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.

Lieke Michielsen, Marcel J.T. Reinders, Ahmed Mahfouz (2021), Hierarchical progressive learning of cell identities in single-cell data, In Nature Communications Volume 12.

Rodrigo Coutinho de Almeida, Ahmed Mahfouz, Hailiang Mei, Evelyn Houtman, Wouter den Hollander, Jamie Soul, Eka Suchiman, Rob G.H.H. Nelissen, Marcel Reinders, More Authors (2021), Identification and characterization of two consistent osteoarthritis subtypes by transcriptome and clinical data integration, In Rheumatology (Oxford, England) Volume 60 p.1166-1175.

Mandy Meijer, Arlin Keo, Judith M.C. van Leeuwen, Oleh Dzyubachyk, Onno C. Meijer, Christiaan H. Vinkers, Ahmed Mahfouz (2021), Molecular characterization of the stress network in individuals at risk for schizophrenia, In Neurobiology of Stress Volume 14.