Nature MethodsPub Date : 2026-01-15DOI: 10.1038/s41592-025-02948-0
Archibald Enninful, Zhaojun Zhang, Dmytro Klymyshyn, Matthew Ingalls, Mingyu Yang, Hailing Zong, Zhiliang Bai, Negin Farzad, Graham Su, Alev Baysoy, Jungmin Nam, Yao Lu, Shuozhen Bao, Siyan Deng, Nancy R Zhang, Oliver Braubach, Mina L Xu, Zongming Ma, Rong Fan
{"title":"Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus.","authors":"Archibald Enninful, Zhaojun Zhang, Dmytro Klymyshyn, Matthew Ingalls, Mingyu Yang, Hailing Zong, Zhiliang Bai, Negin Farzad, Graham Su, Alev Baysoy, Jungmin Nam, Yao Lu, Shuozhen Bao, Siyan Deng, Nancy R Zhang, Oliver Braubach, Mina L Xu, Zongming Ma, Rong Fan","doi":"10.1038/s41592-025-02948-0","DOIUrl":"10.1038/s41592-025-02948-0","url":null,"abstract":"<p><p>Spatially mapping the transcriptome and proteome in the same tissue section can profoundly advance our understanding of cellular heterogeneity and function. Here we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multimodal spatial omics approach combining sequencing-based spatial transcriptomics and multiplexed protein imaging on the same section, enabling both single-cell-resolution cell typing and transcriptome-wide interrogation of biological pathways. DBiTplus utilizes spatial barcoding and RNase H-mediated cDNA retrieval, preserving tissue architecture for multiplexed protein imaging. We developed computational pipelines to integrate these modalities, allowing imaging-guided deconvolution to generate single-cell-resolved spatial transcriptome atlases. We demonstrate DBiTplus across diverse samples including frozen mouse embryos, and formalin-fixed paraffin-embedded human lymph nodes and lymphoma tissues, highlighting its compatibility with challenging clinical specimens. DBiTplus uncovered mechanisms of lymphomagenesis, progression and transformation in human lymphomas. Thus, DBiTplus is a unified workflow for spatially resolved single-cell atlasing and unbiased exploration of biological mechanisms in a cell-by-cell manner at transcriptome scale.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":32.1,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145985213","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 : 2026-01-14DOI: 10.1038/s41592-025-02994-8
Rachel S. G. Sealfon, Chandra L. Theesfeld, Julien Funk, Natalie Sauerwald, Aaron K. Wong, Olga G. Troyanskaya
{"title":"HumanBase: an interactive AI platform for human biology","authors":"Rachel S. G. Sealfon, Chandra L. Theesfeld, Julien Funk, Natalie Sauerwald, Aaron K. Wong, Olga G. Troyanskaya","doi":"10.1038/s41592-025-02994-8","DOIUrl":"10.1038/s41592-025-02994-8","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 3","pages":"483-484"},"PeriodicalIF":32.1,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145970951","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 : 2026-01-12DOI: 10.1038/s41592-025-02999-3
Michelle Korda
{"title":"Bioprinting a human small intestine","authors":"Michelle Korda","doi":"10.1038/s41592-025-02999-3","DOIUrl":"10.1038/s41592-025-02999-3","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 1","pages":"10-10"},"PeriodicalIF":32.1,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145950759","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 : 2026-01-12DOI: 10.1038/s41592-025-02998-4
Aparna Anantharaman
{"title":"Trans-RNAs to program translation initiation","authors":"Aparna Anantharaman","doi":"10.1038/s41592-025-02998-4","DOIUrl":"10.1038/s41592-025-02998-4","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 1","pages":"9-9"},"PeriodicalIF":32.1,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145950799","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 : 2026-01-12DOI: 10.1038/s41592-025-02997-5
{"title":"Year in review 2025","authors":"","doi":"10.1038/s41592-025-02997-5","DOIUrl":"10.1038/s41592-025-02997-5","url":null,"abstract":"We highlight some of the Nature Methods team’s favorite papers published in 2025, reflecting on some trends and new technology developments.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 1","pages":"1-1"},"PeriodicalIF":32.1,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41592-025-02997-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145950808","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 : 2026-01-06DOI: 10.1038/s41592-025-02996-6
{"title":"Computational generation of high-content digital organs at single-cell resolution","authors":"","doi":"10.1038/s41592-025-02996-6","DOIUrl":"10.1038/s41592-025-02996-6","url":null,"abstract":"Complex digital representations of organs were reconstructed by computationally generating virtual slices from sparsely sampled planar spatial transcriptomic data, exemplified by a 38-million-cell mouse brain atlas that bridges gaps between tissue sections and preserves the continuous three-dimensional (3D) molecular landscape at single-cell resolution.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 2","pages":"293-294"},"PeriodicalIF":32.1,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145912401","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 : 2026-01-05DOI: 10.1038/s41592-025-02991-x
Vivien Marx
{"title":"What nanobodies can do for you","authors":"Vivien Marx","doi":"10.1038/s41592-025-02991-x","DOIUrl":"10.1038/s41592-025-02991-x","url":null,"abstract":"Since the chance discovery of nanobodies in the late 1980s, their uses and applications have kept growing. Researchers are now exploring new ways to harness nanobody versatility.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 1","pages":"11-15"},"PeriodicalIF":32.1,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145906264","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 : 2026-01-05DOI: 10.1038/s41592-025-02990-y
Vivien Marx
{"title":"Conference daycare","authors":"Vivien Marx","doi":"10.1038/s41592-025-02990-y","DOIUrl":"10.1038/s41592-025-02990-y","url":null,"abstract":"Not all conferences offer childcare, but when they do, these scientists, who are also mothers, rejoice. The toys are pretty good, too.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"23 1","pages":"2-2"},"PeriodicalIF":32.1,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145906203","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 : 2025-12-31DOI: 10.1038/s41592-025-02995-7
Henry Pinkard, Nils Norlin
{"title":"The missing data for intelligent scientific instruments.","authors":"Henry Pinkard, Nils Norlin","doi":"10.1038/s41592-025-02995-7","DOIUrl":"https://doi.org/10.1038/s41592-025-02995-7","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":32.1,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145878879","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}