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
Acellular, bioresorbable, ultra-purified alginate gel implantation for intervertebral disc herniation: Phase 1/2, open-label, non-randomized clinical trials

An acellular, bioresorbable, ultra-purified alginate gel implantation system to prevent lumbar intervertebral disc (IVD) degeneration after discectomy demonstrated its feasibility and safety in phase 1/2 clinical trials for herniated intervertebral disc degeneration.

Katsuhisa Yamada
Takahiko Hyakumachi
Hideki Sudo
ResearchOpen Access08 May 2025
Nature Communications

Volume: 16, P: 1-13
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
Mapping the human genetic architecture of COVID-19

A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

Mari E. K. Niemi
Juha Karjalainen
Chloe Donohue
ResearchOpen Access08 Jul 2021
Nature

Volume: 600, P: 472-477
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
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
Three-dimensional visualization of the total mesorectal excision plane for dissection in rectal cancer surgery and its ability to predict surgical difficulty

Yuzo Nagai
Kazushige Kawai
Soichiro Ishihara
ResearchOpen Access06 Feb 2023
Scientific Reports

Volume: 13, P: 1-8
Structural basis for cofilin binding and actin filament disassembly

Cofilin is a small actin-binding protein that accelerates actin turnover by disassembling actin filaments. Here the authors present the 3.8 Å cryo-EM structure of a cofilin-decorated actin filament and discuss mechanistic implications.

Kotaro Tanaka
Shuichi Takeda
Akihiro Narita
ResearchOpen Access10 May 2018
Nature Communications

Volume: 9, P: 1-12
A second update on mapping the human genetic architecture of COVID-19

Masahiro Kanai
Shea J. Andrews
Matthew Solomonson
ResearchOpen Access06 Sept 2023
Nature

Volume: 621, P: E7-E26
Post-extubation dysphagia in pediatric trauma patients: a single-center case-series study

Naoki Yogo
Takeru Abe
Katsuki Hirai
ResearchOpen Access12 Feb 2024
Scientific Reports

Volume: 14, P: 1-6
Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy

This study identifies TTTCA- and TTTTA-repeat expansions in benign adult familial myoclonic epilepsy. Cortical neurons from affected people exhibit RNA foci containing these expanded repeats, suggesting RNA toxicity as the mechanism underlying disease pathogenesis.

Hiroyuki Ishiura
Koichiro Doi
Shoji Tsuji
Research05 Mar 2018
Nature Genetics

Volume: 50, P: 581-590
Association of variations in HLA class II and other loci with susceptibility to EGFR-mutated lung adenocarcinoma

EGFR mutations in lung adenocarcinoma are more frequent in East Asians compared to other populations. Here, the authors carry out a genome-wide association study in EGFRmutant cancers and identify loci that are associated with risk of developing this molecular subtype of cancer.

Kouya Shiraishi
Yukinori Okada
Takashi Kohno
ResearchOpen Access09 Aug 2016
Nature Communications

Volume: 7, P: 1-7
In vivo deformation of anatomically pre-bent rods in thoracic adolescent idiopathic scoliosis

Hideki Sudo
Hiroyuki Tachi
Norimasa Iwasaki
ResearchOpen Access16 Jun 2021
Scientific Reports

Volume: 11, P: 1-9
Convolutional neural network for classification of two-dimensional array images generated from clinical information may support diagnosis of rheumatoid arthritis

Jun Fukae
Masato Isobe
Takao Koike
ResearchOpen Access27 Mar 2020
Scientific Reports

Volume: 10, P: 1-7
Three-dimensional depth sensor imaging to identify adolescent idiopathic scoliosis: a prospective multicenter cohort study

Terufumi Kokabu
Noriaki Kawakami
Hideki Sudo
ResearchOpen Access04 Jul 2019
Scientific Reports

Volume: 9, P: 1-8
Fusible, Elastic, and Biodegradable Polyesters of 2-Pyrone-4,6-Dicarboxylic Acid (PDC)

Tsuyoshi Michinobu
Masami Bito
Kiyotaka Shigehara
Research09 Oct 2009
Polymer Journal

Volume: 41, P: 1111-1116
Rapid diagnosis of lymph node metastasis in breast cancer using a new fluorescent method with γ-glutamyl hydroxymethyl rhodamine green

Yoshiaki Shinden
Hiroki Ueo
Koshi Mimori
ResearchOpen Access09 Jun 2016
Scientific Reports

Volume: 6, P: 1-7
Preliminary analysis of the Hayabusa2 samples returned from C-type asteroid Ryugu

The Hayabusa2 spacecraft returned 5.4 g of material from the asteroid Ryugu. A first analysis of the samples found an estimated density of 1,282 ± 231 kg m⁻³, considerably lower than even the most porous meteorites. Together with preliminary spectral analysis, these results indicate that Ryugu is similar to CI chondrites, but darker, more porous and more brittle.

Toru Yada
Masanao Abe
Yuichi Tsuda
ResearchOpen Access20 Dec 2021
Nature Astronomy

Volume: 6, P: 214-220
Characterization of polychaetes inhabiting estuaries and inner bays by composition analysis of amino acids and lactate enantiomers

Mayu Onozato
Wataru Shinohara
Takeshi Fukushima
ResearchOpen Access06 Mar 2024
Scientific Reports

Volume: 14, P: 1-11
Age-related differences in the survival benefit of the administration of antithrombin, recombinant human thrombomodulin, or their combination in sepsis

Takeshi Wada
Kazuma Yamakawa
Satoshi Gando
ResearchOpen Access03 Jun 2022
Scientific Reports

Volume: 12, P: 1-10
Four-dimensional anatomical spinal reconstruction using pre-bent rods in thoracic adolescent idiopathic scoliosis

Akira Fukushima
Takashi Ohnishi
Hideki Sudo
ResearchOpen Access02 Jan 2025
Scientific Reports

Volume: 15, P: 1-9
Validation of the obesity paradox by body mass index and waist circumference in patients undergoing percutaneous coronary intervention

Yuichiro Shirahama
Noriaki Tabata
Junichi Matsubara
Research28 Jul 2022
International Journal of Obesity

Volume: 46, P: 1840-1848
Frequency dispersion amplifies tsunamis caused by outer-rise normal faults

Toshitaka Baba
Naotaka Chikasada
Shuichi Kodaira
ResearchOpen Access08 Oct 2021
Scientific Reports

Volume: 11, P: 1-11
Prevalence of unilateral hyperaldosteronism in primary aldosteronism: impact of a novel chemiluminescent immunoassay for measuring plasma aldosterone in Japan

Hiroki Kobayashi
Yoshihiro Nakamura
Michio Otsuki
Research29 Jul 2024
Hypertension Research

Volume: 47, P: 3035-3044
Space weathering acts strongly on the uppermost surface of Ryugu

Samples returned from Ryugu contain fresher material than the space weathered outer asteroid surface observed by remote sensing, according to a comparison of spectral data from returned samples, orbital observations and Murchison meteorite samples.

Moe Matsuoka
Ei-ichi Kagawa
Yuichi Tsuda
ResearchOpen Access27 Sept 2023
Communications Earth & Environment

Volume: 4, P: 1-12
Development of a deep learning method for improving diagnostic accuracy for uterine sarcoma cases

Yusuke Toyohara
Kenbun Sone
Yutaka Osuga
ResearchOpen Access16 Nov 2022
Scientific Reports

Volume: 12, P: 1-11
Prognosis and diastolic dysfunction predictors in patients with heart failure and recovered ejection fraction

Takuma Takada
Katsuhisa Matsuura
Nobuhisa Hagiwara
ResearchOpen Access24 May 2022
Scientific Reports

Volume: 12, P: 1-11
Association between low body mass index and increased 28-day mortality of severe sepsis in Japanese cohorts

Takehiko Oami
Satoshi Karasawa
Yasuaki Mizushima
ResearchOpen Access15 Jan 2021
Scientific Reports

Volume: 11, P: 1-7
Disseminated intravascular coagulation immediately after trauma predicts a poor prognosis in severely injured patients

Takeshi Wada
Atsushi Shiraishi
Yasuhiro Otomo
ResearchOpen Access26 May 2021
Scientific Reports

Volume: 11, P: 1-12
Automated noninvasive detection of idiopathic scoliosis in children and adolescents: A principle validation study

Hideki Sudo
Terufumi Kokabu
Satoshi Kanai
ResearchOpen Access07 Dec 2018
Scientific Reports

Volume: 8, P: 1-10
Characteristics and outcomes of bacteremia among ICU-admitted patients with severe sepsis

Akira Komori
Toshikazu Abe
Yasuaki Mizushima
ResearchOpen Access19 Feb 2020
Scientific Reports

Volume: 10, P: 1-8
Regulation of vanillate and syringate catabolism by a MarR-type transcriptional regulator DesR in Sphingobium sp. SYK-6

Takuma Araki
Shusuke Umeda
Eiji Masai
ResearchOpen Access02 Dec 2019
Scientific Reports

Volume: 9, P: 1-15
Behavior of light elements in iron-silicate-water-sulfur system during early Earth’s evolution

Riko Iizuka-Oku
Hirotada Gotou
Hiroyuki Kagi
ResearchOpen Access24 Jun 2021
Scientific Reports

Volume: 11, P: 1-10
CD9-positive exosomes from cancer-associated fibroblasts stimulate the migration ability of scirrhous-type gastric cancer cells

Yuichiro Miki
Masakazu Yashiro
Masaichi Ohira
ResearchOpen Access13 Feb 2018
British Journal of Cancer

Volume: 118, P: 867-877
Associated factors and effects of comorbid atrial fibrillation in hypertensive patients due to primary aldosteronism

Shintaro Sakaguchi
Ryuji Okamoto
Mitsuhide Naruse
Research24 Sept 2022
Journal of Human Hypertension

Volume: 37, P: 757-766
Influence of hospital capabilities and prehospital time on outcomes of thrombectomy for stroke in Japan from 2013 to 2016

Ai Kurogi
Daisuke Onozuka
Masayuki Yokota
ResearchOpen Access28 Feb 2022
Scientific Reports

Volume: 12, P: 1-17
Solution properties of poly(N-methylethylene imine), a highly hydrophilic polycation

Poly(N-methylethylene imine) (PMEI) has a wide solubility similar to poly(ethylene oxide) and a high protonation capacity similar to poly(ethylene imine). In addition, PMEI forms aggregates with negatively charged macromolecules, such as polystyrene latex particles, and acts as either a flocculant or a dispersant depending on the environment. An aqueous solution containing the as-synthesized PMEI (weight-average molecular weight: 26 kDa) exhibited an LCST of 116 °C, and a toluene solution exhibited a UCST of 36 °C. Therefore, PMEI is expected to be used as a highly hydrophilic polycation for various applications.

Yuichiro Fukuda
Daisuke Abe
Yuji Sasanuma
Research17 Aug 2016
Polymer Journal

Volume: 48, P: 1065-1072
The tale of TILs in breast cancer: A report from The International Immuno-Oncology Biomarker Working Group

Khalid El Bairi
Harry R. Haynes
Paul J. Van Diest
ReviewsOpen Access01 Dec 2021
npj Breast Cancer

Volume: 7, P: 1-17

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