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 mitotic STAG3–cohesin complex shapes male germline nucleome

Nagano et al. identify the third mitotic cohesin complex, STAG3–cohesin, which, with its unique biophysical properties, weakens insulation and rewires regulatory interactions of spermatogonial stem cells, shaping the male germline nucleome.

Masahiro Nagano
Bo Hu
Mitinori Saitou
Research25 Aug 2025
Nature Structural & Molecular Biology

P: 1-16
Palmar dermatoglyphics of the patients with Klinefelter's syndrome (47,XXY)

Yosuke Komatz
Osamu Yoshida
Research01 Sept 1978
Japanese journal of human genetics

Volume: 23, P: 245-248
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
Terminations of palmar main lines and mainline indices in 47, XXY Klinefelter's syndrome

Yosuke Komatz
Osamu Yoshida
Research01 Dec 1977
Japanese journal of human genetics

Volume: 22, P: 281-286
Extra interphalangeal transverse creases of the little finger

Yosuke Komatz
Kazuyuki Daijo
Osamu Yoshida
Research01 Mar 1978
Japanese journal of human genetics

Volume: 23, P: 31-37
Mechanically activated switching of Si-based single-molecule junction as imaged with three-dimensional dynamic probe

Mechanically induced conformational modulation can be used to control the conductance of single molecules junctions, but it is hard to be realized due to broken junctions. Here, the authors probe three-dimensional dynamics of Si/single-molecule/Si junctions, whose conductance shows a binary change.

Miki Nakamura
Shoji Yoshida
Hidemi Shigekawa
ResearchOpen Access06 Oct 2015
Nature Communications

Volume: 6, P: 1-8
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
Real-space imaging of transient carrier dynamics by nanoscale pump–probe microscopy

By combining advanced ultrashort-pulse laser technology with scanning tunneling microscopy, scientists demonstrate that they can directly image transient carrier dynamics in nanostructures in real space.

Yasuhiko Terada
Shoji Yoshida
Hidemi Shigekawa
Research24 Oct 2010
Nature Photonics

Volume: 4, P: 869-874
A one-base deletion (183delC) and a missense mutation (D276H) in the T-protein gene from a Japanese family with nonketotic hyperglycinemia

S. Kure
Toshikatsu Shinka
Kuniaki Narisawa
Research01 Jun 1998
Journal of Human Genetics

Volume: 43, P: 135-137
An unbiased tissue transcriptome analysis identifies potential markers for skin phenotypes and therapeutic responses in atopic dermatitis

Atopic dermatitis (AD) with complex manifestations and genetic associations. Here the author profile the transcriptome of 951 skin samples from patients with AD to link skin phenotypes, clinical severity, and efficacy of dupilumab treatment to specific types of immune responses and gene features to serve clues for personalized medicine.

Ayano Fukushima-Nomura
Hiroshi Kawasaki
Masayuki Amagai
ResearchOpen Access02 Jun 2025
Nature Communications

Volume: 16, P: 1-22
Ha-ras oncogenes are activated by somatic alterations in human urinary tract tumours

Jun Fujita
Osamu Yoshida
Stuart A. Aaronson
Research31 May 1984
Nature

Volume: 309, P: 464-466
In situ 3D crystallographic characterization of deformation-induced martensitic transformation in a metastable Fe–Cr–Ni austenitic alloy by X-ray microtomography

Osamu Takakuwa
Tatsuya Iwano
Masayuki Uesugi
ResearchOpen Access24 Jun 2024
Scientific Reports

Volume: 14, P: 1-7
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
Association between bowel movement frequency and erectile dysfunction in patients with ulcerative colitis: a cross-sectional study

Shinya Furukawa
Teruki Miyake
Yoichi Hiasa
Research08 Apr 2024
International Journal of Impotence Research

Volume: 37, P: 139-144
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
L1 family of repetitive DNA sequences in primates may be derived from a sequence encoding a reverse transcriptase-related protein

Masahira Hattori
Satoru Kuhara
Yoshiyuki Sakaki
Research05 Jun 1986
Nature

Volume: 321, P: 625-628
Structural insights into the mechanism of rhodopsin phosphodiesterase

Rhodopsin phosphodiesterase (Rh-PDE) hydrolyzes both cAMP and cGMP in a light-dependent manner. Structural and functional analyses of the Rh-PDE from Salpingoeca rosetta reveal unusual rhodopsin topology comprising 8 transmembrane helices (TMs) and suggest that TM0 plays a crucial role in the enzymatic photoactivity.

Tatsuya Ikuta
Wataru Shihoya
Osamu Nureki
ResearchOpen Access05 Nov 2020
Nature Communications

Volume: 11, P: 1-12
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
Association between allergic diseases and mucosal healing in ulcerative colitis

Yasunori Yamamoto
Shinya Furukawa
Yoichi Hiasa
ResearchOpen Access08 Jan 2025
Scientific Reports

Volume: 15, P: 1-7
Removal of Diazonaphthoquinone/Novolak Resist Using UV Laser (266 nm)

Hideo Horibe
Tomosumi Kamimura
Kunio Yoshida
Research07 Nov 2005
Polymer Journal

Volume: 37, P: 813-817
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
Effect of texture and color enhancement imaging on the visibility of gastric tumors

Hiroaki Sakai
Naoto Iwai
Yoshito Itoh
ResearchOpen Access18 Aug 2024
Scientific Reports

Volume: 14, P: 1-8
Microscopic basis for the band engineering of Mo_1−xW_xS₂-based heterojunction

Shoji Yoshida
Yu Kobayashi
Hidemi Shigekawa
ResearchOpen Access07 Oct 2015
Scientific Reports

Volume: 5, P: 1-6
Small-Angle X-Ray Scattering of Poly(tetraoxane) Obtained by the Radiation-Induced Solid-State Polymerization

Yoshiaki Nakase
Toshio Kato
Akira Odajima
Research01 Nov 1977
Polymer Journal

Volume: 9, P: 605-611
Structure and mechanism of the mammalian fructose transporter GLUT5

This study has determined the X-ray crystal structures of GLUT5 from Rattus norvegicus in an open, outward-facing conformation and GLUT5 from Bos taurus in an open, inward-facing conformation; comparison of these structures with previously published structures of the related Escherichia coli d-xylose:H⁺ symporter XylE suggests that transport in GLUT5 is controlled by both a global ‘rocker-switch’-type motion and a local ‘gated-pore’-type transport mechanism.

Norimichi Nomura
Grégory Verdon
David Drew
Research30 Sept 2015
Nature

Volume: 526, P: 397-401
Structure and dynamics of the pyroglutamylated RF-amide peptide QRFP receptor GPR103

GPR103, a GPCR activated by pyroglutamylated RF-amide peptide QRFP, has various physiological functions, such as energy metabolism and appetite regulation. Here, the authors determined the cryoEM structure of the QRFP26- GPR103-Gq complex, revealing its peptide recognition mechanism.

Aika Iwama
Ryoji Kise
Osamu Nureki
ResearchOpen Access19 Jun 2024
Nature Communications

Volume: 15, P: 1-13
Nanoscale terahertz spectroscopy

The advent of terahertz spectroscopy schemes that offer single-photon sensitivity, femtosecond time resolution and nanometre spatial resolution is creating new opportunities for investigating ultrafast charge dynamics in semiconductor structures.

Hidemi Shigekawa
Shoji Yoshida
Osamu Takeuchi
News & Views31 Oct 2014
Nature Photonics

Volume: 8, P: 815-817
Randomized study of two endo-knives for the traction-assisted endoscopic submucosal dissection of early esophageal squamous cell carcinoma

Yoshiyasu Kitagawa
Asuka Ishigaki
Takuto Suzuki
ResearchOpen Access17 Mar 2022
Scientific Reports

Volume: 12, P: 1-8
Probing ultrafast spin dynamics with optical pump–probe scanning tunnelling microscopy

Spin dynamics in semiconductor heterostructures can be probed by a modified scanning tunnelling microscopy technique with a temporal resolution of a few picoseconds.

Shoji Yoshida
Yuta Aizawa
Hidemi Shigekawa
Research29 Jun 2014
Nature Nanotechnology

Volume: 9, P: 588-593
Structural insights into ligand recognition by the lysophosphatidic acid receptor LPA₆

Determination of the crystal structure of the zebrafish LPA₆ receptor shows that the lipid ligand binds to an unusual ligand-binding pocket in the receptor that is laterally accessible through the membrane.

Reiya Taniguchi
Asuka Inoue
Osamu Nureki
Research09 Aug 2017
Nature

Volume: 548, P: 356-360
Direct Evidence for Main Chain Scissions of Polymers in Solution Caused by High Speed Stirring

Masayoshi Tabata
Yoichi Hosokawa
Junkichi Sohma
Research01 Oct 1986
Polymer Journal

Volume: 18, P: 699-712
Endothelial PI3K-C2α, a class II PI3K, has an essential role in angiogenesis and vascular barrier function

Although type I phosphatidylinositol 3-kinases (PI3Ks) are well studied signaling proteins, the functions of other PI3Ks are more enigmatic. Kazuaki Yoshioka et al. find that the type II PI3K-2α isoform regulates endosomal trafficking and cell signaling in endothelial cells. Angiogenic and vascular permeability responses are attenuated in mice lacking PI3K-2α, pointing to this enzyme as a potential target for treating vascular disease.

Kazuaki Yoshioka
Kotaro Yoshida
Yoh Takuwa
Research16 Sept 2012
Nature Medicine

Volume: 18, P: 1560-1569
Identifying the origin of nitrous oxide dissolved in deep ocean by concentration and isotopocule analyses

Sakae Toyoda
Osamu Yoshida
Shuichi Watanabe
ResearchOpen Access24 May 2019
Scientific Reports

Volume: 9, P: 1-9
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
Frequent mutations that converge on the NFKBIZ pathway in ulcerative colitis

In patients with ulcerative colitis, chronic inflammation can lead to remodelling of the colorectal epithelium through positive selection of clones with mutations in genes related to IL-17 signalling, which, however, might be negatively selected during colitis-associated carcinogenesis.

Nobuyuki Kakiuchi
Kenichi Yoshida
Seishi Ogawa
Research18 Dec 2019
Nature

Volume: 577, P: 260-265
Soft chromophore featured liquid porphyrins and their utilization toward liquid electret applications

Though electret materials are attractive for realizing flexible mechanoelectrical devices, these materials are typically solid films. Here, the authors report stretchable ‘liquid-electret’ devices consisting solvent-free liquid porphyrins that show piezoelectric and electroacoustic functionality.

Avijit Ghosh
Manabu Yoshida
Takashi Nakanishi
ResearchOpen Access30 Sept 2019
Nature Communications

Volume: 10, P: 1-9
Possible Formation of Living Polymers of p-Methoxystyrene by Iodine

Toshinobu Higashimura
Osamu Kishiro
Research01 Jan 1977
Polymer Journal

Volume: 9, P: 87-93
Lamellar Structure in Poly(tetraoxane) Obtained by the Radiation-Induced Polymerization in the Solid State

Toshio Kato
Yoshiaki Nakase
Akira Odajima
Research01 Jul 1976
Polymer Journal

Volume: 8, P: 331-339
Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases

Genome-wide analysis in 212,453 Japanese individuals identifies loci associated with 42 diseases. Comparative analysis with European populations identifies East Asian–specific associations.

Kazuyoshi Ishigaki
Masato Akiyama
Yoichiro Kamatani
Research08 Jun 2020
Nature Genetics

Volume: 52, P: 669-679
Blood pressure during long-term cilostazol-based dual antiplatelet therapy after stroke: a post hoc analysis of the CSPS.com trial

Kazunori Toyoda
Masatoshi Koga
Hiroaki Tanaka
ResearchOpen Access09 Jul 2024
Hypertension Research

Volume: 47, P: 2238-2249
Alternative splicing of CD44 mRNA by ESRP1 enhances lung colonization of metastatic cancer cell

CD44 is a cell surface protein that is a marker for stem cell-like cancer cells and has a role in invasion and metastasis. Here, epithelial splicing regulatory protein 1 is shown to generate a CD44 variant protein that enhances metastasis in a mouse model and protects cells from oxidative stress.

Toshifumi Yae
Kenji Tsuchihashi
Osamu Nagano
Research06 Jun 2012
Nature Communications

Volume: 3, P: 1-9
Partially hydrolyzed guar gum increased colonic mucus layer in mice via succinate-mediated MUC2 production

Mariko Kajiwara-Kubota
Kazuhiko Uchiyama
Yuji Naito
ResearchOpen Access28 Mar 2023
npj Science of Food

Volume: 7, P: 1-7
Protein kinase R regulates pancreatic ductal adenocarcinoma progression by modulating the cell cycle via GADD45A

Yuki Numata
Mitsuhito Koizumi
Yoichi Hiasa
ResearchOpen Access10 Jul 2025
Scientific Reports

Volume: 15, P: 1-12
Identification of trypsin-degrading commensals in the large intestine

Colonization of trypsin-degrading commensal bacteria may contribute to the maintenance of intestinal homeostasis and protection against pathogen infection in humans and mice.

Youxian Li
Eiichiro Watanabe
Kenya Honda
ResearchOpen Access07 Sept 2022
Nature

Volume: 609, P: 582-589
Usefulness of circulating tumor DNA by targeting human papilloma virus-derived sequences as a biomarker in p16-positive oropharyngeal cancer

Ken Akashi
Toshihiko Sakai
Tatsuya Yamasoba
ResearchOpen Access12 Jan 2022
Scientific Reports

Volume: 12, P: 1-7
Author Correction: Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Yoshiki Tanaka
Christopher J. Hipolito
Osamu Nureki
Amendments and Corrections30 Jan 2020
Nature

Volume: 578, P: E19
A prospective, randomized, double-blind, placebo-controlled trial of the Kampo formula daiobotanpito combined with antibiotic therapy for acute diverticulitis

Keiko Ogawa-Ochiai
Shigetsugu Tsuji
Hideki Ishikawa
ResearchOpen Access01 Jul 2025
Scientific Reports

Volume: 15, P: 1-10

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