| decoupleR: ensemble of computational methods to infer biological activities from omics data P Badia-i-Mompel, J Vélez Santiago, J Braunger, C Geiss, D Dimitrov, ... Bioinformatics Advances 2 (1), vbac016, 2022 | 343 | 2022 |
| Gene regulatory network inference in the era of single-cell multi-omics P Badia-i-Mompel, L Wessels, S Müller-Dott, R Trimbour, ... Nature Reviews Genetics 24 (11), 739-754, 2023 | 177 | 2023 |
| Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities S Müller-Dott, E Tsirvouli, M Vazquez, RO Ramirez Flores, ... Nucleic acids research 51 (20), 10934-10949, 2023 | 111 | 2023 |
| GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks A Kamal, C Arnold, A Claringbould, R Moussa, NH Servaas, M Kholmatov, ... Molecular Systems Biology 19 (6), e11627, 2023 | 39 | 2023 |
| Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities B Salovska, E Gao, S Müller‐Dott, W Li, CC Cordon, S Wang, A Dugourd, ... Clinical and Translational Medicine 13 (2), e1179, 2023 | 12 | 2023 |
| Hepatocytes reprogram liver macrophages involving control of TGF-β activation, influencing liver regeneration and injury SD Wolf, C Ehlting, S Müller-Dott, G Poschmann, P Petzsch, T Lautwein, ... Hepatology Communications 7 (8), e0208, 2023 | 4 | 2023 |
| Evaluating signaling pathway inference from kinase-substrate interactions and phosphoproteomics data M Garrido-Rodriguez, C Potel, ML Burtscher, I Becher, P Rodriguez-Mier, ... bioRxiv, 2024.10. 21.619348, 2024 | 1 | 2024 |
| Comprehensive evaluation of phosphoproteomic-based kinase activity inference S Mueller-Dott, EJ Jaehnig, KP Munchic, W Jiang, TM Yaron-Barir, ... bioRxiv, 2024.06. 27.601117, 2024 | 1 | 2024 |
| NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks V Paton, D Türei, O Ivanova, S Müller-Dott, P Rodriguez-Mier, V Venafra, ... Bioinformatics, btaf048, 2025 | | 2025 |
| TGF-β critically determines the activation state of both, the macrophage subpopulation that is particularly recruited in the context of MASH progression, as well as of TAMs SD Wolf, S Hammad, S Müller-Dott, T Lautwein, K Köhrer, ... Zeitschrift für Gastroenterologie 63 (01), P4. 15, 2025 | | 2025 |
| PhosX: data-driven kinase activity inference from phosphoproteomics experiments A Lussana, S Müller-Dott, J Saez-Rodriguez, E Petsalaki Bioinformatics 40 (12), btae697, 2024 | | 2024 |
| Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data P Badia-i-Mompel, R Casals-Franch, L Wessels, S Müller-Dott, ... bioRxiv, 2024.12. 20.629764, 2024 | | 2024 |
| Progression of MASLD goes along with significant changes of a recruited and TGFb sensitive macrophage population SD Wolf, MC Malms, S Müller-Dott, T Lautwein, S Hammad, K Köhrer, ... Zeitschrift für Gastroenterologie 62 (01), P3. 04, 2024 | | 2024 |