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Natsuhiko Kumasaka

@natsuhiko83.bsky.social
36 followers 57 following 11 posts

Professor, Division of Digital Genomics, Institute of Medical Science, The University of Tokyo / Team leader, National Center for Child Health and Development

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Natsuhiko Kumasaka @natsuhiko83.bsky.social · 10/09/2026
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Linda Kachuri @lindakachuri.bsky.social · 16/07/2026
📢 #TOPMed e/sQTL atlas is out in @science.org today! Happy to contribute to this amazing team effort and rich resource for the genomics community: 69k cis-eQTL + 35k cis-sQTL across 6 tissues/cell types and diverse ancestries. Still more to discover 😉🧬 www.science.org/doi/10.1126/...
science.org
Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed
Most genetic variants associated with complex traits are hypothesized to regulate gene expression. To understand the genetics underlying gene expression variability, we characterized 14,324 RNA-sequen...
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Kaur Alasoo @kauralasoo.bsky.social · 23/10/2024
Happy to share our most recent GWAS meta-analysis of 249 circulating metabolic biomarkers (Nightingale Health platform) in up to 619,372 individuals. www.medrxiv.org/content/10.1...
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Fabian Theis @fabiantheis.bsky.social · 12/05/2026
Excited to share our RegVelo paper in Cell www.cell.com/cell/fulltex... We unify RNA velocity + GRNs into one model → better OOD prediction of perturbations (e.g. gene KOs), with examples incl. neural crest KO predictions 🔬 Big thanks to W Wang, Z Hu & T Sauka-Spengler 🙏
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Michela Palamin @mpalamin.bsky.social · 24/03/2026
ChromSMF preprint is out!🚀 tinyurl.com/ChromSMF We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting! In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬 What does this unlock? ⬇️
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
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Fabian Theis @fabiantheis.bsky.social · 10/02/2026
🚀 New preprint: population-aware single-cell dynamics Collab w/ Bertie Göttgens’ lab, led by Weizhong. pseudodynamics+ goes beyond pseudotime to infer birth/death, differentiation & interpolate time in scalable fashion - directly from snapshot scRNA-seq. 👉 www.biorxiv.org/content/10.6...
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Robert Warmerdam @robertwarmerdam.bsky.social · 06/02/2026
🧬 New preprint alert! After years of collaborative work across 52 datasets we are presenting eQTLGen phase 2: a genome-wide eQTL meta-analysis covering 43,301 blood samples: www.medrxiv.org/content/10.6... (1/8)
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Kaur Alasoo @kauralasoo.bsky.social · 07/01/2026
If you like larger sample sizes, then do check out our reprocessed and fine mapped cis-eQTLs and cis-sQTLs (leafCutter and MAJIQ!) from the INTERVAL cohort (whole blood, n up to 4,729)! zenodo.org/records/1795... These will be on the eQTL Catalogue FTP soon as well. cc @yosephbarash.bsky.social
zenodo.org
Fine mapped eQTL and sQTL summary statistics from the INTERVAL RNA-seq study (part 1)
This repository contains fine mapped eQTL and sQTL summary statistics from the INTERVAL RNA-seq study (Tokolyi et al, 2025). Datasets QTD001000-QTD001002 are based on the whole cohort of 4,729 samples...
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Natsuhiko Kumasaka @natsuhiko83.bsky.social · 04/11/2025
#エコチル調査 の成果を #NHK で報道していただきました。次は遺伝子解析研究についても取り上げてもらえるよう精進していきたいと思います! news.web.nhk/newsweb/na/n...
news.web.nhk
子どもが育つ環境と健康との関連を調べた研究成果伝える催し | NHKニュース
【NHK】子どもが育つ環境と健康との関連を10年以上にわたって調べている「エコチル調査」について、調査の意義や研究成果を伝える催し
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Natsuhiko Kumasaka @natsuhiko83.bsky.social · 17/10/2025
Our group present two posters this afternoon at #ASHG2025!
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Natsuhiko Kumasaka @natsuhiko83.bsky.social · 07/10/2025
Excited to share my poster at #ASHG2025 (Board 9173F)! Can’t wait to see everyone next week!
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Kaur Alasoo @kauralasoo.bsky.social · 27/09/2025
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:
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Open Targets @opentargets.org · 26/08/2025
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
biorxiv.org
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. ...
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Adriaan @adriaan-vd-graaf.bsky.social · 04/07/2025
Our paper, MR-link-2 has just been published! Offering pleiotropy robust Mendelian randomization from a single region! www.nature.com/articles/s41...
A network of metabolites and their potential causal relationships. Green edges are Detected by the statistical causal inference method MR-link-2
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Zixuan (Eleanor) Zhang @elezzx.bsky.social · 27/01/2025
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...
medrxiv.org
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...
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Open Targets @opentargets.org · 26/06/2025
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...
UMAP of the 9 populations and 86 cell types identified after quality control and clustering
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Yoav Gilad @ygilad.bsky.social · 09/06/2025
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.
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Robin Hofmeister @rjhfmstr.bsky.social · 21/01/2025
🚨 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...
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Haky Im @hakyim.bsky.social · 14/05/2025
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.
cell.com
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 ...
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Mike Inouye @mikeinouye.bsky.social · 07/05/2025
📣📣 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
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Sasha Gusev @sashagusevposts.bsky.social · 05/05/2025
Nice! Environmentally responsive eQTLs are enriched for being more distal and for constrained genes relative to conventional QTLs.
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Pradeep Natarajan @pnatarajanmd.bsky.social · 23/04/2025
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
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Anna Cuomo @annasecuomo.bsky.social · 24/03/2025
📢 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)
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Shai Carmi @shaicarmi.bsky.social · 10/03/2025
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...
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Natsuhiko Kumasaka @natsuhiko83.bsky.social · 20/03/2025
Thrilled to share that our paper has been accepted to #ESHG2025 as an oral presentation! bsky.app/profile/nats...
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Mike Inouye @mikeinouye.bsky.social · 04/03/2025
📣 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!
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Seppe De Winter @seppedewinter.bsky.social · 28/02/2025
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...
nature.com
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...
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Yoav Gilad @ygilad.bsky.social · 26/02/2025
studies of regulatory variation and GxE interactions in the heart. here's the preprint: www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Jonathan Pritchard @jkpritch.bsky.social · 26/01/2025
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 🧵
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Linda Kachuri @lindakachuri.bsky.social · 25/02/2025
📢 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 🧬
medrxiv.org
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...
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Natsuhiko Kumasaka @natsuhiko83.bsky.social · 26/02/2025
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...
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