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The companion website. 伴游网站。
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-13 DOI: 10.1038/s41592-026-03276-7
Andreas Bueckle, Matthias Stahl, Kelly Krause, Torsten Möller, Helena Klara Jambor
{"title":"The companion website.","authors":"Andreas Bueckle, Matthias Stahl, Kelly Krause, Torsten Möller, Helena Klara Jambor","doi":"10.1038/s41592-026-03276-7","DOIUrl":"https://doi.org/10.1038/s41592-026-03276-7","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149183178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Near-infrared photochromic miniprotein enables photoacoustic molecular imaging of acute inflammation and intracellular antigens. 近红外光致变色微小蛋白可实现急性炎症和细胞内抗原的光声分子成像。
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-13 DOI: 10.1038/s41592-026-03255-y
Olena S Oliinyk, Yirui Xu, Jinhuan Luo, Kateryna O Tokarchuk, Kyrylo Yu Manoilov, Josie van de Klashorst, Matthew P Eyring, Mu-En Wang, Ming Chen, Pengfei Song, John W Hickey, Junjie Yao, Vladislav V Verkhusha
{"title":"Near-infrared photochromic miniprotein enables photoacoustic molecular imaging of acute inflammation and intracellular antigens.","authors":"Olena S Oliinyk, Yirui Xu, Jinhuan Luo, Kateryna O Tokarchuk, Kyrylo Yu Manoilov, Josie van de Klashorst, Matthew P Eyring, Mu-En Wang, Ming Chen, Pengfei Song, John W Hickey, Junjie Yao, Vladislav V Verkhusha","doi":"10.1038/s41592-026-03255-y","DOIUrl":"https://doi.org/10.1038/s41592-026-03255-y","url":null,"abstract":"<p><p>Using near-infrared photoswitchable photochromic genetically encoded probes, differential photoacoustic tomography (PAT) enables deep-tissue imaging with high resolution and sensitivity; however, current bacteriophytochrome-based probes are bulky multidomain proteins exceeding 55 kDa, which constrains their use for designing PAT molecular reporters. Here we engineer rsmiRFPnano, a compact cyanobacteriochrome-derived photoswitchable PAT probe. With a molecular weight below 19 kDa, rsmiRFPnano efficiently incorporates biliverdin, exhibits high extinction coefficients in both photochromic states and demonstrates robust performance in live cells. We established rsmiRFPnano-based reporters for NF-κB and AP-1 pathways, which display low basal activity and strong activation-dependent responses. These reporters effectively visualized acute inflammation using noninvasive PAT in vivo, further validated through cellular-level spatial omics mapping. We then created photoswitchable nanobody probes, rsNIR-Fbs, stabilized upon antigen binding and rapidly degraded otherwise, enabling selective photoacoustic immuno-imaging of intracellular antigens in vivo. Together, these results establish rsmiRFPnano as an ultracompact and versatile platform for molecular PAT.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149183188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Early-career balancing act: training, moving, relationships and language learning. 早期职业平衡:培训、搬家、人际关系和语言学习。
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-12 DOI: 10.1038/s41592-026-03267-8
Vivien Marx
{"title":"Early-career balancing act: training, moving, relationships and language learning.","authors":"Vivien Marx","doi":"10.1038/s41592-026-03267-8","DOIUrl":"https://doi.org/10.1038/s41592-026-03267-8","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An integrated open-source acquisition and analysis ecosystem for high-throughput single-molecule imaging. 集成的开源采集和分析生态系统,用于高通量单分子成像。
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-09 DOI: 10.1038/s41592-026-03265-w
Daniel S Terry, Roman Kiselev, Manuel F Juette, Zeliha Kilic, Ryan A Brady, Yuansheng Sun, Scott C Blanchard
{"title":"An integrated open-source acquisition and analysis ecosystem for high-throughput single-molecule imaging.","authors":"Daniel S Terry, Roman Kiselev, Manuel F Juette, Zeliha Kilic, Ryan A Brady, Yuansheng Sun, Scott C Blanchard","doi":"10.1038/s41592-026-03265-w","DOIUrl":"https://doi.org/10.1038/s41592-026-03265-w","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149148824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tangermeme: a toolkit for understanding cis-regulatory logic using deep learning models. Tangermeme:一个使用深度学习模型来理解顺式调控逻辑的工具包。
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-08 DOI: 10.1038/s41592-026-03254-z
Jacob Schreiber
{"title":"Tangermeme: a toolkit for understanding cis-regulatory logic using deep learning models.","authors":"Jacob Schreiber","doi":"10.1038/s41592-026-03254-z","DOIUrl":"https://doi.org/10.1038/s41592-026-03254-z","url":null,"abstract":"<p><p>Deep learning models have achieved state-of-the-art performance at predicting diverse genomic modalities, yet their promise for biological discovery lies in how they are used after demonstrating their predictive performance. Here we describe the functionality of tangermeme, a highly optimized toolkit for 'everything-but-the-model' when it comes to genomic deep learning, and demonstrate how tangermeme can be used to distill the learned cis-regulatory patterns from models into human-interpretable insights.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149137619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Designing rhodamine-binding proteins from scratch 从零开始设计罗丹明结合蛋白
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-07 DOI: 10.1038/s41592-026-03259-8
Fariha Rahman
{"title":"Designing rhodamine-binding proteins from scratch","authors":"Fariha Rahman","doi":"10.1038/s41592-026-03259-8","DOIUrl":"10.1038/s41592-026-03259-8","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 10","pages":"1939-1939"},"PeriodicalIF":28.3,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149090232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recording time via brain organoids 通过大脑类器官记录时间
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-07 DOI: 10.1038/s41592-026-03257-w
Madhura Mukhopadhyay
{"title":"Recording time via brain organoids","authors":"Madhura Mukhopadhyay","doi":"10.1038/s41592-026-03257-w","DOIUrl":"10.1038/s41592-026-03257-w","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 10","pages":"1938-1938"},"PeriodicalIF":28.3,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149092125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
How to write a rebuttal letter 如何写一封反驳信
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-07 DOI: 10.1038/s41592-026-03261-0
{"title":"How to write a rebuttal letter","authors":"","doi":"10.1038/s41592-026-03261-0","DOIUrl":"10.1038/s41592-026-03261-0","url":null,"abstract":"The rebuttal letter is a vitally important document when revising a manuscript for a journal. Here we discuss how to communicate about your manuscript revisions in the best possible light.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 10","pages":"1919-1919"},"PeriodicalIF":28.3,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41592-026-03261-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149100852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Generalizable perturbation prediction 广义微扰预测
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-07 DOI: 10.1038/s41592-026-03260-1
Lin Tang
{"title":"Generalizable perturbation prediction","authors":"Lin Tang","doi":"10.1038/s41592-026-03260-1","DOIUrl":"10.1038/s41592-026-03260-1","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 10","pages":"1939-1939"},"PeriodicalIF":28.3,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149100765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Extracting brain-wide interactions with CURBD 提取与CURBD的全脑相互作用
IF 28.3 1区 生物学
Nature Methods Pub Date : 2026-10-07 DOI: 10.1038/s41592-026-03258-9
Nina Vogt
{"title":"Extracting brain-wide interactions with CURBD","authors":"Nina Vogt","doi":"10.1038/s41592-026-03258-9","DOIUrl":"10.1038/s41592-026-03258-9","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 10","pages":"1938-1938"},"PeriodicalIF":28.3,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149090231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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