Publications

2024

1. sctree: Discovering cellular hierarchies in the presence of batch effects in scrna-seq data

   Moritz Vandenhirtz^*, Florian Barkmann^*, Laura Manduchi, Julia E Vogt, and Valentina Boeva

   arXiv preprint arXiv:2406.19300, 2024

   Spotlight

2. CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer

   Alexander Theus^*, Florian Barkmann^*, David Wissel, and Valentina Boeva

   bioRxiv, 2024
3. Benchmarking Self-Supervised Learning for Single-Cell Data

   Philip Toma^*, Olga Ovcharenko^*, Imant Daunhawer, Julia Vogt, Florian Barkmann^**, and Valentina Boeva^**

   bioRxiv, 2024

2023

1. scROSHI: robust supervised hierarchical identification of single cells

   Michael Prummer, Anne Bertolini, Lars Bosshard, Florian Barkmann, Josephine Yates, Valentina Boeva, Daniel Stekhoven, and Franziska Singer

   NAR Genomics and Bioinformatics, 2023
2. Superiorization of projection algorithms for linearly constrained inverse radiotherapy treatment planning

   Florian Barkmann, Yair Censor, and Niklas Wahl

   Frontiers in Oncology, 2023
3. ANS: Adjusted Neighborhood Scoring to improve assessment of gene signatures in single-cell RNA-seq data

   Laure Ciernik, Agnieszka Kraft, Florian Barkmann, Josephine Yates, and Valentina Boeva

   bioRxiv, 2023

2022

1. CanSig: discovery of shared transcriptional states across cancer patients from single-cell RNA sequencing data

   Josephine Yates^*, Florian Barkmann^*, Pawel Czyz^*, Agnieszka Kraft, Marc Glettig, Frederieke Lohmann, Elia Saquand, Richard Horst, and 3 more authors

   bioRxiv, 2022