BEAT IT publications

Dietrich A*, Merotto L*, Pelz K, Eder B, Zackl C, Reinisch K, Edenhofer F, Marini F, Sturm G, List M†, Finotello F†. Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data. Genome Biology. 2026; 27(1):6. https://doi.org/10.1186/s13059-026-03955-w

Ausserhofer M, Rieder D, Facciolla M, Gronauer R, Lamberti G, Lisandrelli R, Pellegatta S, Trajanoski Z, Finotello F†. NovumRNA: accurate prediction of non-canonical tumor antigens from RNA sequencing data. iScience, 2025; 28(10):113448.  https://doi.org/10.1016/j.isci.2025.113448

van Santvoort M, Lapuente-Santana Ó, Finotello F, van der Hoorn P, Eduati F. Mathematically mapping the network of cells in the tumor microenvironment. Cell Report Methods, 2025; 5(2):100985. https://doi.org/10.1016/j.crmeth.2025.100985

Lapuente-Santana Ó, Sturm G, Kant J, Ausserhofer M, Zackl C, Zopoglou M, McGranahan N, Rieder D, Trajanoski Z, da Cunha Carvalho de Miranda NF, Eduati F†, Finotello F†. Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion. iScience, 2024; 27(8):110529. https://doi.org/10.1016/j.isci.2024.110529

Spathopoulou A, Podlesnic M, De Gaetano L, Kirsch EM, Tisch M, Finotello F, Aigner L, Günther K, Edenhofer F. Single-cell Profiling of Reprogrammed Human Neural Stem Cells Unveils High Similarity to Neural Progenitors in the Developing Central Nervous System. Stem Cell Reviews and Reports. 2024; 20(5):1325-1339.  https://doi.org/10.1007/s12015-024-10698-3

Merotto L, Sturm G, Dietrich A, List M, Finotello F†. Making mouse transcriptomics deconvolution accessible with immunedeconv, Bioinformatics Advances, 2024; 4(1):vbae032. https://doi.org/10.1093/bioadv/vbae032