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decoupleR: ensemble of computational methods to infer biological activities from omics data.
Badia-I-Mompel P, Vélez Santiago J, Braunger J, Geiss C, Dimitrov D, Müller-Dott S, Taus P, Dugourd A, Holland CH, Ramirez Flores RO, Saez-Rodriguez J. Badia-I-Mompel P, et al. Among authors: muller dott s. Bioinform Adv. 2022 Mar 8;2(1):vbac016. doi: 10.1093/bioadv/vbac016. eCollection 2022. Bioinform Adv. 2022. PMID: 36699385 Free PMC article.
Hepatocytes reprogram liver macrophages involving control of TGF-β activation, influencing liver regeneration and injury.
Wolf SD, Ehlting C, Müller-Dott S, Poschmann G, Petzsch P, Lautwein T, Wang S, Helm B, Schilling M, Saez-Rodriguez J, Vucur M, Stühler K, Köhrer K, Tacke F, Dooley S, Klingmüller U, Luedde T, Bode JG. Wolf SD, et al. Among authors: muller dott s. Hepatol Commun. 2023 Jul 24;7(8):e0208. doi: 10.1097/HC9.0000000000000208. eCollection 2023 Aug 1. Hepatol Commun. 2023. PMID: 37486964 Free PMC article.
Gene regulatory network inference in the era of single-cell multi-omics.
Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J. Badia-I-Mompel P, et al. Among authors: muller dott s. Nat Rev Genet. 2023 Nov;24(11):739-754. doi: 10.1038/s41576-023-00618-5. Epub 2023 Jun 26. Nat Rev Genet. 2023. PMID: 37365273 Review.