LASSIM - A network inference toolbox for genome-wide mechanistic modeling. - Rasmus Magnusson; Guido Pio Mariotti; Mattias Köpsén; William Lövfors; Danuta R. Gawel; Rebecka Jörnsten; Jörg Linde; Torbjörn E. M. Nordling; Elin Nyman; Sylvie Schulze; Colm E. Nestor; Huan Zhang; et al. (PLoS Comput. Biol., 2017)

LiPLike: towards gene regulatory network predictions of high certainty. - Rasmus Magnusson; Mika Gustafsson (Bioinform., 2020)

ComHub: Community predictions of hubs in gene regulatory networks. - Julia Åkesson; Zelmina Lubovac-Pilav; Rasmus Magnusson; Mika Gustafsson (BMC Bioinform., 2021)

TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes. - Rasmus Magnusson; Zelmina Lubovac-Pilav (BMC Bioinform., 2021)

Latent space arithmetic on data embeddings from healthy multi-tissue human RNA-seq decodes disease modules. - Hendrik A. de Weerd; Dimitri Guala; Mika Gustafsson; Jane Synnergren; Jesper Tegnér; Zelmina Lubovac-Pilav; Rasmus Magnusson (Patterns, 2024)