Tessa Dieckman, Mette Schreurs, Ciska Lindelauf, Ahmed Mahfouz, Caroline R. Meijer, Louise Pigeaud, Vincent van Unen, Gerd Bouma, Frits Koning (2025), Activated CD27⁺PD-1⁺ CD8 T Cells and CD4 T Regulatory Cells Dominate the Tumor Microenvironment in Refractory Celiac Disease Type II, In Gastro Hep Advances Volume 4.

Felipe Correa-da-Silva, Jari B. Berkhout, Pim Schouten, Margje Sinnema, Constance T.R.M. Stumpel, Leopold M.G. Curfs, Charlotte Höybye, Ahmed Mahfouz, Onno C. Meijer, More Authors (2025), Selective changes in vasopressin neurons and astrocytes in the suprachiasmatic nucleus of Prader–Willi syndrome subjects, In Journal of Neuroendocrinology.

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.

Maud Heredia, Mohammed Charrout, Renz C.W. Klomberg, Martine A. Aardoom, Maria M.E. Jongsma, Polychronis Kemos, Danielle H. Hulleman-van Haaften, Ahmed Mahfouz, Marcel J.T. Reinders, More Authors (2024), Combined plasma protein and memory T cell profiling discern IBD-patient-immunotypes related to intestinal disease and treatment outcomes, In Mucosal Immunology Volume 18 (2025) p.76-89.

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.