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.

Akash Singh, Kirti Biharie, Marcel J.T. Reinders, Ahmed Mahfouz, Tamim Abdelaal (2023), scTopoGAN: unsupervised manifold alignment of single-cell data, In Bioinformatics Advances Volume 3.

Gangqi Wang, Bram Heijs, Sarantos Kostidis, Ahmed Mahfouz, Rosalie G.J. Rietjens, Roel Bijkerk, Angela Koudijs, Loïs A.K. van der Pluijm, Cathelijne W. van den Berg, More Authors (2022), Analyzing cell-type-specific dynamics of metabolism in kidney repair, In Nature Metabolism Volume 4 p.1109-1118.

F. Ferraro, Christina Fevga, Vincenzo Bonifati, Wim Mandemakers, A.M.E.T.A. Mahfouz, M.J.T. Reinders (2022), Correcting Differential Gene Expression Analysis for Cyto—Architectural Alterations in Substantia Nigra of Parkinson’s Disease Patients Reveals Known and Potential Novel Disease—Associated Genes and Pathways, In Cells Volume 11.

Vincent van Unen, Laura F. Ouboter, Na Li, Mette Schreurs, Tamim Abdelaal, Yvonne Kooy-Winkelaar, Guillaume Beyrend, Thomas Höllt, P. W.Jeroen Maljaars, M. Luisa Mearin, Ahmed Mahfouz, Anne M.C. Witte, Cornelis H.M. Clemens, Sunje Abraham, Johanna C. Escher, Boudewijn P.F. Lelieveldt, M. Fernanda Pascutti, Andrea E. van der Meulen – de Jong, Frits Koning (2022), Identification of a Disease-Associated Network of Intestinal Immune Cells in Treatment-Naive Inflammatory Bowel Disease, In Frontiers in Immunology Volume 13.