Nature Search

Enzyme specificity prediction using cross attention graph neural networks

Haiyang Cui
Yufeng Su
Huimin Zhao
Research08 Oct 2025
Nature

P: 1-3
Brain–cervical lymph node crosstalk contributes to brain injury induced by subarachnoid hemorrhage in mice

Crosstalk between the brain and CLNs is critical in brain pathologies. Here, the authors show in a mouse model that extravasated erythrocytes following SAH are degraded by cathepsin S of medullary LECs in CLNs, which plays an important role in SAH pathology.

Jinman Chen
Jie Wang
Qianqian Liang
ResearchOpen Access29 Sept 2025
Nature Communications

Volume: 16, P: 1-17
A generalized platform for artificial intelligence-powered autonomous enzyme engineering

The authors integrate artificial intelligence with laboratory automation to create a widely applicable autonomous platform for efficient and scalable enzyme engineering.

Nilmani Singh
Stephan Lane
Huimin Zhao
ResearchOpen Access01 Jul 2025
Nature Communications

Volume: 16, P: 1-13
Metabolism archetype cancer cells induce protumor TREM2⁺ macrophages via oxLDL-mediated metabolic interplay in hepatocellular carcinoma

Tumour cells can alter the function and metabolism of immune cells to reduce anti-tumour responses. Here the authors use single cell sequencing of HCC and show three tumour archetypes; metabolism, inflammation and stemness and the metabolism archetype are found in association with TREM⁺ macrophages which restrict immune cell infiltration into the tumour microenvironment.

Tianhao Chu
Guiqi Zhu
Yinghong Shi
ResearchOpen Access23 Jul 2025
Nature Communications

Volume: 16, P: 1-25
Migration direction in a songbird explained by two loci

The genetic determinants of long-distance migration in birds are largely unknown. Sokolovskis et al. tracked genotyped hybrid willow warblers from a migratory divide in Sweden and find that autumn migration direction is consistent with a dominant inheritance pattern of two large effect loci that interact through epistasis.

Kristaps Sokolovskis
Max Lundberg
Staffan Bensch
ResearchOpen Access11 Jan 2023
Nature Communications

Volume: 14, P: 1-6
Synthesis of zero-dimensional octahedral metal halides through solvent incorporation and their photophysical properties

Zero-dimensional metal halides exhibit intriguing photophysical properties; however, developing their general design principles remains challenging. Now it has been shown that two-dimensional perovskites can be converted into zero-dimensional octahedral metal halides through solvent incorporation. The resulting materials feature near-unity photoluminescence quantum yields. Structural rigidity and the choice of metal cation are key parameters to tune the exciton recombination dynamics.

Nanlong Zheng
Songqi Cao
Zhiwei Liu
Research04 Aug 2025
Nature Chemistry

Volume: 17, P: 1401-1409
Plume-induced emissions of deep methane linked to the end-Guadalupian mass extinction

Abiogenic methane was generated in the mantle and brought to the surface in the Emeishan large igneous province magmas. Release of this magmatic methane could have induced strong warming and contributed to the end-Guadalupian mass extinctions.

Sheng-Ao Liu
Zhili Xiong
Mingyu Zhao
ResearchOpen Access01 Jul 2025
Nature Communications

Volume: 16, P: 1-12
Ultra-conformal skin electrodes with synergistically enhanced conductivity for long-time and low-motion artifact epidermal electrophysiology

Novel dry electrodes with enhanced mechano-electrical stability and conformability are attractive for long-time electrophysiological signal monitoring. Here, the authors report polymer-covered CVD-grown graphene with enhanced optoelectronic performance for biopotential monitoring.

Yan Zhao
Song Zhang
Nan Liu
ResearchOpen Access12 Aug 2021
Nature Communications

Volume: 12, P: 1-12
Association between endogenous lactate accumulation and dysregulated activation of the NLRP3 inflammasome pathway in schizophrenia

Yingying Zhang
Yanjun Wang
Tianhao Bao
ResearchOpen Access04 Jun 2025
Scientific Reports

Volume: 15, P: 1-19
An epitaxial graphene platform for zero-energy edge state nanoelectronics

Here, the authors show robust edge state transport in patterned nanoribbon networks produced on epigraphene—graphene that is epitaxially grown on non-polar faces of SiC wafers. The edge state forms a zero-energy, one-dimensional ballistic network with dissipationless nodes at ribbon–ribbon junctions.

Vladimir S. Prudkovskiy
Yiran Hu
Walt A. de Heer
ResearchOpen Access19 Dec 2022
Nature Communications

Volume: 13, P: 1-11
Anomalous magnetoresistance by breaking ice rule in Bi₂Ir₂O₇/Dy₂Ti₂O₇ heterostructure

Spin ice compounds are typically insulating and introducing carriers can destroy the spin ice state, making integration into electronic devices problematic. Here the authors report a transport response to an ice-rule-breaking transition in a heterostructure of a pyrochlore spin ice and a nonmagnetic metal.

Han Zhang
Chengkun Xing
Jian Liu
ResearchOpen Access14 Mar 2023
Nature Communications

Volume: 14, P: 1-7
Magneto-transport evidence for strong topological insulator phase in ZrTe₅

It remains difficult to identify non-trivial band topology through electronic transport in narrow-gap topological materials. Here, the authors demonstrate that an inverted band leads to a four-fold splitting of non-zero Landau levels and an anomalous zero Landau level peak in the density of states of ZrTe₅, hence can serve as an indicator to explore non-trivial topology.

Jingyue Wang
Yuxuan Jiang
Zhigang Jiang
ResearchOpen Access19 Nov 2021
Nature Communications

Volume: 12, P: 1-7
ECNet is an evolutionary context-integrated deep learning framework for protein engineering

Protein engineering is an active area of research in which machine learning has proven quite powerful. Here, the authors present a deep learning method that integrates both general and protein-specific sequence representations to improve the engineering of one’s protein of interest.

Yunan Luo
Guangde Jiang
Jian Peng
ResearchOpen Access30 Sept 2021
Nature Communications

Volume: 12, P: 1-14
Tumor-secreted LCN2 impairs gastric cancer progression via autocrine inhibition of the 24p3R/JNK/c-Jun/SPARC axis

Zhixin Huang
Ying Li
Jianhui Chen
ResearchOpen Access18 Oct 2024
Cell Death & Disease

Volume: 15, P: 1-15
Estrogen receptor 1 signaling in hepatic stellate cells designates resistance to liver fibrosis

Tianhao Li
Gang Wang
Jing Yang
CorrespondenceOpen Access15 Apr 2025
Cell Discovery

Volume: 11, P: 1-4
An individualised signature for predicting response with concordant survival benefit for lung adenocarcinoma patients receiving platinum-based chemotherapy

Lishuang Qi
Yang Li
Zheng Guo
ResearchOpen Access17 Nov 2016
British Journal of Cancer

Volume: 115, P: 1513-1519
Machine learning-enabled retrobiosynthesis of molecules

Retrobiosynthesis aims to create novel biosynthetic pathways for the beneficial production of molecules of interest. This Review outlines how machine learning can help to advance retrobiosynthesis by improving retrosynthesis planning, enzyme identification and selection, and the engineering of enzymes and pathways.

Tianhao Yu
Aashutosh Girish Boob
Huimin Zhao
Reviews16 Feb 2023
Nature Catalysis

Volume: 6, P: 137-151
Embryonic liver developmental trajectory revealed by single-cell RNA sequencing in the Foxa2^eGFP mouse

The authors report a single cell-resolution gene expression atlas for the developing mouse liver and gallbladder using a transgenic Foxa2^eGFP mouse line. By tracing the development of cells from gut endoderm to hepatoblasts they identify key transcriptional changes during liver specification.

Tianhao Mu
Liqin Xu
Yong Hou
ResearchOpen Access03 Nov 2020
Communications Biology

Volume: 3, P: 1-12
Recent progress in triplet energy transfer systems toward organic afterglow materials

Artificial light-harvesting systems based on phosphorescence-type energy transfer from the triplet excited states of organic room-temperature phosphorescence emitters have emerged as promising candidates for organic afterglow materials. Here, the authors review our fundamental understanding of phosphorescence-type energy transfer processes and highlight recent advances in the design, modulation and application of such systems.

Kaiwen Wu
Dan Liu
Ben Zhong Tang
ReviewsOpen Access21 Mar 2025
Communications Chemistry

Volume: 8, P: 1-18
Structure and assembly of double-headed Sendai virus nucleocapsids

The authors present the reconstruction of the Sendai Virus N-RNA complex at atomic resolution, including the helical part and a clam-shaped joint, resolved to 2.9 and 3.9 Å respectively, via cryo-EM. They also demonstrate the presence of an additional, ring like structural motif stabilising Nprotein interactions.

Na Zhang
Hong Shan
Qing-Tao Shen
ResearchOpen Access22 Apr 2021
Communications Biology

Volume: 4, P: 1-10
Structural plasticity of mumps virus nucleocapsids with cryo-EM structures

Shan et al. describes the high-resolution structures of Nucleoprotein in two different oligomeric states and four different higher-order helical structures. They further describe the structural rearrangements required to transition between the different helical assemblies obtained, highlighting the basis for structural plasticity among different MuV nucleocapsids.

Hong Shan
Xin Su
Qing-Tao Shen
ResearchOpen Access02 Jul 2021
Communications Biology

Volume: 4, P: 1-11
Application of machine learning standardized integral area algorithm in measuring the scoliosis

Shuman Han
Hongyu Zhao
Wenjuan Wu
ResearchOpen Access07 Nov 2023
Scientific Reports

Volume: 13, P: 1-10
Prim-O-glucosylcimifugin ameliorates aging-impaired endogenous tendon regeneration by rejuvenating senescent tendon stem/progenitor cells

Yu Wang
Shanshan Jin
Yan Liu
ResearchOpen Access23 Oct 2023
Bone Research

Volume: 11, P: 1-19
High aspartate aminotransferase to alanine aminotransferase ratio on admission as risk factor for poor prognosis in COVID-19 patients

Cheng Qin
Yingxin Wei
Yujun Wang
ResearchOpen Access05 Oct 2020
Scientific Reports

Volume: 10, P: 1-10
Spindle function and Wnt pathway inhibition by PBX1 to suppress tumor progression via downregulating DCDC2 in colorectal cancer

Weigang Dai
Yinan Liu
Jianhui Chen
ResearchOpen Access04 Feb 2023
Oncogenesis

Volume: 12, P: 1-11
Rational development of a human antibody cocktail that deploys multiple functions to confer Pan-SARS-CoVs protection

Hangping Yao
Yao Sun
Xiangxi Wang
ResearchOpen Access01 Dec 2020
Cell Research

Volume: 31, P: 25-36
Formaldehyde initiates memory and motor impairments under weightlessness condition

Tianhao Mei
Ying Chen
Zhiqian Tong
ReviewsOpen Access28 Oct 2024
npj Microgravity

Volume: 10, P: 1-14
G9A promotes tumor cell growth and invasion by silencing CASP1 in non-small-cell lung cancer cells

Tianhao Huang
Peng Zhang
Fan Zhang
ResearchOpen Access06 Apr 2017
Cell Death & Disease

Volume: 8, P: e2726
Knockout of Stat5 in T cells ameliorates high cholesterol and high fat diet-induced hypercholesterolemia by influencing cholesterol metabolism in the liver

Zhongnan Ma
Na Sheng
Xin-Yuan Fu
Correspondence05 Mar 2020
Cellular & Molecular Immunology

P: 1-3
HPV E6/E7: insights into their regulatory role and mechanism in signaling pathways in HPV-associated tumor

Qiu Peng
Lujuan Wang
Qianjin Liao
Reviews15 Dec 2023
Cancer Gene Therapy

Volume: 31, P: 9-17

Search

Enzyme specificity prediction using cross attention graph neural networks

Brain–cervical lymph node crosstalk contributes to brain injury induced by subarachnoid hemorrhage in mice

A generalized platform for artificial intelligence-powered autonomous enzyme engineering

Metabolism archetype cancer cells induce protumor TREM2⁺ macrophages via oxLDL-mediated metabolic interplay in hepatocellular carcinoma

Migration direction in a songbird explained by two loci

Synthesis of zero-dimensional octahedral metal halides through solvent incorporation and their photophysical properties

Plume-induced emissions of deep methane linked to the end-Guadalupian mass extinction

Ultra-conformal skin electrodes with synergistically enhanced conductivity for long-time and low-motion artifact epidermal electrophysiology

Association between endogenous lactate accumulation and dysregulated activation of the NLRP3 inflammasome pathway in schizophrenia

An epitaxial graphene platform for zero-energy edge state nanoelectronics

Anomalous magnetoresistance by breaking ice rule in Bi₂Ir₂O₇/Dy₂Ti₂O₇ heterostructure

Magneto-transport evidence for strong topological insulator phase in ZrTe₅

ECNet is an evolutionary context-integrated deep learning framework for protein engineering

Tumor-secreted LCN2 impairs gastric cancer progression via autocrine inhibition of the 24p3R/JNK/c-Jun/SPARC axis

Estrogen receptor 1 signaling in hepatic stellate cells designates resistance to liver fibrosis

An individualised signature for predicting response with concordant survival benefit for lung adenocarcinoma patients receiving platinum-based chemotherapy

Machine learning-enabled retrobiosynthesis of molecules

Embryonic liver developmental trajectory revealed by single-cell RNA sequencing in the Foxa2^eGFP mouse

Recent progress in triplet energy transfer systems toward organic afterglow materials

Structure and assembly of double-headed Sendai virus nucleocapsids

Structural plasticity of mumps virus nucleocapsids with cryo-EM structures

Application of machine learning standardized integral area algorithm in measuring the scoliosis

Prim-O-glucosylcimifugin ameliorates aging-impaired endogenous tendon regeneration by rejuvenating senescent tendon stem/progenitor cells

High aspartate aminotransferase to alanine aminotransferase ratio on admission as risk factor for poor prognosis in COVID-19 patients

Spindle function and Wnt pathway inhibition by PBX1 to suppress tumor progression via downregulating DCDC2 in colorectal cancer

Rational development of a human antibody cocktail that deploys multiple functions to confer Pan-SARS-CoVs protection

Formaldehyde initiates memory and motor impairments under weightlessness condition

G9A promotes tumor cell growth and invasion by silencing CASP1 in non-small-cell lung cancer cells

Knockout of Stat5 in T cells ameliorates high cholesterol and high fat diet-induced hypercholesterolemia by influencing cholesterol metabolism in the liver

HPV E6/E7: insights into their regulatory role and mechanism in signaling pathways in HPV-associated tumor

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