Nature MethodsPub Date : 2025-08-07DOI: 10.1038/s41592-025-02790-4
Arunima Singh
{"title":"Spatiotemporal lipidomics in living tissue","authors":"Arunima Singh","doi":"10.1038/s41592-025-02790-4","DOIUrl":"10.1038/s41592-025-02790-4","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 8","pages":"1622-1622"},"PeriodicalIF":32.1,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799721","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}
Nature MethodsPub Date : 2025-08-07DOI: 10.1038/s41592-025-02789-x
Lin Tang
{"title":"Combating hallucination in digital pathology","authors":"Lin Tang","doi":"10.1038/s41592-025-02789-x","DOIUrl":"10.1038/s41592-025-02789-x","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 8","pages":"1621-1621"},"PeriodicalIF":32.1,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799716","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}
Nature MethodsPub Date : 2025-08-07DOI: 10.1038/s41592-025-02744-w
Dominik Vonficht, Lea Jopp-Saile, Schayan Yousefian, Viktoria Flore, Inés Simó Vesperinas, Ruth Teuber, Bogdan Avanesyan, Yanjiang Luo, Caroline Röthemeier, Florian Grünschläger, Mirian Fernandez-Vaquero, Vincent Fregona, Diana Ordoñez-Rueda, Laura K. Schmalbrock, Luca Deininger, Angelo Jovin Yamachui Sitcheu, Zuguang Gu, Maja C. Funk, Ralf Mikut, Mathias Heikenwälder, Angelika Eggert, Arend von Stackelberg, Sebastian Kobold, Jan Krönke, Ulrich Keller, Andreas Trumpp, Ahmed N. Hegazy, Cornelia Eckert, Daniel Hübschmann, Simon Haas
{"title":"Ultra-high-scale cytometry-based cellular interaction mapping","authors":"Dominik Vonficht, Lea Jopp-Saile, Schayan Yousefian, Viktoria Flore, Inés Simó Vesperinas, Ruth Teuber, Bogdan Avanesyan, Yanjiang Luo, Caroline Röthemeier, Florian Grünschläger, Mirian Fernandez-Vaquero, Vincent Fregona, Diana Ordoñez-Rueda, Laura K. Schmalbrock, Luca Deininger, Angelo Jovin Yamachui Sitcheu, Zuguang Gu, Maja C. Funk, Ralf Mikut, Mathias Heikenwälder, Angelika Eggert, Arend von Stackelberg, Sebastian Kobold, Jan Krönke, Ulrich Keller, Andreas Trumpp, Ahmed N. Hegazy, Cornelia Eckert, Daniel Hübschmann, Simon Haas","doi":"10.1038/s41592-025-02744-w","DOIUrl":"10.1038/s41592-025-02744-w","url":null,"abstract":"Cellular interactions are of fundamental importance, orchestrating organismal development, tissue homeostasis and immunity. Recently, powerful methods that use single-cell genomic technologies to dissect physically interacting cells have been developed. However, these approaches are characterized by low cellular throughput, long processing times and high costs and are typically restricted to predefined cell types. Here we introduce Interact-omics, a cytometry-based framework to accurately map cellular landscapes and cellular interactions across all immune cell types at ultra-high resolution and scale. We demonstrate the utility of our approach to study kinetics, mode of action and personalized response prediction of immunotherapies, and organism-wide shifts in cellular composition and cellular interaction dynamics following infection in vivo. Our scalable framework can be applied a posteriori to existing cytometry datasets or incorporated into newly designed cytometry-based studies to map cellular interactions with a broad range of applications from fundamental biology to applied biomedicine. Interact-omics, a high-throughput cytometry-based framework, resolves the cellular interaction landscape.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 9","pages":"1887-1899"},"PeriodicalIF":32.1,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12446065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799713","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}
Nature MethodsPub Date : 2025-08-07DOI: 10.1038/s41592-025-02765-5
Morgan V. Farrell, Emily Darin, Nicholas J. Shikuma
{"title":"The biofouling tubeworm Hydroides elegans","authors":"Morgan V. Farrell, Emily Darin, Nicholas J. Shikuma","doi":"10.1038/s41592-025-02765-5","DOIUrl":"10.1038/s41592-025-02765-5","url":null,"abstract":"The globally distributed marine tubeworm Hydroides elegans is emerging as a powerful model for studying bacteria-induced metamorphosis, and offers insights into developmental biology, marine ecology and host–microbe interactions.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 8","pages":"1607-1609"},"PeriodicalIF":32.1,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799722","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}
Nature MethodsPub Date : 2025-08-07DOI: 10.1038/s41592-025-02743-x
{"title":"Unravelling cellular interactions using flow cytometry","authors":"","doi":"10.1038/s41592-025-02743-x","DOIUrl":"10.1038/s41592-025-02743-x","url":null,"abstract":"We present a cost-effective ultra-high-throughput cytometry-based framework for the detection of physical interactions between cells, along with the characterization of complex cellular landscapes. Application of our approach can offer a systems-level understanding of immunity and facilitate study of the kinetics, mode of action and personalized response prediction of immunotherapies.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 9","pages":"1770-1771"},"PeriodicalIF":32.1,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799714","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}
Nature MethodsPub Date : 2025-08-07DOI: 10.1038/s41592-025-02786-0
{"title":"Push-button science","authors":"","doi":"10.1038/s41592-025-02786-0","DOIUrl":"10.1038/s41592-025-02786-0","url":null,"abstract":"Technological advances change not only what we can learn as scientists, but also how science is conducted. Here we explore how automation and outsourcing are affecting the act of doing science.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 8","pages":"1605-1605"},"PeriodicalIF":32.1,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41592-025-02786-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799720","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}
Nature MethodsPub Date : 2025-08-07DOI: 10.1038/s41592-025-02787-z
Madhura Mukhopadhyay
{"title":"Capturing host–microbe interactions","authors":"Madhura Mukhopadhyay","doi":"10.1038/s41592-025-02787-z","DOIUrl":"10.1038/s41592-025-02787-z","url":null,"abstract":"A combination of organoid technology and genetic methods enables studies of human pathogens.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 8","pages":"1620-1620"},"PeriodicalIF":32.1,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799715","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}
Nature MethodsPub Date : 2025-08-06DOI: 10.1038/s41592-025-02740-0
Matthew J. Styles, Joshua A. Pixley, Tongyao Wei, Christopher Basile, Shannon S. Lu, Bryan C. Dickinson
{"title":"PANCS-Binders: a rapid, high-throughput binder discovery platform","authors":"Matthew J. Styles, Joshua A. Pixley, Tongyao Wei, Christopher Basile, Shannon S. Lu, Bryan C. Dickinson","doi":"10.1038/s41592-025-02740-0","DOIUrl":"10.1038/s41592-025-02740-0","url":null,"abstract":"Proteins that selectively bind to a target of interest are foundational in research, diagnostics and therapeutics. Current approaches for discovering binders are laborious and time-consuming, taking months or more, and have a high failure rate. Here we establish phage-assisted noncontinuous selection of protein binders (PANCS-Binders), an in vivo selection platform that links the life cycle of M13 phage to target protein binding through proximity-dependent split RNA polymerase biosensors, allowing for comprehensive screening of whether a variant binds a target with high fidelity. We showcase PANCS-Binders by screening multiple protein libraries each against a panel of 95 separate targets, thereby individually assessing more than 1011 protein–protein interaction pairs, in 2 days. These selections yielded large, high-quality datasets and hundreds of novel binders, which can be affinity matured or directly used in mammalian cells to inhibit or degrade targets. We believe that PANCS-Binders accelerates and simplifies the binder discovery process, which will help unlock new creative potential in proteome targeting with engineered binder-based biotechnologies. Phage-assisted noncontinuous selection of protein binders (PANCS-Binders) allows multiple high-diversity protein libraries to each be screened against a panel of dozens of targets for high-throughput protein binder discovery.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 8","pages":"1720-1730"},"PeriodicalIF":32.1,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12328212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794913","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}
Nature MethodsPub Date : 2025-08-06DOI: 10.1038/s41592-025-02767-3
Vivien Marx
{"title":"Is single-molecule protein sequencing here yet?","authors":"Vivien Marx","doi":"10.1038/s41592-025-02767-3","DOIUrl":"10.1038/s41592-025-02767-3","url":null,"abstract":"As instruments and approaches emerge for single-molecule protein analysis, some developers and early users share their first impressions.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 8","pages":"1623-1628"},"PeriodicalIF":32.1,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794912","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}
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