J. B. Berkhout, D. Poormoghadam, C. Yi, A. Kalsbeek, O. C. Meijer, A. Mahfouz (2024), An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptomic and functional types, In Journal of Neuroendocrinology Volume 36.

Adam Tisch, Siddharth Madapoosi, Stephen Blough, Jan Rosa, Sean Eddy, Laura Mariani, Abhijit Naik, Ahmed Mahfouz, Fadhl Alakwaa, More Authors (2024), Identification of kidney cell types in scRNA-seq and snRNA-seq data using machine learning algorithms, In Heliyon Volume 10.

Joana B. Nunes, Marieke E. Ijsselsteijn, Tamim Abdelaal, Rick Ursem, Manon van der Ploeg, Martin Giera, Bart Everts, Ahmed Mahfouz, Bram Heijs, Noel F.C.C. de Miranda (2024), Integration of mass cytometry and mass spectrometry imaging for spatially resolved single-cell metabolic profiling, In Nature Methods Volume 21 p.1796-1800.

Lieke Michielsen, Marcel J. T. Reinders, Ahmed Mahfouz (2024), Predicting cell population-specific gene expression from genomic sequence, In Frontiers in Bioinformatics Volume 4.

Tamim Abdelaal, Laurens M. Grossouw, R. Jeroen Pasterkamp, Boudewijn P.F. Lelieveldt, Marcel J.T. Reinders, Ahmed Mahfouz (2024), SIRV: Spatial inference of RNA velocity at the single-cell resolution, In NAR Genomics and Bioinformatics Volume 6.

Dongxu Zheng, Annelot Wondergem, Susan Kloet, Iris Willemsen, Judit Balog, Stephen J. Tapscott, Ahmed Mahfouz, Anita Van Den Heuvel, Silvère M. Van Der Maarel (2024), snRNA-seq analysis in multinucleated myogenic FSHD cells identifies heterogeneous FSHD transcriptome signatures associated with embryonic-like program activation and oxidative stress-induced apoptosis, In Human Molecular Genetics Volume 33 p.284-298.

Claudio Novella-Rausell, Magda Grudniewska, Dorien J.M. Peters, Ahmed Mahfouz (2023), A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery, In iScience Volume 26.

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 .

Kirti Biharie, Lieke Michielsen, Marcel J.T. Reinders, Ahmed Mahfouz (2023), Cell type matching across species using protein embeddings and transfer learning, In Bioinformatics (Oxford, England) Volume 39 p.i404-i412.

Gerard A. Bouland, Ahmed Mahfouz, Marcel J.T. Reinders (2023), Consequences and opportunities arising due to sparser single-cell RNA-seq datasets, In Genome biology Volume 24.