Tetsuya Yamada
@tyamadat.bsky.social
PhD student @UniHeidelberg | Kaessmann lab | UTokyo alumn
Pinned
Tetsuya Yamada
@tyamadat.bsky.social
· Oct 17
Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
So excited to see this out on bioRxiv! Huge thanks to @kaessmannlab.bsky.social and the amazing cerebellum team (@marisepp.bsky.social and @ioansarr.bsky.social) for all the support and insightful discussions that made this work possible!!
Reposted by Tetsuya Yamada
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
February 7, 2026 at 8:50 AM
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
Reposted by Tetsuya Yamada
The new updates for Charles McAnany’s preprint “Positional Interpretation of Cis-Regulatory Code and Nucleosome Organization with Deep Learning Models” (www.biorxiv.org/content/10.1...) are up!
We introduce PISA, a tool to visualize the cis-regulatory code. See a recap below:
We introduce PISA, a tool to visualize the cis-regulatory code. See a recap below:
www.biorxiv.org
February 5, 2026 at 7:29 PM
The new updates for Charles McAnany’s preprint “Positional Interpretation of Cis-Regulatory Code and Nucleosome Organization with Deep Learning Models” (www.biorxiv.org/content/10.1...) are up!
We introduce PISA, a tool to visualize the cis-regulatory code. See a recap below:
We introduce PISA, a tool to visualize the cis-regulatory code. See a recap below:
Reposted by Tetsuya Yamada
Happy to announce that our latest paper is now out! Have you ever wondered how neural tissues control their size? In this paper, we show that cell division orientation is critical in both the cortex and retina. www.science.org/doi/10.1126/...
Oriented cell divisions induce basal progenitors and regulate neural expansion across tissues and species
A fundamental role for division orientation in progenitor output driving cortical and retinal growth is revealed.
www.science.org
February 4, 2026 at 7:16 PM
Happy to announce that our latest paper is now out! Have you ever wondered how neural tissues control their size? In this paper, we show that cell division orientation is critical in both the cortex and retina. www.science.org/doi/10.1126/...
Reposted by Tetsuya Yamada
It is finally out! If you are interested in TE-derived CREs, and newly described, but evolutionary old KZFP-TE mechanistic modalities, read it at www.cell.com/cell-reports....
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨
Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity
Milovanović et al. uncover a mechanism by which KZFPs restrict the activity of transposon-derived
cis-regulatory elements to safeguard cardiomyocyte functionality. This work extends
the classical TE-K...
www.cell.com
January 29, 2026 at 2:20 PM
It is finally out! If you are interested in TE-derived CREs, and newly described, but evolutionary old KZFP-TE mechanistic modalities, read it at www.cell.com/cell-reports....
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨
Reposted by Tetsuya Yamada
A genome language model for mapping DNA replication origins [new]
predicts specific DNA replication origin sequences by learning rich sequence features beyond known motifs, enabling fast genome-wide mapping across vertebrates.
predicts specific DNA replication origin sequences by learning rich sequence features beyond known motifs, enabling fast genome-wide mapping across vertebrates.
January 30, 2026 at 4:15 PM
A genome language model for mapping DNA replication origins [new]
predicts specific DNA replication origin sequences by learning rich sequence features beyond known motifs, enabling fast genome-wide mapping across vertebrates.
predicts specific DNA replication origin sequences by learning rich sequence features beyond known motifs, enabling fast genome-wide mapping across vertebrates.
Reposted by Tetsuya Yamada
I've started my own lab 🎉
PhD/postdoc positions available - reach out if curious about cerebellum evo-devo and autism spectrum disorders.
We’re based at Uni Tartu, Institute of Genomics (home to Estonian Biobank), and funded by @simonsfoundation.org @embo.org, and the Estonian Research Council.
PhD/postdoc positions available - reach out if curious about cerebellum evo-devo and autism spectrum disorders.
We’re based at Uni Tartu, Institute of Genomics (home to Estonian Biobank), and funded by @simonsfoundation.org @embo.org, and the Estonian Research Council.
January 29, 2026 at 8:33 PM
I've started my own lab 🎉
PhD/postdoc positions available - reach out if curious about cerebellum evo-devo and autism spectrum disorders.
We’re based at Uni Tartu, Institute of Genomics (home to Estonian Biobank), and funded by @simonsfoundation.org @embo.org, and the Estonian Research Council.
PhD/postdoc positions available - reach out if curious about cerebellum evo-devo and autism spectrum disorders.
We’re based at Uni Tartu, Institute of Genomics (home to Estonian Biobank), and funded by @simonsfoundation.org @embo.org, and the Estonian Research Council.
Very happy to see this work finally published!
I am truly grateful to all the collaborators who made this work possible, especially @ioansarr.bsky.social, @marisepp.bsky.social, and @kaessmannlab.bsky.social. It’s been a pleasure working with you!
I am truly grateful to all the collaborators who made this work possible, especially @ioansarr.bsky.social, @marisepp.bsky.social, and @kaessmannlab.bsky.social. It’s been a pleasure working with you!
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 30, 2026 at 7:25 AM
Very happy to see this work finally published!
I am truly grateful to all the collaborators who made this work possible, especially @ioansarr.bsky.social, @marisepp.bsky.social, and @kaessmannlab.bsky.social. It’s been a pleasure working with you!
I am truly grateful to all the collaborators who made this work possible, especially @ioansarr.bsky.social, @marisepp.bsky.social, and @kaessmannlab.bsky.social. It’s been a pleasure working with you!
Reposted by Tetsuya Yamada
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
www.biorxiv.org
January 29, 2026 at 12:07 PM
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
Reposted by Tetsuya Yamada
Our paper on the evolution of XIST regulatory network in primates is now published in Science Advances! Check out the paper www.science.org/doi/10.1126/... or a digest of our findings emmanuelczt.github.io/posts/2026/0... A short 🧵 of our main findings 👇
Remodeling of XIST regulatory landscape during primate evolution
How gene regulation strategies rapidly evolve across short evolutionary timescales is explored.
www.science.org
January 28, 2026 at 3:48 PM
Our paper on the evolution of XIST regulatory network in primates is now published in Science Advances! Check out the paper www.science.org/doi/10.1126/... or a digest of our findings emmanuelczt.github.io/posts/2026/0... A short 🧵 of our main findings 👇
Reposted by Tetsuya Yamada
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
Reposted by Tetsuya Yamada
1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Dissecting gene regulatory networks governing human cortical cell fate - Nature
Systematic screening of transcription factors reveals conserved mechanisms governing cortical radial glia lineage progression across primates and provides a framework for functional dissecti...
www.nature.com
January 23, 2026 at 1:16 AM
1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Tetsuya Yamada
It’s out! 🐟 We compared three regeneration superstars—axolotl, zebrafish, and Polypterus—to ask how animals regrow limbs and fins. We find shared core processes, and other programs fine-tuned by evolution in surprising, lineage-specific ways. tinyurl.com/mpftkn7y
January 22, 2026 at 5:38 PM
It’s out! 🐟 We compared three regeneration superstars—axolotl, zebrafish, and Polypterus—to ask how animals regrow limbs and fins. We find shared core processes, and other programs fine-tuned by evolution in surprising, lineage-specific ways. tinyurl.com/mpftkn7y
Reposted by Tetsuya Yamada
Our review “A competition model of multilineage priming and cell-fate decisions” is out: www.cell.com/cell-reports...
A competition model of multilineage priming and cell-fate decisions
In development, cells navigate highly complex gene-regulatory landscapes to make fate
choices. Steinschaden et al. synthesize concepts of multilineage priming, microheterogeneity,
and collective multi...
www.cell.com
January 19, 2026 at 11:05 PM
Our review “A competition model of multilineage priming and cell-fate decisions” is out: www.cell.com/cell-reports...
Reposted by Tetsuya Yamada
New preprint from the @wittbrodtlab.bsky.social. The group developed an "infinity pool" setup to test visual acuity and swimming behavior in medaka.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
A Scalable, High-Throughput Optomotor Response Pipeline for Quantitative Analysis of Vision Using Infinity-Pools
The optomotor response (OMR) provides a robust readout assay for evaluating visually guided locomotion and has been widely applied to various animal models. We present a scalable, high-throughput OMR ...
www.biorxiv.org
January 17, 2026 at 6:34 AM
Reposted by Tetsuya Yamada
We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.
January 15, 2026 at 11:57 AM
We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.
Reposted by Tetsuya Yamada
New Year, New Paper!🎊
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...
Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...
Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
Transposable elements (TEs) make up about half of the human and mouse genomes and play important regulatory roles in immune responses. However, the cis -regulatory contribution of TEs to immune cell d...
www.biorxiv.org
January 7, 2026 at 7:45 PM
New Year, New Paper!🎊
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...
Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...
Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵
Reposted by Tetsuya Yamada
Our work on the evolution of the regulatory genome of echinoderms is now out in @natecoevo.nature.com. Led by my former PhD Marta Magri, Danila Voronov & Saoirse Foley. Great collaboration of Arnone, Hinman & Maeso labs, started long time ago with our missed José Luis Gomez-Skarmeta: rdcu.be/eXX8l
Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes
Nature Ecology & Evolution - Analysis of the 3D chromatin architecture and cis-regulatory elements in a sea urchin and a sea star reveals mechanisms of 3D chromatin organization in echinoderms...
rdcu.be
January 7, 2026 at 7:33 PM
Our work on the evolution of the regulatory genome of echinoderms is now out in @natecoevo.nature.com. Led by my former PhD Marta Magri, Danila Voronov & Saoirse Foley. Great collaboration of Arnone, Hinman & Maeso labs, started long time ago with our missed José Luis Gomez-Skarmeta: rdcu.be/eXX8l
Reposted by Tetsuya Yamada
DNA sequence quantitatively encodes CTCF-binding affinity at genome scale https://www.biorxiv.org/content/10.64898/2026.01.05.696797v1
January 6, 2026 at 7:31 AM
DNA sequence quantitatively encodes CTCF-binding affinity at genome scale https://www.biorxiv.org/content/10.64898/2026.01.05.696797v1
Reposted by Tetsuya Yamada
Cross-species insights into placental evolution and diseases at the single-cell resolution https://www.biorxiv.org/content/10.64898/2025.12.26.696571v1
December 26, 2025 at 6:31 PM
Cross-species insights into placental evolution and diseases at the single-cell resolution https://www.biorxiv.org/content/10.64898/2025.12.26.696571v1
Reposted by Tetsuya Yamada
Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Decoding cnidarian cell type gene regulation - Nature Ecology & Evolution
This study reconstructs the gene regulatory networks that define cell types in the sea anemone Nematostella vectensis, providing a valuable resource for comparative regulatory genomics and the evoluti...
www.nature.com
December 22, 2025 at 10:12 AM
Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Tetsuya Yamada
🧬👁️ Our Science Advances paper is published! snATAC-seq analysis across lamprey to human retina uncovers deeply conserved cis-regulatory codes in all six retinal cell types — even with extensive enhancer turnover. Immensely grateful to my coauthors and collaborators. 🙏 www.science.org/doi/10.1126/...
Conservation of cis-regulatory codes over half a billion years of evolution
The regulatory codes controlling vertebrate retinal gene expression have been conserved over more than half a billion years.
www.science.org
December 16, 2025 at 2:17 PM
🧬👁️ Our Science Advances paper is published! snATAC-seq analysis across lamprey to human retina uncovers deeply conserved cis-regulatory codes in all six retinal cell types — even with extensive enhancer turnover. Immensely grateful to my coauthors and collaborators. 🙏 www.science.org/doi/10.1126/...
Reposted by Tetsuya Yamada
New paper alert!!...🤩 Led by @blogeman.bsky.social, we identify how cell type-specific hormonal responses in the hypothalamus tunes parenting behavior in males and females 🐭🧠🍼. Highlights in thread 👇 1/6
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Cell Type-Specific Hormonal Signaling Configures Hypothalamic Circuits for Parenting
Parenting behavior emerges from hormonally sensitive circuits, but how distinct circuit components are affected by, and contribute to, sex and state dependent changes in infant caregiving remains uncl...
www.biorxiv.org
December 13, 2025 at 2:03 PM
New paper alert!!...🤩 Led by @blogeman.bsky.social, we identify how cell type-specific hormonal responses in the hypothalamus tunes parenting behavior in males and females 🐭🧠🍼. Highlights in thread 👇 1/6
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Tetsuya Yamada
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
www.nature.com
December 11, 2025 at 5:54 PM
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Reposted by Tetsuya Yamada
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...
Reposted by Tetsuya Yamada
Thank you Alex! Excited to see our paper published in @nature.com ! Huge thanks to @jeffspence.github.io , @tkyzeng.bsky.social , @emmamarydann.bsky.social, @nikhilmilind.dev, @marsonlab.bsky.social, @jkpritch.bsky.social, and all the members of the Pritchard and Marson labs for your enormous help!
December 11, 2025 at 3:04 AM
Thank you Alex! Excited to see our paper published in @nature.com ! Huge thanks to @jeffspence.github.io , @tkyzeng.bsky.social , @emmamarydann.bsky.social, @nikhilmilind.dev, @marsonlab.bsky.social, @jkpritch.bsky.social, and all the members of the Pritchard and Marson labs for your enormous help!