Horvath, P. & Coscia, F.* Spatial proteomics in translational and clinical research. Mol. Syst. Biol. 21, 526 - 530 (2025)
Pietzner, M.* et al. Machine learning-guided deconvolution of plasma protein levels. Mol. Syst. Biol., DOI: 10.1038/s44320-025-00158-6 (2025)
Stock, M. et al. Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data. Mol. Syst. Biol. 21, 214-230 (2025)
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)
Mitic, N.* et al. Dissecting the spatiotemporal diversity of adult neural stem cells. Mol. Syst. Biol. 20, 321-337 (2024)
Tomaz da Silva, P.* et al. Cellular energy regulates mRNA degradation in a codon-specific manner. Mol. Syst. Biol. 20, 506-520 (2024)
Lotfollahi, M. et al. Predicting cellular responses to complex perturbations in high-throughput screens. Mol. Syst. Biol. 19:e11517 (2023)
Polychronidou, M.* et al. Single-cell biology: What does the future hold? Mol. Syst. Biol. 19:e11799 (2023)
Thielert, M.* et al. Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Mol. Syst. Biol. 19:e11503 (2023)
Urban, L. et al. Real-time genomics for One Health. Mol. Syst. Biol. 19:e11686 (2023)
Brunner, A.D.* et al. Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation. Mol. Syst. Biol. 18:e10798 (2022)
Hersbach, B.A. et al. Probing cell identity hierarchies by fate titration and collision during direct reprogramming. Mol. Syst. Biol. 18:e11129 (2022)
Ibarra Del Rio, I.A. et al. Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements. Mol. Syst. Biol. 18:e10473 (2022)
Bergen, V. ; Soldatov, R.A.* ; Kharchenko, P.V.* & Theis, F.J. RNA velocity-current challenges and future perspectives. Mol. Syst. Biol. 17:e10282 (2021)
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)
Ostaszewski, M.* et al. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms. Mol. Syst. Biol. 17:e10387 (2021)
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)
Türei, D.* et al. Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Mol. Syst. Biol. 17:e9923 (2021)
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)
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)
Luecken, M. & Theis, F.J. Current best practices in single-cell RNA-seq analysis: A tutorial. Mol. Syst. Biol. 15:e8746 (2019)
Niu, L.* et al. Plasma proteome profiling discovers novel proteins associated with non-alcoholic fatty liver disease. Mol. Syst. Biol. 15:e8793 (2019)
Argelaguet, R.* et al. Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. Mol. Syst. Biol. 14:e8124 (2018)
Griffiths, J.A.* ; Scialdone, A. & Marioni, J.C.* Using single-cell genomics to understand developmental processes and cell fate decisions. Mol. Syst. Biol. 14:e8046 (2018)
Schiller, H. B.* et al. Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair. Mol. Syst. Biol. 11:819 (2015)
Iskar, M.* et al. Characterization of drug-induced transcriptional modules: Towards drug repositioning and functional understanding. Mol. Syst. Biol. 9:662 (2013)
Kuhn, M.* et al. Systematic identification of proteins that elicit drug side effects. Mol. Syst. Biol. 9:663 (2013)
Wang-Sattler, R. et al. Novel biomarkers for pre-diabetes identified by metabolomics. Mol. Syst. Biol. 8:615 (2012)
Kiel, C.* et al. Structural and functional protein network analyses predict novel signaling functions for rhodopsin. Mol. Syst. Biol. 7:551 (2011)