Learning Tn5 Sequence Bias from ATAC-seq on Naked Chromatin. - Meshal Ansari; David S. Fischer; Fabian J. Theis (ICANN (1), 2020)

Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data. - Philipp Angerer; David S. Fischer; Fabian J. Theis; Antonio Scialdone; Carsten Marr (Bioinform., 2020)

EpiScanpy: integrated single-cell epigenomic analysis. - Anna Danese; Maria L. Richter; Kridsadakorn Chaichoompu; David S. Fischer; Fabian J. Theis; Maria Colomé-Tatché (Zenodo, 2020)

[DEPRECATED] Theislab sfaira Model Repository. - Leander Dony; David S. Fischer; Fabian J. Theis (Zenodo, 2020)

Theislab sfaira Model Repository. - Leander Dony; David S. Fischer; Fabian J. Theis (Zenodo, 2021)

Modeling fragment counts improves single-cell ATAC-seq analysis. - Laura D. Martens; David S. Fischer; Vicente A. Yépez; Fabian J. Theis; Julien Gagneur (Zenodo, 2023)

Delineating the effective use of self-supervised learning in single-cell genomics. - Till Richter; Mojtaba Bahrami; Yufan Xia; David S. Fischer; Fabian J. Theis (Nat. Mac. Intell., 2025)

The Cell Ontology in the age of single-cell omics. - Shawn Zheng Kai Tan; Aleix Puig-Barbe; Damien Goutte-Gattat; Caroline Eastwood; Brian D. Aevermann; Alida Avola; James P. Balhoff; Ismail Ugur Bayindir; Jasmine Belfiore; Anita R. Caron; David S. Fischer; Nancy George; et al. (CoRR, 2025)