Nature Search

SON-dependent nuclear speckle rehabilitation alleviates proteinopathies

Here the authors show that rehabilitating nuclear speckles, membraneless organelles involved in mRNA processing and gene regulation, can boost protein quality control and reduce toxic protein buildup, as well as ameliorate models of diseases like tauopathy and retinal degeneration.

William Dion
Yuren Tao
Bokai Zhu
ResearchOpen Access05 Aug 2025
Nature Communications

Volume: 16, P: 1-23
A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment

The interaction between the host immune response and the component organisms forming the microbiota is critical during homeostatic but all pathological contexts. Here the authors use a multi-omics spatial approach to dissect and characterise host and microbiome in a murine model of intestinal inflammation.

Bokai Zhu
Yunhao Bai
Sizun Jiang
ResearchOpen Access31 Jan 2025
Nature Communications

Volume: 16, P: 1-20
Quantitative characterization of tissue states using multiomics and ecological spatial analysis

Multiomics and ecological spatial analysis (MESA) calculates ecodiversity-inspired metrics in spatially resolved omics integrated with single-cell data, enabling the quantitative comparison of tissue states across a range of conditions.

Daisy Yi Ding
Zeyu Tang
Garry P. Nolan
ResearchOpen Access01 Apr 2025
Nature Genetics

Volume: 57, P: 910-921
CellLENS enables cross-domain information fusion for enhanced cell population delineation in single-cell spatial omics data

In this Technical Report, the authors present CellLENS, a computational method that enhances immune cell identification and analyses by integrating cross-domain information in spatial multiomics data.

Bokai Zhu
Sheng Gao
Zongming Ma
Research22 May 2025
Nature Immunology

Volume: 26, P: 963-974
The relationship between the ratio of triglyceride to high-density lipoprotein cholesterol and left ventricular hypertrophy in Chinese hypertension adults

Jiabin Hu
Shuang Cai
Ping Zhu
ResearchOpen Access24 Apr 2025
Scientific Reports

Volume: 15, P: 1-7
Integration of spatial and single-cell data across modalities with weakly linked features

MaxFuse enables data integration between modalities even when features are weakly correlated.

Shuxiao Chen
Bokai Zhu
Zongming Ma
ResearchOpen Access07 Sept 2023
Nature Biotechnology

Volume: 42, P: 1096-1106
Robust single-cell matching and multimodal analysis using shared and distinct features

MARIO is a robust tool for accurately matching multimodal single-cell datasets.

Bokai Zhu
Shuxiao Chen
Sizun Jiang
ResearchOpen Access09 Jan 2023
Nature Methods

Volume: 20, P: 304-315
Association between insulin resistance and vascular damage in an adult population in China: a cross-sectional study

Cong Ma
Bokai Cheng
Shuxia Wang
ResearchOpen Access09 Aug 2024
Scientific Reports

Volume: 14, P: 1-8
Organization of the human intestine at single-cell resolution

Intestinal cell types are organized into distinct neighbourhoods and communities within the healthy human intestine, with distinct immunological niches.

John W. Hickey
Winston R. Becker
Michael Snyder
ResearchOpen Access19 Jul 2023
Nature

Volume: 619, P: 572-584
MAPS: pathologist-level cell type annotation from tissue images through machine learning

Current cell annotation methods using high-plex spatial proteomics data are resource intensive and demand iterative expert input. Here, the authors present MAPS (Machine learning for Analysis of Proteomics in Spatial biology), an approach that facilitates rapid and precise cell type identification with human-level accuracy from spatial proteomics data.

Muhammad Shaban
Yunhao Bai
Faisal Mahmood
ResearchOpen Access02 Jan 2024
Nature Communications

Volume: 15, P: 1-11
Full electrical manipulation of perpendicular exchange bias in ultrathin antiferromagnetic film with epitaxial strain

Manipulating exchange bias is crucial for advancing spintronic devices. Here, the authors demonstrate full electrical switching of perpendicular exchange bias in multilayers featuring an antiferromagnetic layer with anisotropic epitaxial strain.

Jie Qi
Yunchi Zhao
Shouguo Wang
ResearchOpen Access03 Jun 2024
Nature Communications

Volume: 15, P: 1-9
Leveraging large language models to assist philosophical counseling: prospective techniques, value, and challenges

Bokai Chen
Weiwei Zheng
Xiaojun Ding
ResearchOpen Access06 Mar 2025
Humanities and Social Sciences Communications

Volume: 12, P: 1-15
The relationship between the weight-adjusted-waist index and left ventricular hypertrophy in Chinese hypertension adults

Shuang Cai
Tianyu Zhu
Shuxia Wang
Research01 Nov 2022
Hypertension Research

Volume: 46, P: 253-260
Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging

Multiplexed ion beam imaging can provide subcellular localisation information but with limited resolution. Here the authors report an ion beam imaging method with nanoscale resolution which they use to assess the subcellular distribution of cisplatin.

Xavier Rovira-Clavé
Sizun Jiang
Garry P. Nolan
ResearchOpen Access30 Jul 2021
Nature Communications

Volume: 12, P: 1-18
XBP1 links the 12-hour clock to NAFLD and regulation of membrane fluidity and lipid homeostasis

Hepatocyte 12-hour rhythms have a role in cellular stress and metabolic functions. Here, the authors demonstrate disrupting the 12-hour clock through deletion of XBP1 is associated with the development of NAFLD as well as disruption of phospholipid composition and the maintenance of lipid homeostasis.

Huan Meng
Naomi M. Gonzales
Bert W. O’Malley
ResearchOpen Access04 Dec 2020
Nature Communications

Volume: 11, P: 1-16
Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology

Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Here, the authors propose a spatial histopathology tool that allows for high-plex protein staining and physical expansion, while retaining the lateral tissue expansion.

Yunhao Bai
Bokai Zhu
Sizun Jiang
ResearchOpen Access07 Jul 2023
Nature Communications

Volume: 14, P: 1-18
Restoration of the molecular clock is tumor suppressive in neuroblastoma

MYCN is frequently amplified in neuroblastomas. Here, the authors show that MYCN disrupts the molecular clock by downregulating clock activator RORα and that the reactivation of RORα restores BMAL1 activity, and inhibits lipid metabolism and neuroblastoma growth

Myrthala Moreno-Smith
Giorgio Milazzo
Eveline Barbieri
ResearchOpen Access28 Jun 2021
Nature Communications

Volume: 12, P: 1-16
Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

Sanjay Jain
Liming Pei
Michael P. Snyder
Amendments and Corrections01 Mar 2024
Nature Cell Biology

Volume: 26, P: 839
Metabolic enzyme PFKFB4 activates transcriptional coactivator SRC-3 to drive breast cancer

The glycolytic enzyme PFKFB4 directly phosphorylates and regulates binding of the coactivator SRC-3 to ATF4 and thereby increases the transcriptional activity of this complex, leading to increased expression of metabolic genes, and enhancing tumour growth and metastasis.

Subhamoy Dasgupta
Kimal Rajapakshe
Bert W. O’Malley
Research03 Apr 2018
Nature

Volume: 556, P: 249-254
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

The Human BioMolecular Atlas Program (HuBMAP) presents its production phase: the generation of spatial maps of functional tissue units across organs from diverse populations and the creation of tools and infrastructure to advance biomedical research.

Sanjay Jain
Liming Pei
Michael P. Snyder
Reviews19 Jul 2023
Nature Cell Biology

Volume: 25, P: 1089-1100
Acetylation of histone H3K27 signals the transcriptional elongation for estrogen receptor alpha

Gao et al. study the relationship between AFF4 and acetylated histone H3K27 in the context of estrogen receptor alpha signaling. They use a series of pull down assays, genetic backgrounds, and global sequencing analysis and show that AFF4 binds to H2K27ac at promoters and influences the ER alpha signaling and breast cancer cell growth.

Yujing Gao
Lijia Chen
Qin Feng
ResearchOpen Access07 Apr 2020
Communications Biology

Volume: 3, P: 1-10
Evidence for ~12-h ultradian gene programs in humans

Bokai Zhu
Silvia Liu
Matthew L. Steinhauser
ResearchOpen Access09 Aug 2024
npj Biological Timing and Sleep

Volume: 1, P: 1-10

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