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Nature Methods|March 29, 2025
Atomic context-conditioned protein sequence design using LigandMPNNJustas Dauparas, Gyu Rie Lee, Robert Pecoraro, et al.Nature Methods|March 31, 2025
Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagementIno de Bruijn, Milen Nikolov, Clarisse Lau, et al.Nature Methods|March 25, 2025
Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerabilityDongsheng Bai, Zhenkun Cao, Nivedita Attada, et al.Nature Methods|November 20, 2025
4Pi-SIMFLUX: 4Pi single-molecule localization microscopy with structured illuminationQian Wang, Bei Zheng, Zijing Yu, et al.Nature Methods|November 3, 2025
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transportGeert-Jan Huizing, Jules Samaran, Daniele Capocefalo, et al.Nature Methods|October 30, 2025
Annotating the genome at single-nucleotide resolution with DNA foundation modelsBernardo P de Almeida, Hugo Dalla-Torre, Guillaume Richard, et al.Nature Methods|September 23, 2025
Kilohertz volumetric imaging of in vivo dynamics using squeezed light field microscopyZhaoqiang Wang, Ruixuan Zhao, Daniel A Wagenaar, et al.Nature Methods|September 23, 2025
Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropodsOtso Ovaskainen, Steven Winter, Gleb Tikhonov, et al.Nature Methods|September 15, 2025
MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysisTeresa Zulueta-Coarasa, Florian Jug, Aastha Mathur, et al.Nature Methods|September 15, 2025
The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbesYingjie Li, Anjun Ma, Evan Johnson, et al.Pageof 337