Publications

Michał Patryk Miazga, Daniel Abitz, Matthias Täschner, und 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, und Sebastian J. Vollmer. Beyond the black box with biologically informed neural networks. Nature Reviews Genetics, 04.03.2025. [PUMA: topic_lifescience yaff] URL

Kristina Vogel, Johanna Moeller, Nina G. Bozhanova, Markus Voehler, Anja Penk, Jens Meiler, und 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

David Antony Selby, Rashika Jakhmola, Maximilian Sprang, Gerrit Grossmann, Hind Raki, Niloofar Maani, Daria Pavliuk, Jan Ewald, und 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, und 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, und Jan Ewald. A generalized and versatile framework to train and evaluate autoencoders for biological representation learning and beyond: AUTOENCODIX. bioRxiv, Cold Spring Harbor Laboratory, Dezember 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, und 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, Januar 2025. [PUMA: Yaff melanoma myown single-cell topic_lifescience transcriptomics] URL

Sahar Vahdati, Deepankan Bharathi Nagaraj, Maximilian Bryan, Sobhan Moazemi, Sabine Gründer-Fahrer, und 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, und 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, und 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, und 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, und 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]

Luke Sorensen, Adam Humenick, Sabrina SB Poon, Myat Noe Han, Narges S Mahdavian, Matthew C Rowe, Ryan Hamnett, Estibaliz Gómez-de Mariscal, Peter H Neckel, Ayame Saito, Robert Haase, und others. Gut Analysis Toolbox--automating quantitative analysis of enteric neurons. Journal of Cell Science, (137)20The Company of Biologists, 2024. [PUMA: topic_lifescience yaff]

Merlin Lange, Alejandro Granados, Shruthi VijayKumar, Jordao Bragantini, Sarah Ancheta, Sreejith Santhosh, Michael Borja, Hirofumi Kobayashi, Erin McGeever, Ahmet Can Solak, Robert Haase, und others. Zebrahub--Multimodal zebrafish developmental atlas reveals the State-transition dynamics of late-vertebrate pluripotent axial progenitors. BioRxiv, 2023--03, Cold Spring Harbor Laboratory, 2023. [PUMA: topic_lifescience zno]

Johannes Soltwedel, Theresa Suckert, Elke Beyreuther, Moritz Schneider, Marc Boucsein, Elisabeth Bodenstein, Sindi Nexhipi, Liane Stolz-Kieslich, Mechthild Krause, Cläre von Neubeck, Robert Haase, und others. Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D. Radiotherapy and Oncology, (182):109591, Elsevier, 2023. [PUMA: topic_lifescience zno]

Robert Haase. Towards Transparency and Knowledge Exchange in AI- assisted Data Analysis Code Generation. Zenodo, Oktober 2024. [PUMA: topic_language topic_lifescience unit_transfer xack] URL

Abhinav Singh, Philipp H. Suhrcke, Pietro Incardona, und Ivo F. Sbalzarini. A numerical solver for active hydrodynamics in three dimensions and its application to active turbulence. Physics of fluids, (35)10American Institute of Physics, 01.10.2023. [PUMA: FIS_scads imported topic_lifescience xack yaff]

Suryanarayana Maddu, Bevan L. Cheeseman, Ivo F Sbalzarini, und Christian L. Müller. Stability selection enables robust learning of differential equations from limited noisy data. Proceedings of the Royal Society of London : Series A, Mathematical, physical and engineering sciences, (478)2262Royal Society Publishing, Juni 2022. [PUMA: FIS_scads topic_lifescience xack]

Sarah Perez, Suryanarayana Maddu, Ivo F. Sbalzarini, und Philippe Poncet. Adaptive weighting of Bayesian physics informed neural networks for multitask and multiscale forward and inverse problems. Journal of computational physics, (491)Academic Press Inc., 15.10.2023. [PUMA: topic_lifescience yaff]

Pietro Incardona, Aryaman Gupta, Serhii Yaskovets, und Ivo F. Sbalzarini. A C++ Library for Memory Layout and Performance Portability of Scientific Applications. In Jeremy Singer, Yehia Elkhatib, Dora Blanco Heras, Patrick Diehl, Nick Brown, und Aleksandar Ilic (Hrsg.), Euro-Par 2022, 109--120, Springer Science and Business Media B.V., Germany, 2023. [PUMA: nopdf topic_lifescience]