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1.
Lobentanzer, S.* ; Rodriguez-Mier, P.* ; Bauer, S. & Saez-Rodriguez, J.*: Molecular causality in the advent of foundation models. Mol. Syst. Biol., DOI: 10.1038/s44320-024-00041-w (2024)
2.
Mitic, N.* et al.: Dissecting the spatiotemporal diversity of adult neural stem cells. Mol. Syst. Biol. 20, 321-337 (2024)
3.
Tomaz da Silva, P.* et al.: Cellular energy regulates mRNA degradation in a codon-specific manner. Mol. Syst. Biol. 20, 506-520 (2024)
4.
Lotfollahi, M. et al.: Predicting cellular responses to complex perturbations in high-throughput screens. Mol. Syst. Biol. 19:e11517 (2023)
5.
Polychronidou, M.* et al.: Single-cell biology: What does the future hold? Mol. Syst. Biol. 19:e11799 (2023)
6.
Thielert, M.* et al.: Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Mol. Syst. Biol. 19:e11503 (2023)
7.
Urban, L. et al.: Real-time genomics for One Health. Mol. Syst. Biol. 19:e11686 (2023)
8.
Brunner, A.D.* et al.: Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation. Mol. Syst. Biol. 18:e10798 (2022)
9.
Hersbach, B.A. et al.: Probing cell identity hierarchies by fate titration and collision during direct reprogramming. Mol. Syst. Biol. 18:e11129 (2022)
10.
Ibarra Del Rio, I.A. et al.: Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements. Mol. Syst. Biol. 18:e10473 (2022)
11.
Bergen, V. ; Soldatov, R.A.* ; Kharchenko, P.V.* & Theis, F.J.: RNA velocity-current challenges and future perspectives. Mol. Syst. Biol. 17:e10282 (2021)
12.
Molbay, M. ; Kolabas, Z.I. ; Todorov, M.I. ; Ohn, T.-L. & Ertürk, A.: A guidebook for DISCO tissue clearing. Mol. Syst. Biol. 17:e9807 (2021)
13.
Ostaszewski, M.* et al.: COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms. Mol. Syst. Biol. 17:e10387 (2021)
14.
Ostaszewski, M.* et al.: COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms (vol 17, e10387, 2021). Mol. Syst. Biol. 17:e10851 (2021)
15.
Türei, D.* et al.: Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Mol. Syst. Biol. 17:e9923 (2021)
16.
Fischer, D.S. ; Wu, Y. ; Schubert, B. & Theis, F.J.: Predicting antigen specificity of single T cells based on TCR CDR3 regions. Mol. Syst. Biol. 16:e9416 (2020)
17.
Eraslan, B.* et al.: Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues. Mol. Syst. Biol. 15:e8513 (2019)
18.
Luecken, M. & Theis, F.J.: Current best practices in single-cell RNA-seq analysis: A tutorial. Mol. Syst. Biol. 15:e8746 (2019)
19.
Niu, L.* et al.: Plasma proteome profiling discovers novel proteins associated with non-alcoholic fatty liver disease. Mol. Syst. Biol. 15:e8793 (2019)
20.
Argelaguet, R.* et al.: Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. Mol. Syst. Biol. 14:e8124 (2018)
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