Oasis: online analysis of small RNA deep sequencing data. - Vincenzo Capece; Julio C. Garcia Vizcaino; Ramon Vidal; Raza-Ur Rahman; Tonatiuh Pena Centeno; Orr Shomroni; Irantzu Suberviola; André Fischer; Stefan Bonn (Bioinform., 2015)

Root demotion: efficient post-processing of layered graphs to reduce dummy vertices for hierarchical graph drawing. - Daniel Sumner Magruder; Stefan Bonn (J. Graph Algorithms Appl., 2017)

A semantic data integration methodology for translational neurodegenerative disease research. - Sumit Madan; Maksims Fiosins; Stefan Bonn; Juliane Fluck (SWAT4LS, 2018)

Oasis 2: improved online analysis of small RNA-seq data. - Raza-Ur Rahman; Abhivyakti Gautam; Jörn Bethune; Abdul Sattar 004; Maksims Fiosins; Daniel Sumner Magruder; Vincenzo Capece; Orr Shomroni; Stefan Bonn (BMC Bioinform., 2018)

Deep Learning and Random Forest-Based Augmentation of sRNA Expression Profiles. - Jelena Fiosina; Maksims Fiosins; Stefan Bonn (ISBRA, 2019)

Explainable Deep Learning for Augmentation of sRNA Expression Profiles. - Jelena Fiosina; Maksims Fiosins; Stefan Bonn (CoRR, 2019)

Explainable Deep Learning for Augmentation of Small RNA Expression Profiles. - Jelena Fiosina; Maksims Fiosins; Stefan Bonn (J. Comput. Biol., 2020)

SEAweb: the small RNA Expression Atlas web application. - Raza-Ur Rahman; Anna-Maria Liebhoff; Vikas Bansal; Maksims Fiosins; Ashish Rajput; Abdul Sattar 004; Daniel Sumner Magruder; Sumit Madan; Ting Sun; Abhivyakti Gautam; Sven Heins; Timur Liwinski; et al. (Nucleic Acids Res., 2020)

Deep Learning-Based Bias Transfer for Overcoming Laboratory Differences of Microscopic Images. - Ann-Katrin Thebille; Esther Dietrich; Martin Klaus; Lukas Gernhold; Maximilian Lennartz; Christoph Kuppe; Rafael Kramann; Tobias B. Huber; Guido Sauter; Victor G. Puelles; Marina Zimmermann; Stefan Bonn (MIUA, 2021)

Towards Explainable End-to-End Prostate Cancer Relapse Prediction from H&E Images Combining Self-Attention Multiple Instance Learning with a Recurrent Neural Network. - Esther Dietrich; Patrick Fuhlert; Anne Ernst; Guido Sauter; Maximilian Lennartz; H. Siegfried Stiehl; Marina Zimmermann; Stefan Bonn (ML4H@NeurIPS, 2021)

Interactive gene networks with KNIT. - Daniel Sumner Magruder; Anna-Maria Liebhoff; Jörn Bethune; Stefan Bonn (Bioinform., 2021)

Uncertainty Estimation for Single-cell Label Transfer. - Robin Khatri; Stefan Bonn (COPA, 2022)

Deep Learning-Based Discrete Calibrated Survival Prediction. - Patrick Fuhlert; Anne Ernst; Esther Dietrich; Fabian Westhaeusser; Karin Kloiber; Stefan Bonn (ICDH, 2022)

Pathogen detection in RNA-seq data with Pathonoia. - Anna-Maria Liebhoff; Kevin Menden; Alena Laschtowitz; Andre Franke; Christoph Schramm; Stefan Bonn (BMC Bioinform., 2023)

A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles. - Sina Abdollahi; Darius P. Schaub; Madalena Barroso; Nora C. Laubach; Wiebke Hutwelker; Ulf Panzer; Søren W. Gersting; Stefan Bonn (J. Cheminformatics, 2024)