Regression-based Deep-Learning predicts molecular biomarkers from pathology slides. - Omar S. M. El Nahhas; Chiara Maria Lavinia Loeffler; Zunamys I. Carrero; Marko van Treeck; Fiona R. Kolbinger; Katherine Jane Hewitt; Hannah Sophie Muti; Mara Graziani; Qinghe Zeng; Julien Calderaro; Nadina Ortiz-Brüchle; Tanwei Yuan; et al. (CoRR, 2023)

From Whole-slide Image to Biomarker Prediction: A Protocol for End-to-End Deep Learning in Computational Pathology. - Omar S. M. El Nahhas; Marko van Treeck; Georg Wölflein; Michaela Unger; Marta Ligero; Tim Lenz; Sophia J. Wagner; Katherine Jane Hewitt; Firas Khader; Sebastian Foersch; Daniel Truhn; Jakob Nikolas Kather (CoRR, 2023)

Joint Multi-task Learning Improves Weakly-Supervised Biomarker Prediction in Computational Pathology. - Omar S. M. El Nahhas; Georg Wölflein; Marta Ligero; Tim Lenz; Marko van Treeck; Firas Khader; Daniel Truhn; Jakob Nikolas Kather (MICCAI (4), 2024)

Benchmarking foundation models as feature extractors for weakly-supervised computational pathology. - Peter Neidlinger; Omar S. M. El Nahhas; Hannah Sophie Muti; Tim Lenz; Michael Hoffmeister; Hermann Brenner; Marko van Treeck; Rupert Langer; Bastian Dislich; Hans-Michael Behrens; Christoph Röcken; Sebastian Foersch; et al. (CoRR, 2024)

Privacy-preserving large language models for structured medical information retrieval. - Isabella C. Wiest; Dyke Ferber; Jiefu Zhu; Marko van Treeck; Sonja K. Meyer; Radhika Juglan; Zunamys I. Carrero; Daniel Paech; Jens Kleesiek; Matthias P. Ebert; Daniel Truhn; Jakob Nikolas Kather (npj Digit. Medicine, 2024)

Unsupervised Foundation Model-Agnostic Slide-Level Representation Learning. - Tim Lenz; Peter Neidlinger; Marta Ligero; Georg Wölflein; Marko van Treeck; Jakob Nikolas Kather (CVPR, 2025)

Diagnosis with Nanoscale Protein Distributions: Single-Molecule Fluorescence Localization Microscopy and Attention-Based Learning. - Alistair Curd; Hayley Slaney; Scarlet F. Brockmöller; Andras-Gabor Miklosi; Deep Arora; Andrew Lewington; James H. Felce; Omar S. M. El Nahhas; Marko van Treeck; Jakob Nikolas Kather; Phil Quirke (ISBI, 2025)