Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel Reinders (2024), An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics, In Briefings in Bioinformatics.

Mostafa Eltager, Tamim Abdelaal, Mohammed Charrout, A.M.E.T.A. Mahfouz, M.J.T. Reinders, Stavros Makrodimitris (2023), Benchmarking variational AutoEncoders on cancer transcriptomics data, In PLoS ONE Volume 18 .

Pia Keukeleire, Stavros Makrodimitris, Marcel Reinders (2023), Cell type deconvolution of methylated cell-free DNA at the resolution of individual reads, In NAR Genomics and Bioinformatics Volume 5.

Elisabeth M. Jongbloed, Maurice P.H.M. Jansen, Vanja de Weerd, Jean A. Helmijr, Corine M. Beaufort, Marcel J.T. Reinders, Ronald van Marion, Wilfred F.J. van IJcken, Stavros Makrodimitris (2023), Machine learning-based somatic variant calling in cell-free DNA of metastatic breast cancer patients using large NGS panels, In Scientific Reports Volume 13.

Irene van den Bent, Stavros Makrodimitris, Marcel Reinders (2021), The Power of Universal Contextualized Protein Embeddings in Cross-species Protein Function Prediction, In Evolutionary Bioinformatics Volume 17.

S. Makrodimitris (2021), What does that gene do?: Gene function prediction by machine learning with applications to plants, PhD Thesis Delft University of Technology.

Stavros Makrodimitris, Marcel Reinders, Roeland van Ham (2020), A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins, In PLoS ONE Volume 15 p.1-18.

Stavros Makrodimitris, Roeland C.H.J. Van Ham, Marcel J.T. Reinders (2020), Automatic gene function prediction in the 2020’s, In Genes p.1-18.

Erik B. van den Akker, Stavros Makrodimitris, Marc Hulsman, Martijn H. Brugman, Tatjana Nikolic, Ted Bradley, Quinten Waisfisz, Frank Baas, Marcel J.T. Reinders, Henne Holstege, More Authors (2020), Dynamic clonal hematopoiesis and functional T-cell immunity in a supercentenarian.

Katja Geertruida Schmahl, Tom Julian Viering, Stavros Makrodimitris, Arman Naseri Jahfari, David Tax, Marco Loog (2020), Is Wikipedia succeeding in reducing gender bias? Assessing changes in gender bias in Wikipedia using word embeddings, In Proceedings of the Fourth Workshop on Natural Language Processing and Computational Social Science p.94-103, Association for Computational Linguistics.