Nature Search

Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution

A single-cell multiomic immune cell atlas from 235 Japanese, including patients with COVID-19 and healthy individuals, linked with host genetics including germline and somatic mutation, plasma proteomics and metagenomics data reveals that immune cells are dynamically regulated in a cell state-dependent manner.

Ryuya Edahiro
Go Sato
Yukinori Okada
ResearchOpen Access28 Jul 2025
Nature Genetics

Volume: 57, P: 1905-1921
The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

Genetic mechanisms influencing COVID-19 susceptibility are not well understood. Here, the authors analyzed whole blood RNA-seq data of 465 Japanese individuals with COVID-19, highlighting thousands of fine-mapped variants affecting expression and splicing of genes, as well as the presence of COVID-19 severity-interaction eQTLs.

Qingbo S. Wang
Ryuya Edahiro
Yukinori Okada
ResearchOpen Access22 Aug 2022
Nature Communications

Volume: 13, P: 1-19
DOCK2 is involved in the host genetics and biology of severe COVID-19

A genome-wide association study highlights a variant in DOCK2, which is common in East Asian populations but rare in Europeans, as a host genetic risk factor for severe COVID-19.

Ho Namkoong
Ryuya Edahiro
Yukinori Okada
ResearchOpen Access08 Aug 2022
Nature

Volume: 609, P: 754-760
Blood DNA virome associates with autoimmune diseases and COVID-19

Analysis of the blood DNA virome in patients with COVID-19 and autoimmune disease associates endogenous HHV-6 (eHHV-6) and high anellovirus load with increased disease risk, most notably for systemic lupus erythematosus. eHHV-6 carriers show a distinct immune response.

Noah Sasa
Shohei Kojima
Yukinori Okada
ResearchOpen Access03 Jan 2025
Nature Genetics

Volume: 57, P: 65-79
Trans-ancestry mutational landscape of hepatocellular carcinoma genomes

Tatsuhiro Shibata, David Wheeler, Hiroyuki Aburatani and colleagues report the genomic, exomic and oncoviral sequencing of hundreds of liver cancers from the United States and Japan. The authors analyzed mutation patterns and identified signatures unique to the Asian cases.

Yasushi Totoki
Kenji Tatsuno
Tatsuhiro Shibata
Research02 Nov 2014
Nature Genetics

Volume: 46, P: 1267-1273
Genomic spectra of biliary tract cancer

Tatsuhiro Shibata and colleagues molecularly characterize 260 biliary tract cancer samples by a combination of exome and transcriptome sequencing. They find genomic alterations that could potentially be therapeutic targets.

Hiromi Nakamura
Yasuhito Arai
Tatsuhiro Shibata
Research10 Aug 2015
Nature Genetics

Volume: 47, P: 1003-1010
Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity

Peripheral blood mononuclear cells from 73 Japanese patients with coronavirus disease 2019 (COVID-19) and 75 healthy controls were analyzed using single-cell transcriptomics. Combining these data with genotyping data highlights the interplay between host genetics and the immune response in modulating disease severity.

Ryuya Edahiro
Yuya Shirai
Yukinori Okada
ResearchOpen Access24 Apr 2023
Nature Genetics

Volume: 55, P: 753-767
How the kinetochore couples microtubule force and centromere stretch to move chromosomes

Using mathematical simulations and a FRET tension sensor inserted into the microtubule-binding complex Ndc80, Suzuki and colleagues obtain insights into how force is generated at the budding yeast kinetochore.

Aussie Suzuki
Benjamin L. Badger
Kerry Bloom
Research14 Mar 2016
Nature Cell Biology

Volume: 18, P: 382-392
Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators

Hidewaki Nakagawa and colleagues report the whole-genome sequencing of 27 hepatocellular carcinomas. They find that chromatin regulators were mutated in approximately 50% of tumors.

Akihiro Fujimoto
Yasushi Totoki
Hidewaki Nakagawa
Research27 May 2012
Nature Genetics

Volume: 44, P: 760-764
High-resolution characterization of a hepatocellular carcinoma genome

Tatsuhiro Shibata and colleagues report the sequencing of a hepatocellular carcinoma. The authors identified 63 somatic non-synonymous substitutions and 22 somatic chromosomal rearrangements in this liver tumor.

Yasushi Totoki
Kenji Tatsuno
Tatsuhiro Shibata
Research17 Apr 2011
Nature Genetics

Volume: 43, P: 464-469
Identification and replication of sex-dimorphic protein quantitative trait loci across multiple ancestries and their associations with diseases

Youngjune Bhak
Vasilis Raptis
Albert Tenesa
ResearchOpen Access28 Aug 2025
Scientific Reports

Volume: 15, P: 1-16
Dyssegmental dysplasia Rolland–Desbuquois type is caused by pathogenic variants in HSPG2 - a founder haplotype shared in five patients

Paniz Farshadyeganeh
Takahiro Yamada
Kinji Ohno
ResearchOpen Access29 Feb 2024
Journal of Human Genetics

Volume: 69, P: 235-244
Determinants of Tenascin-C and HIV-1 envelope binding and neutralization

Riley J. Mangan
Lisa Stamper
Sallie R. Permar
Research11 Apr 2019
Mucosal Immunology

Volume: 12, P: 1004-1012
Irisin – a myth rather than an exercise-inducible myokine

Elke Albrecht
Frode Norheim
Steffen Maak
ResearchOpen Access09 Mar 2015
Scientific Reports

Volume: 5, P: 1-10

Search

Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

DOCK2 is involved in the host genetics and biology of severe COVID-19

Blood DNA virome associates with autoimmune diseases and COVID-19

Trans-ancestry mutational landscape of hepatocellular carcinoma genomes

Genomic spectra of biliary tract cancer

Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity

How the kinetochore couples microtubule force and centromere stretch to move chromosomes

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators

High-resolution characterization of a hepatocellular carcinoma genome

Identification and replication of sex-dimorphic protein quantitative trait loci across multiple ancestries and their associations with diseases

Dyssegmental dysplasia Rolland–Desbuquois type is caused by pathogenic variants in HSPG2 - a founder haplotype shared in five patients

Determinants of Tenascin-C and HIV-1 envelope binding and neutralization

Irisin – a myth rather than an exercise-inducible myokine

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