
to 406 prevalent diseases, 660 incident diseases, and 986 health-related traits, identifying
promising biomarkers for disease discrimination and potential therapeutic targets
and paving the way for precision medicine.
www.cell.com
January 10, 2025 at 9:09 PM
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...
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...
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...
meetings.embo.org/event/embo-j...
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…
meetings.embo.org
January 9, 2025 at 2:42 AM
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...
meetings.embo.org/event/embo-j...
Reposted by Ryuichiro Nakato
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.
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.
Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling go.nature.com/4hXER5O
Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling - Nature Biotechnology
MultiPerturb-seq profiles gene expression and chromatin accessibility in single-cell pooled CRISPR screen.
go.nature.com
November 26, 2024 at 1:42 PM
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.
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.
Reposted by Ryuichiro Nakato
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 😊!
December 3, 2024 at 5:40 AM
Absolutely! Thanks again for doing most of the planning work.