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Nature Methods|April 17, 2025
A highly stable monomeric red fluorescent protein for advanced microscopyHaiyan Xiong, Qiyuan Chang, Jiayi Ding, et al.Nature Methods|April 9, 2025
Efficient and robust search of microbial genomes via phylogenetic compressionKarel Břinda, Leandro Lima, Simone Pignotti, et al.Nature Methods|April 9, 2025
CAVE: Connectome Annotation Versioning EngineSven Dorkenwald, Casey M Schneider-Mizell, Derrick Brittain, et al.Nature Methods|March 18, 2025
scNET: learning context-specific gene and cell embeddings by integrating single-cell gene expression data with protein-protein interactionsRon Sheinin, Roded Sharan, Asaf MadiNature Methods|March 18, 2025
A computational pipeline for spatial mechano-transcriptomicsAdrien Hallou, Ruiyang He, Benjamin D Simons, et al.Nature Methods|March 14, 2025
Feature selection methods affect the performance of scRNA-seq data integration and queryingLuke Zappia, Sabrina Richter, Ciro Ramírez-Suástegui, et al.Nature Methods|March 13, 2025
Spotiphy enables single-cell spatial whole transcriptomics across an entire sectionJiyuan Yang, Ziqian Zheng, Yun Jiao, et al.Nature Methods|March 3, 2025
Reproducible image-based profiling with PycytominerErik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, et al.Nature Methods|June 14, 2024
The tidyomics ecosystem: enhancing omic data analysesWilliam J Hutchison, Timothy J Keyes, , et al.Nature Methods|June 6, 2024
Large-scale foundation model on single-cell transcriptomicsMinsheng Hao, Jing Gong, Xin Zeng, et al.Pageof 344