Nature Search

Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD

A comprehensive analysis of the cell-specific molecular regulatory mechanisms underlying post-traumatic stress disorder in the human prefrontal cortex.

Ahyeon Hwang
Mario Skarica
Matthew J. Girgenti
ResearchOpen Access18 Jun 2025
Nature

Volume: 643, P: 744-754
SANTO: a coarse-to-fine alignment and stitching method for spatial omics

Spatial omics technologies require alignment and stitching of slices for a 3D molecular profile. Here, the authors present SANTO, a coarse-to-fine method that rapidly determines spatial positions and overlap regions, then refines them, enabling integration across platforms and modalities.

Haoyang Li
Yingxin Lin
Xin Gao
ResearchOpen Access18 Jul 2024
Nature Communications

Volume: 15, P: 1-12
A CD26⁺ tendon stem progenitor cell population contributes to tendon repair and heterotopic ossification

Chen, et al identify peritendon CD26 expressing tendon stem/progenitor cells that contribute to tendon healing, as well as Tenascin-C/YAP dependent heterotopic ossification.

Siwen Chen
Yingxin Lin
Hui Liu
ResearchOpen Access16 Jan 2025
Nature Communications

Volume: 16, P: 1-18
scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links

Single-cell multi-omics integration is challenged by varied feature relationships and modality-specific limitations. Here, the authors present scMODAL, a deep learning framework that leverages known feature links to align single-cell omics, enabling accurate integration and downstream analyses.

Gefei Wang
Jia Zhao
Hongyu Zhao
ResearchOpen Access29 May 2025
Nature Communications

Volume: 16, P: 1-13
BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data

Subcellular in situ spatial transcriptomics offers the promise to address biological problems that were previously inaccessible but requires accurate cell segmentation to uncover insights. Here, authors present BIDCell, a biologically informed, deep learning-based cell segmentation framework.

Xiaohang Fu
Yingxin Lin
Jean Y. H. Yang
ResearchOpen Access13 Jan 2024
Nature Communications

Volume: 15, P: 1-17
Genome of a novel Fangshan bunya-like virus identified in mosquitoes from Shandong Province, China

Yuli Zhang
Yujie Liu
Yujing Zhu
ResearchOpen Access26 Aug 2025
Scientific Reports

Volume: 15, P: 1-13
scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning

Integration of data from single-cell RNA-seq and ATAC-seq is achieved with transfer learning.

Yingxin Lin
Tung-Yu Wu
Y. X. Rachel Wang
Research20 Jan 2022
Nature Biotechnology

Volume: 40, P: 703-710
Study on Phenolic Resins Modified by Copper Nanoparticles

Ronghui Lin
Liang Fang
Ping Sun
Reviews15 Feb 2006
Polymer Journal

Volume: 38, P: 178-183
Ferritin-mediated mitochondrial iron homeostasis is essential for the survival of hematopoietic stem cells and leukemic stem cells

Weiwei Yi
Jinhua Zhang
Zhiyang Chen
Research24 Feb 2024
Leukemia

Volume: 38, P: 1003-1018
Investigating higher-order interactions in single-cell data with scHOT

scHOT enables detection of changes in higher-order interactions in single-cell gene expression data.

Shila Ghazanfar
Yingxin Lin
Jean Yee Hwa Yang
Research13 Jul 2020
Nature Methods

Volume: 17, P: 799-806
Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2

Recent advances in multi-condition single-cell multi-cohort studies enable exploration of diverse cell states. Here, authors present scMerge2, an algorithm that allows integration of a large COVID-19 data collection with over five million cells to uncover distinct signatures of disease progression.

Yingxin Lin
Yue Cao
Jean Y. H. Yang
ResearchOpen Access17 Jul 2023
Nature Communications

Volume: 14, P: 1-13
STV11 encodes a sulphotransferase and confers durable resistance to rice stripe virus

Rice stripe virus (RSV) causes a disease in rice with significant economic consequences. Here, the authors clone an RSV-resistant gene in rice and suggest that this gene encodes a sulphotransferase that catalyses the conversion of salicylic acid (SA) into sulphonated salicylic acid, leading to increased SA accumulation in RSV-infected plants and inhibition of viral replication.

Qi Wang
Yuqiang Liu
Jianmin Wan
ResearchOpen Access09 Sept 2014
Nature Communications

Volume: 5, P: 1-8
Functional and morphologic study of retinal hypoperfusion injury induced by bilateral common carotid artery occlusion in rats

Yali Qin
Meiqi Ji
Ming Jin
ResearchOpen Access14 Jan 2019
Scientific Reports

Volume: 9, P: 1-10
3D reconstruction of spatial expression

A novel approach to probabilistically align adjacent multiple tissue slices from spatially resolved transcriptomics data provides unprecedented depth for the investigation of tissue architecture and paves the way for new developments in 3D spatial analytics.

Yingxin Lin
Jean Y. H. Yang
News & Views16 May 2022
Nature Methods

Volume: 19, P: 526-527
Monolithic integration of a lithium niobate microresonator with a free-standing waveguide using femtosecond laser assisted ion beam writing

Zhiwei Fang
Yingxin Xu
Ya Cheng
ResearchOpen Access30 Mar 2017
Scientific Reports

Volume: 7, P: 1-6
Fabrication of high-Q lithium niobate microresonators using femtosecond laser micromachining

Jintian Lin
Yingxin Xu
Ya Cheng
ResearchOpen Access28 Jan 2015
Scientific Reports

Volume: 5, P: 1-4
Uncovering cell identity through differential stability with Cepo

Defining cell identity is a fundamental task in dissecting the cellular heterogeneity in single-cell data. Here the authors developed Cepo, a method to uncover cell identity genes and enhance the retrieval of cellular identities from scRNA-seq data.

Hani Jieun Kim
Kevin Wang
Pengyi Yang
Research20 Dec 2021
Nature Computational Science

Volume: 1, P: 784-790
Limits on the luminance of dark matter from xenon recoil data

A direct search for effective electromagnetic interactions between dark matter and xenon nuclei that produce a recoil of the latter is carried out and the first constraint on charge radius of dark matter is derived.

Xuyang Ning
Abdusalam Abdukerim
Yubo Zhou
Research17 May 2023
Nature

Volume: 618, P: 47-50
NCAPH, ubiquitinated by TRIM21, promotes cell proliferation by inhibiting autophagy of cervical cancer through AKT/mTOR dependent signaling

Shiqi Wang
Xiaowen Qiao
Xiao Wang
ResearchOpen Access06 Aug 2024
Cell Death & Disease

Volume: 15, P: 1-16
Longitudinal association of carotid endothelial shear stress with renal function decline in aging adults with normal renal function: A population-based cohort study

Yingxin Zhao
Yuanli Dong
Zhendong Liu
ResearchOpen Access14 Feb 2019
Scientific Reports

Volume: 9, P: 1-11
Nature-based Solutions can help restore degraded grasslands and increase carbon sequestration in the Tibetan Plateau

Ecological restoration projects are expected to increase the terrestrial carbon sink of Tibetan Plateau grassland ecosystems by 15 to 21 tetragrams of carbon by 2060, under high to low emissions scenarios, according to a meta-analysis and model simulations over the period 1960-2100.

Jian Sun
Yingxin Wang
Bojie Fu
ResearchOpen Access26 Mar 2024
Communications Earth & Environment

Volume: 5, P: 1-12
simKAP: simulation framework for the kidney allocation process with decision making model

Yunwei Zhang
Anne Hu
Jean Yee Hwa Yang
ResearchOpen Access29 Sept 2023
Scientific Reports

Volume: 13, P: 1-9
Differential gene expression analysis of ‘Chili’ (Pyrus bretschneideri) fruit pericarp with two types of bagging treatments

Yuling Wang
Xinfu Zhang
Shaolan Yang
ResearchOpen Access08 Mar 2017
Horticulture Research

Volume: 4, P: 1-10
In vitro biomimetic platforms featuring a perfusion system and 3D spheroid culture promote the construction of tissue-engineered corneal endothelial layers

Shanyi Li
Yuting Han
Jiansu Chen
ResearchOpen Access10 Apr 2017
Scientific Reports

Volume: 7, P: 1-17
H⁺-type and OH⁻-type biological protonic semiconductors and complementary devices

Yingxin Deng
Erik Josberger
Marco Rolandi
ResearchOpen Access03 Oct 2013
Scientific Reports

Volume: 3, P: 1-9
Nanomedicine-induced programmed cell death in cancer therapy: mechanisms and perspectives

Lin Luobin
He Wanxin
Li Huaqin
ReviewsOpen Access29 Aug 2024
Cell Death Discovery

Volume: 10, P: 1-13
Association between body mass index and semen quality: a systematic review and meta-analysis

Yingxin Li
Yi Lin
Yuewei Liu
Reviews13 Jul 2024
International Journal of Obesity

Volume: 48, P: 1383-1401
Effects of sartans and low-dose statins on cerebral white matter hyperintensities and cognitive function in older patients with hypertension: a randomized, double-blind and placebo-controlled clinical trial

Hua Zhang
Yi Cui
Zhendong Liu
Research14 Dec 2018
Hypertension Research

Volume: 42, P: 717-729
Structural basis of the activation of metabotropic glutamate receptor 3

Wei Fang
Fan Yang
Jianfeng Liu
CorrespondenceOpen Access02 Mar 2022
Cell Research

Volume: 32, P: 695-698
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data

Daniel Kim
Andy Tran
Pengyi Yang
ReviewsOpen Access19 Oct 2023
npj Systems Biology and Applications

Volume: 9, P: 1-13

Search

Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD

SANTO: a coarse-to-fine alignment and stitching method for spatial omics

A CD26⁺ tendon stem progenitor cell population contributes to tendon repair and heterotopic ossification

scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links

BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data

Genome of a novel Fangshan bunya-like virus identified in mosquitoes from Shandong Province, China

scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning

Study on Phenolic Resins Modified by Copper Nanoparticles

Ferritin-mediated mitochondrial iron homeostasis is essential for the survival of hematopoietic stem cells and leukemic stem cells

Investigating higher-order interactions in single-cell data with scHOT

Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2

STV11 encodes a sulphotransferase and confers durable resistance to rice stripe virus

Functional and morphologic study of retinal hypoperfusion injury induced by bilateral common carotid artery occlusion in rats

3D reconstruction of spatial expression

Monolithic integration of a lithium niobate microresonator with a free-standing waveguide using femtosecond laser assisted ion beam writing

Fabrication of high-Q lithium niobate microresonators using femtosecond laser micromachining

Uncovering cell identity through differential stability with Cepo

Limits on the luminance of dark matter from xenon recoil data

NCAPH, ubiquitinated by TRIM21, promotes cell proliferation by inhibiting autophagy of cervical cancer through AKT/mTOR dependent signaling

Longitudinal association of carotid endothelial shear stress with renal function decline in aging adults with normal renal function: A population-based cohort study

Nature-based Solutions can help restore degraded grasslands and increase carbon sequestration in the Tibetan Plateau

simKAP: simulation framework for the kidney allocation process with decision making model

Differential gene expression analysis of ‘Chili’ (Pyrus bretschneideri) fruit pericarp with two types of bagging treatments

In vitro biomimetic platforms featuring a perfusion system and 3D spheroid culture promote the construction of tissue-engineered corneal endothelial layers

H⁺-type and OH⁻-type biological protonic semiconductors and complementary devices

Nanomedicine-induced programmed cell death in cancer therapy: mechanisms and perspectives

Association between body mass index and semen quality: a systematic review and meta-analysis

Effects of sartans and low-dose statins on cerebral white matter hyperintensities and cognitive function in older patients with hypertension: a randomized, double-blind and placebo-controlled clinical trial

Structural basis of the activation of metabotropic glutamate receptor 3

Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data

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