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.

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

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.

Lieke Michielsen, Mohammad Lotfollahi, Daniel Strobl, Lisa Sikkema, Marcel J.T. Reinders, Fabian J. Theis, Ahmed Mahfouz (2023), Single-cell reference mapping to construct and extend cell-type hierarchies, In NAR Genomics and Bioinformatics Volume 5 p.12.

L. G.M. Heezen, T. Abdelaal, M. van Putten, A. Aartsma-Rus, A. Mahfouz, P. Spitali (2023), Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models, In Nature Communications Volume 14.

Philippe C. Habets, Konstantinos Kalafatakis, Oleh Dzyubachyk, Steven J.A. van der Werff, Arlin Keo, Jamini Thakrar, Ahmed Mahfouz, Alberto M. Pereira, Georgina M. Russell, More Authors (2023), Transcriptional and cell type profiles of cortical brain regions showing ultradian cortisol rhythm dependent responses to emotional face stimulation, In Neurobiology of Stress Volume 22.