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1.
Ertürk, A.: Deep 3D histology powered by tissue clearing, omics and AI. Nat. Methods 21, 1153-1165 (2024)
2.
Frenz-Wiessner, S.* et al.: Generation of complex bone marrow organoids from human induced pluripotent stem cells. Nat. Methods, DOI: 10.1038/s41592-024-02172-2 (2024)
3.
Gayoso, A.* et al.: Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells. Nat. Methods 21, 50-59 (2024)
4.
Kaltenecker, D. et al.: Virtual reality-empowered deep-learning analysis of brain cells. Nat. Methods, DOI: 10.1038/s41592-024-02245-2 (2024)
5.
Kretschmer, F.* ; Harrieder, E.-M. ; Hoffmann, M.A.* ; Böcker, S.* & Witting, M.: RepoRT: A comprehensive repository for small molecule retention times. Nat. Methods 21, 153–155 (2024)
6.
Maier-Hein, L.* et al.: Metrics reloaded: Recommendations for image analysis validation. Nat. Methods 21, 195-212 (2024)
7.
Marconato, L.* et al.: SpatialData: An open and universal data framework for spatial omics. Nat. Methods, DOI: 10.1038/s41592-024-02212-x (2024)
8.
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)
9.
Pfeuffer, J.* et al.: OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat. Methods 21, 365-367 (2024)
10.
Reinke, A.* et al.: Understanding metric-related pitfalls in image analysis validation. Nat. Methods 21, 182–194 (2024)
11.
Truong, D.J.J. et al.: Exonuclease-enhanced prime editors. Nat. Methods 21, 455-464 (2024)
12.
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)
13.
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)
14.
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)
15.
De Donno, C. et al.: Population-level integration of single-cell datasets enables multi-scale analysis across samples. Nat. Methods 20, 1683-1692 (2023)
16.
Rosenberger, F.A.* et al.: Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome. Nat. Methods 20, 1530-1536 (2023)
17.
Sandoval-Guzmán, T.: The axolotl. Nat. Methods 20, 1117-1119 (2023)
18.
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)
19.
Bandi, V.G.* et al.: Targeted multicolor in vivo imaging over 1,000 nm enabled by nonamethine cyanines. Nat. Methods 19, 353–358 (2022)
20.
Giansanti, P.* et al.: Mass spectrometry-based draft of the mouse proteome. Nat. Methods 19, 803-811 (2022)
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