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Nature Methods|April 15, 2024
Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choiceHonggui Wu, Jiankun Zhang, Fanchong Jian, et al.Nature Methods|April 11, 2024
brainlife.io: a decentralized and open-source cloud platform to support neuroscience researchSoichi Hayashi, Bradley A Caron, Anibal Sólon Heinsfeld, et al.Nature Methods|January 15, 2026
MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discoveryWilliam A Nickols, Thomas Kuntz, Jiaxian Shen, et al.Nature Methods|February 9, 2026
Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometryMingdu Luo, Tianzhang Kou, Yandong Yin, et al.Nature Methods|December 11, 2025
Benchmarking algorithms for generalizable single-cell perturbation response predictionZhiting Wei, Yiheng Wang, Yicheng Gao, et al.Nature Methods|December 2, 2025
CaBLAM: a high-contrast bioluminescent Ca2+ indicator derived from an engineered Oplophorus gracilirostris luciferaseGerard G Lambert, Emmanuel L Crespo, Jeremy Murphy, et al.Nature Methods|November 25, 2025
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov modelFelix Holst, Anthony M Bolger, Felicitas Kindel, et al.Nature Methods|January 20, 2025
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencingYun Li, Zheng Huang, Lubin Xu, et al.Nature Methods|February 6, 2025
Live imaging of the extracellular matrix with a glycan-binding fluorophoreAntonio Fiore, Guoqiang Yu, Jason J Northey, et al.Nature Methods|December 13, 2024
Considerations for building and using integrated single-cell atlasesKarin Hrovatin, Lisa Sikkema, Vladimir A Shitov, et al.Pageof 338