Publications
Ceccarelli, F., Lio, P., Saez-Rodriguez, J., Holden, S. B., Tanevski, J.
Topography Aware Optimal Transport for Alignment of Spatial Omics Data.
bioRxiv:2025.04.15.648894 (2025).
Schiller, C., Ibarra-Arellano, Miguel A., Bestak, K., Tanevski, J., Schapiro, D.
Comparison and Optimization of Cellular Neighbor Preference Methods for Quantitative Tissue Analysis.
bioRxiv:2025.03.31.646289 (2025).
Tanevski, J., Vuillard, L., Hartmann, F., Saez-Rodriguez, J.
Learning tissue representation by identification of persistent local patterns in spatial omics data.
bioRxiv:2024.03.06.583691 (2024).
Rahimi, A., Vale-Silva, L.A., Faelth Savitski, M., Tanevski, J., Saez-Rodriguez, J.
DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics.
Nature Communications 15 (2024).
Dimitrov, D., Schäfer, P.S.L., Farr, E., et al.
LIANA+ provides an all-in-one framework for cell–cell communication inference.
Nature Cell Biology (2024).
Laury, A. R., Zheng, S., Aho, N. et al.
Opening the black box: spatial transcriptomics and the relevance of AI-detected prognostic regions in high grade serous carcinoma.
Modern Pathology 100508 (2024).
Paton, V., Gabor, A., Ramirez Flores, R.O. et al.
Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results.
Nucleic Acids Research (2024).
Wünnemann, F., Sicklinger, F., Bestak, K., et al.
Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration.
bioRxiv:2024.05.20.594955 (2024).
Heumos, L., Schaar, A.C., Lance, C. et al.
Best practices for single-cell analysis across modalities.
Nature Reviews Genetics 24, 550–572 (2023).
Tanevski, J., Ramirez Flores, R.O., Gabor, A. et al.
Explainable multiview framework for dissecting spatial relationships from highly multiplexed data.
Genome Biology 23, 97 (2022).
Kuppe, C., Ramirez Flores, R.O., Li, Z. et al.
Spatial multi-omic map of human myocardial infarction.
Nature 608, 766–777 (2022).
Gabor, A., Tognetti, M., Driessen, A., Tanevski, J. et al.
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd.
Molecular Systems Biology, 17(10), e10402 (2021).
Schwabenland, M., Salié, H., Tanevski, J. et al.
Deep spatial profiling of human COVID-19 brains reveals neuroinflammation with distinct microanatomical microglia-T-cell interactions.
Immunity 54(70), 1594-1610.e11 (2021)
Holland, C.H., Tanevski, J., Perales-Patón, J. et al.
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.
Genome Biology 21, 36 (2020).
Tanevski, J., Nguyen, T., Truong, B. et al.
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data.
Life Science Alliance 3 (11), e202000867 (2020).
Tanevski, J., Todorovski, L., Džeroski, S.
Combinatorial search for selecting the structure of models of dynamical systems with equation discovery.
Engineering Applications of Artificial Intelligence 89, 103423 (2020).
Tanevski, J., Todorovski, L., Džeroski, S.
Process-based design of dynamical biological systems.
Scientific Reports 6, 34107 (2016).
Tanevski, J., Todorovski, L., Džeroski, S.
Learning stochastic process-based models of dynamical systems from knowledge and data.
BMC Systems Biology 10, 30 (2016).