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

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.

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.

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

Tamim Abdelaal, Lieke C.M. Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J.T. Reinders, Ahmed Mahfouz (2019), A comparison of automatic cell identification methods for single-cell RNA sequencing data, In Genome biology Volume 20 p.1-19.

Sjoerd M.H. Huisman, Baldur Van Lew, Ahmed Mahfouz, Nicola Pezzotti, Thomas Höllt, Lieke Michielsen, Anna Vilanova, Marcel J.T. Reinders, Boudewijn P.F. Lelieveldt (2017), BrainScope: Interactive visual exploration of the spatial and temporal human brain transcriptome, In Nucleic Acids Research Volume 45.