Nature Methods最新文献_第4页

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment. 利用诱捕法对串联质谱分析中的错误发现率控制进行评估。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-01 Epub Date: 2025-06-16 DOI: 10.1038/s41592-025-02719-x

Bo Wen, Jack Freestone, Michael Riffle, Michael J MacCoss, William S Noble, Uri Keich

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引用次数: 0

Advancing time-resolved structural biology: latest strategies in cryo-EM and X-ray crystallography. 推进时间分辨结构生物学：低温电镜和x射线晶体学的最新策略。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-01 Epub Date: 2025-05-01 DOI: 10.1038/s41592-025-02659-6

Amir Banari, Amit K Samanta, Anna Munke, Tim Laugks, Saša Bajt, Kay Grünewald, Thomas C Marlovits, Jochen Küpper, Filipe R N C Maia, Henry N Chapman, Dominik Oberthür, Carolin Seuring

引用次数: 0

A sweet summer of science. 一个甜蜜的科学之夏。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-01 DOI: 10.1038/s41592-025-02739-7

Vivien Marx

引用次数: 0

SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing. SAVANA：利用长读测序可靠地分析体细胞结构变异和拷贝数畸变。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-01 Epub Date: 2025-05-28 DOI: 10.1038/s41592-025-02708-0

Hillary Elrick, Carolin M Sauer, Jose Espejo Valle-Inclan, Katherine Trevers, Melanie Tanguy, Sonia Zumalave, Solange De Noon, Francesc Muyas, Rita Cascão, Angela Afonso, Alistair G Rust, Fernanda Amary, Roberto Tirabosco, Adam Giess, Timothy Freeman, Alona Sosinsky, Katherine Piculell, David T Miller, Claudia C Faria, Greg Elgar, Adrienne M Flanagan, Isidro Cortes-Ciriano

{"title":"SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing.","authors":"Hillary Elrick, Carolin M Sauer, Jose Espejo Valle-Inclan, Katherine Trevers, Melanie Tanguy, Sonia Zumalave, Solange De Noon, Francesc Muyas, Rita Cascão, Angela Afonso, Alistair G Rust, Fernanda Amary, Roberto Tirabosco, Adam Giess, Timothy Freeman, Alona Sosinsky, Katherine Piculell, David T Miller, Claudia C Faria, Greg Elgar, Adrienne M Flanagan, Isidro Cortes-Ciriano","doi":"10.1038/s41592-025-02708-0","DOIUrl":"10.1038/s41592-025-02708-0","url":null,"abstract":"Accurate detection of somatic structural variants (SVs) and somatic copy number aberrations (SCNAs) is critical to study the mutational processes underpinning cancer evolution. Here we describe SAVANA, an algorithm designed to detect somatic SVs and SCNAs at single-haplotype resolution and estimate tumor purity and ploidy using long-read sequencing data with or without a germline control sample. We also establish best practices for benchmarking SV detection algorithms across the entire genome in a data-driven manner using replication and read-backed phasing analysis. Through the analysis of matched Illumina and nanopore whole-genome sequencing data for 99 human tumor-normal pairs, we show that SAVANA has significantly higher sensitivity and 13- and 82-times-higher specificity than the second and third-best performing algorithms. Moreover, SVs reported by SAVANA are highly consistent with those detected using short-read sequencing. In summary, SAVANA enables the application of long-read sequencing to detect SVs and SCNAs reliably.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1436-1446"},"PeriodicalIF":36.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12240814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174108","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

Super-resolution microscopy for structural biology. 结构生物学的超分辨率显微镜。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-06-27 DOI: 10.1038/s41592-025-02731-1

John S H Danial

引用次数: 0

Bioimaging Brasil: democratizing in vivo optical microscopy to drive scientific progress across a vast nation. 生物成像巴西：民主化体内光学显微镜，推动科学进步在一个庞大的国家。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-06-16 DOI: 10.1038/s41592-025-02686-3

Maísa Mota Antunes, André Gustavo Oliveira, Cristina Maria de Paula, Teng-Leong Chew, Heitor A Paula-Neto, Gustavo B Menezes

引用次数: 0

BiaPy: accessible deep learning on bioimages. BiaPy：基于生物图像的可访问深度学习。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-06-01 DOI: 10.1038/s41592-025-02699-y

Daniel Franco-Barranco, Jesús A Andrés-San Román, Ivan Hidalgo-Cenalmor, Lenka Backová, Aitor González-Marfil, Clément Caporal, Anatole Chessel, Pedro Gómez-Gálvez, Luis M Escudero, Donglai Wei, Arrate Muñoz-Barrutia, Ignacio Arganda-Carreras

引用次数: 0

Dark sectioning boosts segmentation accuracy and image quality in fluorescence microscopy. 暗切片提高了荧光显微镜的分割精度和图像质量。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-06-01 DOI: 10.1038/s41592-025-02668-5

引用次数: 0

Super-resolution imaging technique for precision in vivo neuronal activity mapping. 超分辨率成像技术用于精确的体内神经元活动映射。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-06-01 DOI: 10.1038/s41592-025-02691-6

引用次数: 0

Barcoded CRISPR screens reveal RNA regulatory networks. 条形码CRISPR屏幕揭示RNA调控网络。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-06-01 DOI: 10.1038/s41592-025-02703-5

引用次数: 0