Tessa Dieckman, Mette Schreurs, Ahmed Mahfouz, Yvonne Kooy-Winkelaar, Andra Neefjes-Borst, Gerd Bouma, Frits Koning (2022), Single-Cell Analysis of Refractory Celiac Disease Demonstrates Inter- and Intra-Patient Aberrant Cell Heterogeneity, In CMGH Volume 14 p.173-192.

Florencia Morgana, Rianne Opstelten, Manon C. Slot, Andrew M. Scott, René A.W. van Lier, Bianca Blom, Ahmed Mahfouz, Derk Amsen (2022), Single-Cell Transcriptomics Reveals Discrete Steps in Regulatory T Cell Development in the Human Thymus, In Journal of immunology (Baltimore, Md. : 1950) Volume 208 p.384-395.

Gangqi Wang, Bram Heijs, Sarantos Kostidis, Rosalie G.J. Rietjens, Ahmed Mahfouz, Susana M. Chuva de Sousa Lopes, Cathelijne W. van den Berg, Bernard M. van den Berg, Ton J. Rabelink, More Authors (2022), Spatial dynamic metabolomics identifies metabolic cell fate trajectories in human kidney differentiation, In Cell Stem Cell Volume 29 p.1580-1593.e7.

Arno R. Bourgonje, Shixian Hu, Lieke M. Spekhorst, Daria V. Zhernakova, Arnau Vich Vila, Yanni Li, Mohammed Charrout, Ahmed Mahfouz, Marcel J.T. Reinders, More Authors (2022), The Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease, In Journal of Crohn's and Colitis Volume 16 p.414-429.

M.A.M.E. Eltager, T.R.M. Abdelaal, A.M.E.T.A. Mahfouz, M.J.T. Reinders (2022), scMoC: single-cell multi-omics clustering, In Bioinformatics Advances Volume 2 p.1-8.

Anoushka Joglekar, Andreyi Prjibelski, Ahmed Mahfouz, Paul Collier, Susan Lin , Anna Katharina Schlusche, Jordan Marrocco, Stephen R. Williams, Bettina Haase, More Authors (2021), A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain, In Nature Communications Volume 12 p.1-16.

Wenbo Yu, Ahmed Mahfouz, Marcel J.T. Reinders (2021), CBA: Cluster-Guided Batch Alignment for Single Cell RNA-seq, In Frontiers in Genetics Volume 12 p.1-12.

Eva M.G. Viho, Jacobus C. Buurstede, Jari B. Berkhout, Ahmed Mahfouz, Onno C. Meijer (2021), Cell type specificity of glucocorticoid signaling in the adult mouse hippocampus, In Journal of Neuroendocrinology Volume 34 (2022).

Arlin Keo, Oleh Dzyubachyk, Jeroen van der Grond, Anne Hafkemeijer, Wilma D.J. van de Berg, Jacobus J. van Hilten, Marcel J.T. Reinders, Ahmed Mahfouz (2021), Cingulate networks associated with gray matter loss in Parkinson's disease show high expression of cholinergic genes in the healthy brain, In European journal of neuroscience Volume 53 p.3727-3739.

Gerard A. Bouland, Ahmed Mahfouz, Marcel J.T. Reinders (2021), Differential analysis of binarized single-cell RNA sequencing data captures biological variation, In NAR Genomics and Bioinformatics Volume 3.