Natsuhiko Kumasaka
@natsuhiko83.bsky.social
Professor, Division of Digital Genomics, Institute of Medical Science, The University of Tokyo / Team leader, National Center for Child Health and Development
Pinned
I'm delighted to present our nationwide effort to identify genetic determinants of child health and development in Japan.
Preprint: www.medrxiv.org/content/10.1...
Preprint: www.medrxiv.org/content/10.1...
Reposted by Natsuhiko Kumasaka
Perhaps the biggest change is that we have added some practical guidelines for performing MR with proxy exposures. These are summarised on this nice figure prepared by Ida Rahu:
September 27, 2025 at 8:53 AM
Perhaps the biggest change is that we have added some practical guidelines for performing MR with proxy exposures. These are summarised on this nice figure prepared by Ida Rahu:
Reposted by Natsuhiko Kumasaka
Out now on bioRxiv! 🧬🖥️
A team from the Cowley, Bassett, and @gosiatrynka.bsky.social labs integrate pooled iPSC phenotyping, transcriptomics, and CRISPR perturbations to identify genetic drivers of molecular and cellular phenotypes in microglia
www.biorxiv.org/content/10.1...
#neuroskyence
A team from the Cowley, Bassett, and @gosiatrynka.bsky.social labs integrate pooled iPSC phenotyping, transcriptomics, and CRISPR perturbations to identify genetic drivers of molecular and cellular phenotypes in microglia
www.biorxiv.org/content/10.1...
#neuroskyence
Integrated QTL mapping and CRISPR screening in pooled iPSC-derived microglia reveals genetic drivers of neurodegenerative risk
Mounting evidence implicates microglia in neurodegeneration, but linking disease-associated genetic variants to target genes and cellular phenotypes is hindered by the inaccessibility of these cells. ...
www.biorxiv.org
August 26, 2025 at 10:16 AM
Out now on bioRxiv! 🧬🖥️
A team from the Cowley, Bassett, and @gosiatrynka.bsky.social labs integrate pooled iPSC phenotyping, transcriptomics, and CRISPR perturbations to identify genetic drivers of molecular and cellular phenotypes in microglia
www.biorxiv.org/content/10.1...
#neuroskyence
A team from the Cowley, Bassett, and @gosiatrynka.bsky.social labs integrate pooled iPSC phenotyping, transcriptomics, and CRISPR perturbations to identify genetic drivers of molecular and cellular phenotypes in microglia
www.biorxiv.org/content/10.1...
#neuroskyence
Reposted by Natsuhiko Kumasaka
Our paper, MR-link-2 has just been published! Offering pleiotropy robust Mendelian randomization from a single region! www.nature.com/articles/s41...
July 4, 2025 at 8:52 AM
Our paper, MR-link-2 has just been published! Offering pleiotropy robust Mendelian randomization from a single region! www.nature.com/articles/s41...
Reposted by Natsuhiko Kumasaka
Excited to present our work on developing jaxQTL, a fast single-cell eQTL mapping tool that improves power and robustness in identifying sc-eQTLs using count-based models. See details in threads 🧵
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Efficient count-based models improve power and robustness for large-scale single-cell eQTL mapping
Population-scale single-cell transcriptomic technologies (scRNA-seq) enable characterizing variant effects on gene regulation at the cellular level (e.g., single-cell eQTLs; sc-eQTLs). However, existi...
www.medrxiv.org
January 27, 2025 at 6:29 PM
Excited to present our work on developing jaxQTL, a fast single-cell eQTL mapping tool that improves power and robustness in identifying sc-eQTLs using count-based models. See details in threads 🧵
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Natsuhiko Kumasaka
Preprint out today!
A team led by @tobioinformatics.bsky.social and Bradley Harris in @carlanderson.bsky.social ‘s lab has created the largest single-cell atlas of IBD tissues to date
www.medrxiv.org/content/10.1...
A team led by @tobioinformatics.bsky.social and Bradley Harris in @carlanderson.bsky.social ‘s lab has created the largest single-cell atlas of IBD tissues to date
www.medrxiv.org/content/10.1...
June 26, 2025 at 8:29 AM
Preprint out today!
A team led by @tobioinformatics.bsky.social and Bradley Harris in @carlanderson.bsky.social ‘s lab has created the largest single-cell atlas of IBD tissues to date
www.medrxiv.org/content/10.1...
A team led by @tobioinformatics.bsky.social and Bradley Harris in @carlanderson.bsky.social ‘s lab has created the largest single-cell atlas of IBD tissues to date
www.medrxiv.org/content/10.1...
Reposted by Natsuhiko Kumasaka
Why do so many disease risk variants show no regulatory effects in GTEx and/or other standard eQTL studies?
What do we mean when we say a regulatory effect is "context-specific" and how do we define the context?
We explored these questions using brain organoids and oxygen stress.
What do we mean when we say a regulatory effect is "context-specific" and how do we define the context?
We explored these questions using brain organoids and oxygen stress.
June 9, 2025 at 12:03 AM
Why do so many disease risk variants show no regulatory effects in GTEx and/or other standard eQTL studies?
What do we mean when we say a regulatory effect is "context-specific" and how do we define the context?
We explored these questions using brain organoids and oxygen stress.
What do we mean when we say a regulatory effect is "context-specific" and how do we define the context?
We explored these questions using brain organoids and oxygen stress.
Reposted by Natsuhiko Kumasaka
🚨 Preprint update!
We expanded our study on parent-of-origin effects with new findings from the MoBa cohort, now leveraging up to 265,000 individuals!
Discover fresh insights into the genetic architecture of early growth!
Updated preprint: www.medrxiv.org/content/10.1...
We expanded our study on parent-of-origin effects with new findings from the MoBa cohort, now leveraging up to 265,000 individuals!
Discover fresh insights into the genetic architecture of early growth!
Updated preprint: www.medrxiv.org/content/10.1...
🚨 Our preprint on parent-of-origin effects (POEs) is out!
With our novel method, we inferred the parental origin of alleles for >220,000 individuals, uncovering novel insights into genetics, evolution, and health.
👉 Read here: www.medrxiv.org/content/10.1...
👇 Highlights below!
With our novel method, we inferred the parental origin of alleles for >220,000 individuals, uncovering novel insights into genetics, evolution, and health.
👉 Read here: www.medrxiv.org/content/10.1...
👇 Highlights below!
Parent-of-Origin inference and its role in the genetic architecture of complex traits: evidence from ~220,000 individuals
Parent-of-origin effects (POEs) occur when the impact of a genetic variant depends on its parental origin. Traditionally linked to genomic imprinting, these effects are believed to have evolved from p...
www.medrxiv.org
January 21, 2025 at 1:52 PM
🚨 Preprint update!
We expanded our study on parent-of-origin effects with new findings from the MoBa cohort, now leveraging up to 265,000 individuals!
Discover fresh insights into the genetic architecture of early growth!
Updated preprint: www.medrxiv.org/content/10.1...
We expanded our study on parent-of-origin effects with new findings from the MoBa cohort, now leveraging up to 265,000 individuals!
Discover fresh insights into the genetic architecture of early growth!
Updated preprint: www.medrxiv.org/content/10.1...
Reposted by Natsuhiko Kumasaka
Check out our scPrediXcan paper
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework
Zhou et al. introduce scPrediXcan, a novel transcriptome-wide association study framework
that integrates the deep learning-based model ctPred for cell-type-specific expression
prediction. Applied to ...
www.cell.com
May 14, 2025 at 10:41 PM
Check out our scPrediXcan paper
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
Reposted by Natsuhiko Kumasaka
📣📣 Thrilled to see this cool work finally out in the wild! "Genome-wide analyses of variance in blood cell phenotypes provide new insights into complex trait biology & prediction" www.nature.com/articles/s41...
Loads of cool findings including MR for alcohol usage -> increased variance in BC traits
Loads of cool findings including MR for alcohol usage -> increased variance in BC traits
May 7, 2025 at 7:21 PM
📣📣 Thrilled to see this cool work finally out in the wild! "Genome-wide analyses of variance in blood cell phenotypes provide new insights into complex trait biology & prediction" www.nature.com/articles/s41...
Loads of cool findings including MR for alcohol usage -> increased variance in BC traits
Loads of cool findings including MR for alcohol usage -> increased variance in BC traits
Reposted by Natsuhiko Kumasaka
Nice! Environmentally responsive eQTLs are enriched for being more distal and for constrained genes relative to conventional QTLs.
May 5, 2025 at 7:28 PM
Nice! Environmentally responsive eQTLs are enriched for being more distal and for constrained genes relative to conventional QTLs.
Reposted by Natsuhiko Kumasaka
Very excited to share our preprint led by M. Levin @skoyama.bsky.social J. Woerner & with S. Damrauer assessing genome-wide pleiotropy of >1,000 clinical traits across ~1.7M individuals with nearly 30K locus-trait associations!
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
April 23, 2025 at 11:35 AM
Very excited to share our preprint led by M. Levin @skoyama.bsky.social J. Woerner & with S. Damrauer assessing genome-wide pleiotropy of >1,000 clinical traits across ~1.7M individuals with nearly 30K locus-trait associations!
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
www.medrxiv.org/content/10.1... @medrxivpreprint.bsky.social
Reposted by Natsuhiko Kumasaka
I proudly advocate for 2002 as the year GWAS began 🙂
www.nature.com/articles/ng1...
www.nature.com/articles/ng1...
Functional SNPs in the lymphotoxin-α gene that are associated with susceptibility to myocardial infarction - Nature Genetics
Nature Genetics - Functional SNPs in the lymphotoxin-α gene that are associated with susceptibility to myocardial infarction
www.nature.com
April 18, 2025 at 12:29 PM
I proudly advocate for 2002 as the year GWAS began 🙂
www.nature.com/articles/ng1...
www.nature.com/articles/ng1...
Reposted by Natsuhiko Kumasaka
📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1...
🧵👇 (1/n)
🧵👇 (1/n)
March 24, 2025 at 7:47 AM
📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1...
🧵👇 (1/n)
🧵👇 (1/n)
Reposted by Natsuhiko Kumasaka
Looks like a nice resource:
* Array genetic data for 80,638 Japanese children
* 1,163 child health and developmental traits (e.g. food allergy, anthropometric, developmental)
* Parental environmental exposures
www.medrxiv.org/content/10.1...
* Array genetic data for 80,638 Japanese children
* 1,163 child health and developmental traits (e.g. food allergy, anthropometric, developmental)
* Parental environmental exposures
www.medrxiv.org/content/10.1...
March 10, 2025 at 10:18 AM
Looks like a nice resource:
* Array genetic data for 80,638 Japanese children
* 1,163 child health and developmental traits (e.g. food allergy, anthropometric, developmental)
* Parental environmental exposures
www.medrxiv.org/content/10.1...
* Array genetic data for 80,638 Japanese children
* 1,163 child health and developmental traits (e.g. food allergy, anthropometric, developmental)
* Parental environmental exposures
www.medrxiv.org/content/10.1...
Thrilled to share that our paper has been accepted to #ESHG2025 as an oral presentation!
bsky.app/profile/nats...
bsky.app/profile/nats...
I'm delighted to present our nationwide effort to identify genetic determinants of child health and development in Japan.
Preprint: www.medrxiv.org/content/10.1...
Preprint: www.medrxiv.org/content/10.1...
March 20, 2025 at 1:14 PM
Thrilled to share that our paper has been accepted to #ESHG2025 as an oral presentation!
bsky.app/profile/nats...
bsky.app/profile/nats...
Reposted by Natsuhiko Kumasaka
📣 New from the lab: The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes www.nature.com/articles/s41...
Check out the INTERVAL RNAseq portal www.intervalrna.org.uk
Led by @alextokolyi.bsky.social & Elodie Persyn!
Check out the INTERVAL RNAseq portal www.intervalrna.org.uk
Led by @alextokolyi.bsky.social & Elodie Persyn!
March 4, 2025 at 10:27 AM
📣 New from the lab: The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes www.nature.com/articles/s41...
Check out the INTERVAL RNAseq portal www.intervalrna.org.uk
Led by @alextokolyi.bsky.social & Elodie Persyn!
Check out the INTERVAL RNAseq portal www.intervalrna.org.uk
Led by @alextokolyi.bsky.social & Elodie Persyn!
Reposted by Natsuhiko Kumasaka
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Modelling and design of transcriptional enhancers - Nature Reviews Bioengineering
Enhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to unravel the rules underlying enhancer activit...
www.nature.com
February 28, 2025 at 2:45 PM
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Reposted by Natsuhiko Kumasaka
studies of regulatory variation and GxE interactions in the heart. here's the preprint: www.biorxiv.org/content/10.1...
Guided Differentiation of Pluripotent Stem Cells into Heterogeneously Differentiating Cultures of Cardiac Cells
In principle, induced pluripotent stem cells (iPSCs) can differentiate into any cell type in the body. The challenge is to find a way to rapidly expand the dimensionality of cell types and cell states...
www.biorxiv.org
February 26, 2025 at 8:29 PM
studies of regulatory variation and GxE interactions in the heart. here's the preprint: www.biorxiv.org/content/10.1...
Reposted by Natsuhiko Kumasaka
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 12:13 AM
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
Reposted by Natsuhiko Kumasaka
📢 Thrilled to see this out, an atlas of e/sQTL across multiple tissues and diverse ancestries in 14,324 TOPMed participants: www.medrxiv.org/content/10.1...
Grateful to the #TOPMed #Omics WG for giving me an opportunity to learn and contribute to this important work 🧬
Grateful to the #TOPMed #Omics WG for giving me an opportunity to learn and contribute to this important work 🧬
Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed
Most genetic variants associated with complex traits and diseases occur in non-coding genomic regions and are hypothesized to regulate gene expression. To understand the genetics underlying gene expre...
www.medrxiv.org
February 25, 2025 at 8:48 PM
📢 Thrilled to see this out, an atlas of e/sQTL across multiple tissues and diverse ancestries in 14,324 TOPMed participants: www.medrxiv.org/content/10.1...
Grateful to the #TOPMed #Omics WG for giving me an opportunity to learn and contribute to this important work 🧬
Grateful to the #TOPMed #Omics WG for giving me an opportunity to learn and contribute to this important work 🧬
I'm delighted to present our nationwide effort to identify genetic determinants of child health and development in Japan.
Preprint: www.medrxiv.org/content/10.1...
Preprint: www.medrxiv.org/content/10.1...
February 26, 2025 at 12:18 AM
I'm delighted to present our nationwide effort to identify genetic determinants of child health and development in Japan.
Preprint: www.medrxiv.org/content/10.1...
Preprint: www.medrxiv.org/content/10.1...