Nature Biomedical Engineering最新文献_第6页

HisToSpatialCNV: an interpretable deep learning method predicting spatial copy number variations from histopathology images. HisToSpatialCNV：一种可解释的深度学习方法，预测组织病理图像的空间拷贝数变化。

IF 26.3 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-24 DOI: 10.1038/s41551-026-01754-z

Tianao Chen, Thatchayut Unjitwattana, Xuhui Guo, Pooja Thakur, Shu Zhou, Zheng Jing, Yiwen Yang, Yuheng Du, Weiping Zou, Lana X Garmire

{"title":"HisToSpatialCNV: an interpretable deep learning method predicting spatial copy number variations from histopathology images.","authors":"Tianao Chen, Thatchayut Unjitwattana, Xuhui Guo, Pooja Thakur, Shu Zhou, Zheng Jing, Yiwen Yang, Yuheng Du, Weiping Zou, Lana X Garmire","doi":"10.1038/s41551-026-01754-z","DOIUrl":"https://doi.org/10.1038/s41551-026-01754-z","url":null,"abstract":"Copy number variations (CNV) are key drivers of cancer progression, yet methods for predicting spatial CNVs directly from haematoxylin and eosin (H&E) images are currently lacking. We introduce HisToSpatialCNV, a multiscale deep-learning framework that integrates histopathological features from H&E-stained images to infer spatial CNV patterns. Combining interpretable feature extraction with graph neural networks and multihead self-attention, our approach captures both local and global tissue contexts. Applied to HER2+ breast cancer, skin cancer and brain cancer datasets, HisToSpatialCNV outperformed existing methods for spatial gene expression inference and showed strong concordance between predicted CNVs and gene expression. In addition, it enabled tumour subclone identification, phylogenetic reconstruction and detection of pathway alterations linked to tumour progression. HisToSpatialCNV generalized across Visium and Xenium spatial transcriptomics platforms, on HER2+ patients. Applying the HisToSpatialCNV HER2+ model to TCGA HER2+ histopathology data identified spatial-molecular subtypes associated with distinct survival outcomes in TCGA HER2+ patients. By connecting histopathology to spatial genomics, HisToSpatialCNV offers a powerful, cost-effective tool for studying intratumour heterogeneity using only routine pathology images.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":" ","pages":""},"PeriodicalIF":26.3,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148813649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improving outdoor navigation for people with blindness using an AI-driven smartphone application and personalized audio guidance. 使用人工智能驱动的智能手机应用程序和个性化音频引导，改善盲人的户外导航。

IF 26.3 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-24 DOI: 10.1038/s41551-026-01772-x

Raymond Liu, Patrick Slade

{"title":"Improving outdoor navigation for people with blindness using an AI-driven smartphone application and personalized audio guidance.","authors":"Raymond Liu, Patrick Slade","doi":"10.1038/s41551-026-01772-x","DOIUrl":"https://doi.org/10.1038/s41551-026-01772-x","url":null,"abstract":"Globally, 340 million people have blindness or moderate-to-severe visual impairment (BVI), which limits independent outdoor navigation and negatively affects their health and quality of life. We surveyed 112 people with BVI and found that an ideal outdoor navigation aid must be able to perform turn-by-turn directions, path guidance and obstacle detection and avoidance. Existing navigation tools such as white canes, guide dogs and electronic travel aids often lack one or more of these criteria and may be expensive or inaccessible. Here we introduce Mobilio, a smartphone application that incorporates machine learning, sensor fusion algorithms and personalized audio feedback to meet all of the outdoor navigation criteria. We assessed the reliability of the smartphone sensors and models used for navigation with engineering tests in representative navigation scenarios. We performed a series of experiments in which Mobilio personalized audio feedback for participants with BVI (n = 14), guided them along an outdoor community path and helped them to navigate an obstacle course. Participants walking with Mobilio and a white cane navigated a community path in 13 ± 3% less time and reduced environmental contacts by 41 ± 5% compared with using Google Maps and a white cane. Mobilio achieved similar outdoor navigation reliability to a human guide. Participant surveys reported that Mobilio was easy to use, had a low perceived workload and provided intuitive audio feedback. This work provides an accessible and personalized tool that may be an effective outdoor navigation aid to increase independence for people with BVI.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":" ","pages":""},"PeriodicalIF":26.3,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148813607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Targeted lipid nanoparticles unlock in vivo human haematopoietic stem cell gene editing. 靶向脂质纳米颗粒解锁体内人造血干细胞基因编辑。

IF 26.3 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-21 DOI: 10.1038/s41551-026-01770-z

Zhangyi Luo, Audrey T Zhu, Michael J Mitchell

引用次数: 0

Intracellular protein binders for imaging, control and future therapeutics. 用于成像、控制和未来治疗的细胞内蛋白结合物。

IF 26.3 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-20 DOI: 10.1038/s41551-026-01768-7

Natalia V Barykina, Vladislav V Verkhusha

{"title":"Intracellular protein binders for imaging, control and future therapeutics.","authors":"Natalia V Barykina, Vladislav V Verkhusha","doi":"10.1038/s41551-026-01768-7","DOIUrl":"10.1038/s41551-026-01768-7","url":null,"abstract":"Intracellular protein dysregulation underlies many cancers, neurodegenerative disorders and infectious diseases, yet a substantial fraction of the human proteome remains inaccessible to conventional small-molecule drugs or extracellular antibodies. Genetically encoded intracellular binders, including nanobodies, DARPins, affibodies and de novo-designed scaffolds, provide modular platforms for selective recognition, visualization and functional modulation of endogenous proteins in living cells. These binders can engage extended protein surfaces and conformational epitopes and are increasingly applied in preclinical models to inhibit oncogenic signalling, degrade pathogenic proteins, rewire cellular pathways and engineer programmable cell therapies. Here we outline the structural diversity, discovery strategies and design principles of intracellular binders and summarize their emerging applications in imaging, biosensing and targeted protein control. We further discuss recent advances in computationally assisted binder design and optimization. Finally, we examine key translational challenges, including cellular stability, delivery technologies and immunogenicity, that will shape the clinical development of intracellular binder-based therapeutics.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":" ","pages":""},"PeriodicalIF":26.3,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13549425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Analysing long-read CRISPR experiments with CRISPRLungo 使用CRISPRLungo分析长读CRISPR实验

IF 28.1 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-20 DOI: 10.1038/s41551-026-01776-7

Gue-Ho Hwang, Benjamin Vyshedskiy, Timothy Barry, Jing Zeng, Sébastien Levesque, John P. Manis, Akiko Shimamura, Daniel E. Bauer, Luca Pinello

{"title":"Analysing long-read CRISPR experiments with CRISPRLungo","authors":"Gue-Ho Hwang, Benjamin Vyshedskiy, Timothy Barry, Jing Zeng, Sébastien Levesque, John P. Manis, Akiko Shimamura, Daniel E. Bauer, Luca Pinello","doi":"10.1038/s41551-026-01776-7","DOIUrl":"https://doi.org/10.1038/s41551-026-01776-7","url":null,"abstract":"Long-read sequencing can characterize complex genome editing-induced DNA sequence changes such as large deletions, insertions and inversions that are difficult to detect using short-read sequencing. However, PCR amplification and sequencing errors complicate accurate variant detection, and existing analysis tools are not optimized for gene editing specific allelic outcomes. Here we present CRISPRLungo, a computational pipeline specifically designed for long-read amplicon sequencing of gene edited samples. CRISPRLungo incorporates unique molecular identifier-based error correction and statistical filtering to distinguish true editing events from background noise, enabling robust detection of small indels and structural variants. Through systematic benchmarking using simulated datasets, we demonstrate that CRISPRLungo outperforms existing approaches in both accuracy and read recovery. CRISPRLungo supports both Oxford Nanopore and PacBio platforms and identifies previously undetected structural variant edits such as inversions in published CRISPR datasets. To demonstrate allele-specific edit quantification, we applied CRISPRLungo to analyse edited primary cells from a patient harbouring compound heterozygous SBDS mutations, accurately quantifying SBDS editing outcomes despite contaminating reads from the homologous SBDSP1 pseudogene. To maximize accessibility, we developed a fully client-side web application requiring no installation, making advanced long-read analysis accessible to researchers regardless of computational expertise. CRISPRLungo is freely available at https://github.com/pinellolab/CRISPRLungo with a user-friendly web interface available at https://pinellolab.github.io/CRISPRLungo.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":"6 1","pages":""},"PeriodicalIF":28.1,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148769332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A miniature endovascular soft robot for active blood flow regulation in occluded vessels 用于闭塞血管主动血流调节的微型血管内软机器人

IF 28.1 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-17 DOI: 10.1038/s41551-026-01771-y

Kaiwen Fang, Yibin Wang, Jiguang Liang, Zhen Yang, Hui Chen, Xingzhou Du, Xiao Li, Peng Song, Jiangfan Yu

{"title":"A miniature endovascular soft robot for active blood flow regulation in occluded vessels","authors":"Kaiwen Fang, Yibin Wang, Jiguang Liang, Zhen Yang, Hui Chen, Xingzhou Du, Xiao Li, Peng Song, Jiangfan Yu","doi":"10.1038/s41551-026-01771-y","DOIUrl":"https://doi.org/10.1038/s41551-026-01771-y","url":null,"abstract":"Blood flow abnormalities in occluded or narrowed vessels limit drug delivery and contribute to recurrent vascular disease. Existing endovascular or pharmacological approaches do not directly address impaired local flow. Here we propose a miniature endovascular soft robot for active blood flow regulation and enhanced fluid exchange and drug transport in occluded vessels. The soft robot integrates a magnetic body for navigation with cilia that generate metachronal waves to drive the flow. Navigation and flow regulation are decoupled, allowing positioning at target sites followed by local flow enhancement. We investigate the flow regulation mechanism and optimize the structural parameters of the cilia carpet. We validate flow regulation in different vessel phantoms with biologically relevant conditions and in large animal studies. The system restores flow in occluded branches and improves delivery of therapeutic agents, accelerating clot dissolution with reduced residual obstruction and shorter recanalization time both in vitro and in vivo. This technology allows the local modulation of vascular flow, supporting more effective and controlled endovascular therapies.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":"37 1","pages":""},"PeriodicalIF":28.1,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148769175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An explainable biomedical foundation model via large-scale concept-enhanced vision–language pretraining 基于大规模概念增强视觉语言预训练的可解释生物医学基础模型

IF 28.1 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-17 DOI: 10.1038/s41551-026-01764-x

Yuxiang Nie, Sunan He, Yequan Bie, Yihui Wang, Zhixuan Chen, Shu Yang, Zhiyuan Cai, Linshan Wu, Hongmei Wang, Xi Wang, Ngai Shing Cheng, Luyang Luo, Mingxiang Wu, Haibo Jin, Xian Wu, Ronald Cheong Kin Chan, Yuk Ming Lau, Zhengyu Zhang, Sushan Xiao, Can Yang, Yinghua Zhao, Xiaohui Duan, Li Zhang, Li Liang, Yefeng Zheng, Pranav Rajpurkar, Hao Chen

{"title":"An explainable biomedical foundation model via large-scale concept-enhanced vision–language pretraining","authors":"Yuxiang Nie, Sunan He, Yequan Bie, Yihui Wang, Zhixuan Chen, Shu Yang, Zhiyuan Cai, Linshan Wu, Hongmei Wang, Xi Wang, Ngai Shing Cheng, Luyang Luo, Mingxiang Wu, Haibo Jin, Xian Wu, Ronald Cheong Kin Chan, Yuk Ming Lau, Zhengyu Zhang, Sushan Xiao, Can Yang, Yinghua Zhao, Xiaohui Duan, Li Zhang, Li Liang, Yefeng Zheng, Pranav Rajpurkar, Hao Chen","doi":"10.1038/s41551-026-01764-x","DOIUrl":"https://doi.org/10.1038/s41551-026-01764-x","url":null,"abstract":"Artificial intelligence for medical imaging is required to be accurate and interpretable to clinicians. However, current multimodal biomedical foundation models often prioritize performance over explainability. Here we present ConceptCLIP, an explainable biomedical foundation model that achieves state-of-the-art diagnostic accuracy while delivering human-interpretable explanations across diverse imaging modalities. We curate MedConcept-23M, a large-scale dataset comprising 23 million biomedical image–text–concept triplets. Leveraging this dataset, we pretrain ConceptCLIP via joint image–text and region–concept alignment for precise and interpretable medical image analysis. Across a large-scale benchmark covering 78 datasets in 10 imaging modalities, ConceptCLIP demonstrates superior diagnostic performance while providing human-understandable explanations. In a clinician user study spanning three modalities, the concept-based explanations provided by ConceptCLIP help clinicians verify model predictions and identify potential errors. As an explainable biomedical foundation model, ConceptCLIP represents a critical milestone towards the widespread clinical adoption of AI, thereby advancing trustworthy AI in medicine.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":"19 1","pages":""},"PeriodicalIF":28.1,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148769178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A critical look at AI in medicine 人工智能在医学中的应用

IF 26.3 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-14 DOI: 10.1038/s41551-026-01778-5

引用次数: 0

Biomimetic zona pellucida-encapsulated islets for sustained glycaemic control in immunocompetent mice 仿生透明带包封胰岛对免疫功能小鼠持续血糖控制的作用

IF 28.1 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-14 DOI: 10.1038/s41551-026-01775-8

Kyungsene Lee, Xuelin Wang, Connie Wen, Yixun Wang, Jennifer Z. Wang, Brandon Davis, James Coyne, Alexander L. Mark, Chien-Wei Wu, Ana Aviles Vargas, Yuhong Jiang, Thomas I. McDougal, Selina Y. Lin, Xiaojun Lance Lian, Hong Zheng, Yuguo Lei, Yong Wang

引用次数: 0

A practical toolbox for modelling fibrosis in vitro 一个实用的体外纤维化模型工具箱。

IF 26.3 1区医学

Nature Biomedical Engineering Pub Date : 2026-08-13 DOI: 10.1038/s41551-026-01749-w

Margaretha A. J. Morsink, Sharon Fleischer, Trevor R. Nash, Thomas Falcucci, Julie Leonard-Duke, Vanessa Li, Meghan Pinezich, Jugal Kishore Sahoo, Onur Hasturk, Andy Lee, Sophia Theodossiou, Jaewon Choi, Pamela Graney, Clark Hung, David L. Kaplan, Gordana Vunjak-Novakovic

{"title":"A practical toolbox for modelling fibrosis in vitro","authors":"Margaretha A. J. Morsink, Sharon Fleischer, Trevor R. Nash, Thomas Falcucci, Julie Leonard-Duke, Vanessa Li, Meghan Pinezich, Jugal Kishore Sahoo, Onur Hasturk, Andy Lee, Sophia Theodossiou, Jaewon Choi, Pamela Graney, Clark Hung, David L. Kaplan, Gordana Vunjak-Novakovic","doi":"10.1038/s41551-026-01749-w","DOIUrl":"10.1038/s41551-026-01749-w","url":null,"abstract":"Fibrosis is a widespread disease implicated in millions of deaths worldwide and impacting diverse organs, including the heart, lung, kidney, liver and synovium. Characterized by excessive extracellular matrix deposition, fibrosis leads to tissue scarring and dysfunction, ultimately resulting in organ failure. The development of faithful experimental models of fibrosis is challenged by its complexity, limiting the discovery of effective therapeutics. Human in vitro tissue models are emerging as powerful systems that capture the pathophysiology of fibrosis to uncover disease mechanisms, identify biomarkers and facilitate drug discovery. Here we define the hallmarks of fibrosis across organ systems to establish foundational design criteria necessary for modelling human fibrosis in vitro. We provide an overview of state-of-the-art technologies and recent advancements in tissue fibrosis models pointing towards potential future directions. Finally, we offer a practical toolkit for researchers with diverse expertise to implement these considerations into future tissue models. Key tissue features shared by fibrotic diseases are distilled into clear design rules for human in vitro models, with practical guidance on choosing cells, matrices and platforms for mechanistic studies and drug testing.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":"10 10","pages":"1993-2011"},"PeriodicalIF":26.3,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148760128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0