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21.
Marconato, L.* et al.: SpatialData: An open and universal data framework for spatial omics. Nat. Methods, DOI: 10.1038/s41592-024-02212-x (2024)
22.
Martens, L.D. ; Fischer, D.S. ; Yépez, V.A.* ; Theis, F.J. & Gagneur, J.: Modeling fragment counts improves single-cell ATAC-seq analysis. Nat. Methods 21, 28–31 (2024)
23.
Pfeuffer, J.* et al.: OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat. Methods 21, 365-367 (2024)
24.
Reinke, A.* et al.: Understanding metric-related pitfalls in image analysis validation. Nat. Methods 21, 182–194 (2024)
25.
Stiel, A.-C. & Ntziachristos, V.: Controlling the sound of light: photoswitching optoacoustic imaging. Nat. Methods 21, 1996-2007 (2024)
26.
Szałata, A. et al.: Transformers in single-cell omics: A review and new perspectives. Nat. Methods 21, 1430-1443 (2024)
27.
Truong, D.J.J. et al.: Exonuclease-enhanced prime editors. Nat. Methods 21, 455-464 (2024)
28.
Weiler, P. ; Lange, M. ; Klein, M. ; Pe'er, D.* & Theis, F.J.: CellRank 2: Unified fate mapping in multiview single-cell data. Nat. Methods, DOI: 10.1038/s41592-024-02303-9 (2024)
29.
Agam, G.* et al.: Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nat. Methods 20, 523-535 (2023)
30.
Beagrie, R.A.* et al.: Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C. Nat. Methods 20, 1037-1047 (2023)
31.
De Donno, C. et al.: Population-level integration of single-cell datasets enables multi-scale analysis across samples. Nat. Methods 20, 1683-1692 (2023)
32.
Rosenberger, F.A.* et al.: Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome. Nat. Methods 20, 1530-1536 (2023)
33.
Sandoval-Guzmán, T.: The axolotl. Nat. Methods 20, 1117-1119 (2023)
34.
Spitzer, H. ; Berry, S.* ; Donoghoe, M.* ; Pelkmans, L.* & Theis, F.J.: Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps. Nat. Methods 20, 1058-1069 (2023)
35.
Bandi, V.G.* et al.: Targeted multicolor in vivo imaging over 1,000 nm enabled by nonamethine cyanines. Nat. Methods 19, 353–358 (2022)
36.
Giansanti, P.* et al.: Mass spectrometry-based draft of the mouse proteome. Nat. Methods 19, 803-811 (2022)
37.
Lange, M. et al.: CellRank for directed single-cell fate mapping. Nat. Methods 19, 159–170 (2022)
38.
Luecken, M. et al.: Benchmarking atlas-level data integration in single-cell genomics. Nat. Methods 19, 41-50 (2022)
39.
Palla, G. et al.: Squidpy: A scalable framework for spatial omics analysis. Nat. Methods 19, 171–178 (2022)
40.
Matschinske, J.* et al.: The AIMe registry for artificial intelligence in biomedical research. Nat. Methods, DOI: 10.1038/s41592-021-01241-0 (2021)
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