Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel Reinders (2024), An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics, In Briefings in Bioinformatics.

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 .

Liv Cecilie Vestrheim Thomsen, Katrin Kleinmanns, Shamundeeswari Anandan, Stein Erik Gullaksen, Tamim Abdelaal, Grete Alrek Iversen, Lars Andreas Akslen, Emmet McCormack, Line Bjørge (2023), Combining Mass Cytometry Data by CyTOFmerge Reveals Additional Cell Phenotypes in the Heterogeneous Ovarian Cancer Tumor Microenvironment: A Pilot Study, In Cancers Volume 15.

Na Li, Junhui Zhu, Peiru Chen, Chuntong Bao, Jun Wang, Tamim Abdelaal, Dexi Chen, Sibo Zhu, Wenjing Wang, More Authors (2023), High-dimensional analysis reveals an immune atlas and novel neutrophil clusters in the lungs of model animals with Actinobacillus pleuropneumoniae-induced pneumonia, In Veterinary research Volume 54 p.76.

Tetje C. van der Sluis, Guillaume Beyrend, Esmé T.I. van der Gracht, Tamim Abdelaal, Simon P. Jochems, Robert A. Belderbos, Thomas H. Wesselink, Suzanne van Duikeren, Ramon Arens, More Authors (2023), OX40 agonism enhances PD-L1 checkpoint blockade by shifting the cytotoxic T cell differentiation spectrum, In Cell Reports Medicine Volume 4.

Yun Zhang, Jeremy A. Miller, Jeongbin Park, Boudewijn P. Lelieveldt, Tamim Abdelaal, Oleh Dzyubachyk, Ed S. Lein, Richard H. Scheuermann, More Authors (2023), Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain, In Scientific Reports Volume 13.

Chang Li, Julian Thijssen, Thomas Kroes, Mitchell de Boer, Tamim Abdelaal, Thomas Höllt, Boudewijn Lelieveldt (2023), SpaceWalker enables interactive gradient exploration for spatial transcriptomics data, In Cell Reports Methods Volume 3.

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.

Hester Koppejan, Guillaume Beyrend, Marjolijn Hameetman, Tamim Abdelaal, René E.M. Toes, Floris A. van Gaalen (2023), Spondyloarthritis mass cytometry immuno-monitoring: a proof of concept study in the tight-control and treat-to target TiCoSpA trial, In Clinical Rheumatology Volume 42 p.2387-2396.

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.