Publications

Michał Patryk Miazga, Daniel Abitz, Matthias Täschner, and Erhard Rahm. Automated Configuration of Schema Matching Tools: A Reinforcement Learning Approach. Datenbanksysteme für Business, Technologie und Web (BTW 2025), 331--354, Gesellschaft für Informatik, Bonn, 2025. [PUMA: topic_lifescience xack yaff]

David A. Selby, Maximilian Sprang, Jan Ewald, and Sebastian J. Vollmer. Beyond the black box with biologically informed neural networks. Nature Reviews Genetics, Mar 4, 2025. [PUMA: topic_lifescience yaff] URL

Kristina Vogel, Johanna Moeller, Nina G. Bozhanova, Markus Voehler, Anja Penk, Jens Meiler, and Clara T. Schoeder. Computational Engineering of siderocalin to modulate its binding affinity to the antihypertension drug candesartan. Journal of Structural Biology, (217)1:108180, 2025. [PUMA: topic_lifescience xack yaff] URL

Marie-Sophie von Braun, Kristin Starke, Lucas Peter, Daniel Kürsten, Florian Welle, Hans Ralf Schneider, Max Wawrzyniak, Daniel P O Kaiser, Gordian Prasse, Cindy Richter, Elias Kellner, Marco Reisert, Julian Klingbeil, Anika Stockert, Karl-Titus Hoffmann, Gerik Scheuermann, Christina Gillmann, and Dorothee Saur. Prediction of tissue and clinical thrombectomy outcome in acute ischaemic stroke using deep learning. In Masud Husain (Eds.), Brain, awaf013, January 2025. [PUMA: biomarker cdss cnn computer_vision deep_learning neuroimaging neurology nopdf topic_lifescience xack yaff] URL

David Antony Selby, Rashika Jakhmola, Maximilian Sprang, Gerrit Grossmann, Hind Raki, Niloofar Maani, Daria Pavliuk, Jan Ewald, and Sebastian Vollmer. Visible neural networks for multi-omics integration: a critical review. bioRxiv, Cold Spring Harbor Laboratory, 2024. [PUMA: topic_lifescience yaff] URL

Maximilian Joas, Daniel Freund, Robert Haase, Erhard Rahm, and Jan Ewald. Zero-Shot, Big-Shot, Active-Shot - How to estimate cell confluence, lazily. bioRxiv, Cold Spring Harbor Laboratory, 2025. [PUMA: topic_lifescience xack yaff] URL

Maximilian Joas, Neringa Jurenaite, Dusan Prascevic, Nico Scherf, and Jan Ewald. A generalized and versatile framework to train and evaluate autoencoders for biological representation learning and beyond: AUTOENCODIX. bioRxiv, Cold Spring Harbor Laboratory, December 2024. [PUMA: topic_lifescience xack] URL

Antonia Stubenvoll, Maria Schmidt, Johanna Moeller, Max Alexander Lingner Chango, Carolyn Schultz, Olga Antoniadou, Henry Loeffler-Wirth, Stephan Bernhart, Florian Peter Große, Beatrice Thier, Annette Paschen, Ulf Anderegg, Jan C. Simon, Mirjana Ziemer, Clara T. Schoeder, Hans Binder, and Manfred Kunz. Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity. Cancer Communications, (n/a)n/aJohn Wiley & Sons, Ltd, January 2025. [PUMA: Yaff melanoma myown single-cell topic_lifescience transcriptomics] URL

Antonia Stubenvoll, Maria Schmidt, Johanna Moeller, Max Alexander Lingner Chango, Carolyn Schultz, Olga Antoniadou, Henry Loeffler-Wirth, Stephan Bernhart, Florian Peter Große, Beatrice Thier, Annette Paschen, Ulf Anderegg, Jan C. Simon, Mirjana Ziemer, Clara T. Schoeder, Hans Binder, and Manfred Kunz. Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity. Cancer Communications, (n/a)n/aJohn Wiley & Sons, Ltd, January 2025. [PUMA: melanoma myown single-cell topic_lifescience transcriptomics] URL

Marie-Sophie von Braun, Kristin Starke, Lucas Peter, Daniel Kürsten, Florian Welle, Hans Ralf Schneider, Max Wawrzyniak, Daniel P O Kaiser, Gordian Prasse, Cindy Richter, Elias Kellner, Marco Reisert, Julian Klingbeil, Anika Stockert, Karl-Titus Hoffmann, Gerik Scheuermann, Christina Gillmann, and Dorothee Saur. Prediction of tissue and clinical thrombectomy outcome in acute ischaemic stroke using deep learning. In Masud Husain (Eds.), Brain, awaf013, January 2025. [PUMA: biomarker cdss cnn computer_vision deep_learning myown neuroimaging neurology topic_lifescience] URL

Sahar Vahdati, Deepankan Bharathi Nagaraj, Maximilian Bryan, Sobhan Moazemi, Sabine Gründer-Fahrer, and Michael Martin. Utilizing transformers on OCT imagery and metadata for treatment response prediction in macular edema patients. Lecture Notes in Computer Science, 3--15, Springer Nature Switzerland, Cham, 2023. [PUMA: OCT Xack edema macular prediction response topic_lifescience transformers treatment]

Markus Bauer, and Christoph Augenstein. Self-supervised learning in histopathology: New perspectives for prostate cancer grading. Lecture Notes in Computer Science, 348--360, Springer Nature Switzerland, Cham, 2024. [PUMA: Yaff cancer grading histopathology learning prostate self-supervised topic_lifescience]

Bernhard Vogginger, Amirhossein Rostami, Vaibhav Jain, Sirine Arfa, Andreas Hantsch, David Kappel, Michael Schäfer, Ulrike Faltings, Hector A. Gonzalez, Chen Liu, and Christian Mayr. Neuromorphic hardware for sustainable AI data centers. Zenodo, 2024. [PUMA: AI Neuromorphic area_responsibleai centers data hardware sustainable topic_lifescience xack] URL

Merlin Lange, Alejandro Granados, Shruthi VijayKumar, Jordão Bragantini, Sarah Ancheta, Yang-Joon Kim, Sreejith Santhosh, Michael Borja, Hirofumi Kobayashi, Erin McGeever, Robert Haase, and others. A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors. Cell, (187)23:6742--6759, Elsevier, 2024. [PUMA: topic_lifescience zno]

Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Robert Haase, and others. Metrics reloaded: recommendations for image analysis validation. Nature methods, (21)2:195--212, Nature Publishing Group US New York, 2024. [PUMA: topic_lifescience yaff]