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]

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

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

Abhinav Singh, Philipp H. Suhrcke, Pietro Incardona, and 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, Oct 1, 2023. [PUMA: FIS_scads imported topic_lifescience xack yaff]

Suryanarayana Maddu, Quentin Vagne, and Ivo F. Sbalzarini. Learning deterministic hydrodynamic equations from stochastic active particle dynamics. Jan 21, 2022. [PUMA: FIS_scads topic_lifescience xack yaff]

Suryanarayana Maddu, Dominik Sturm, Bevan L. Cheeseman, Christian L. Müller, and Ivo F. Sbalzarini. STENCIL-NET for equation-free forecasting from data. Scientific reports, (13)1Nature Publishing Group, December 2023. [PUMA: FIS_scads imported topic_lifescience xack yaff]

Ali Al-Fatlawi, Michael Schroeder, and A Francis Stewart. The Rad52 SSAP superfamily and new insight into homologous recombination. Communications biology, (6)1Springer Nature, Jan 23, 2023. [PUMA: topic_lifescience xack yaff]

Ali Al-Fatlawi, Martin Menzel, and Michael Schroeder. Is Protein BLAST a thing of the past?. Nature communications, (14)1Nature Publishing Group, Dec 11, 2023. [PUMA: topic_lifescience xack yaff]

Ali Al-Fatlawi, Eka Rusadze, Alexander Shmelkin, Negin Malekian, Cigdem Ozen, Christian Pilarsky, and Michael Schroeder. Netrank: network-based approach for biomarker discovery. BMC bioinformatics, (24)1BioMed Central, London, Jul 29, 2023. [PUMA: topic_lifescience xack yaff]

Fabian Liessmann, Lukas von Bredow, Jens Meiler, and rahm Liebscher, Ines. Targeting adhesion G protein-coupled receptors. Current status and future perspectives. Structure, Elsevier, November 2024. [PUMA: ADGRG1; ADGRG2; ADGRG3; ADGRG5; ADGRG6; ADGRG7; GPCRs; GPR114; GPR126; GPR128; GPR56; GPR64; GPR97; adhesion area_bigdata discovery; drug ep ligands; molecules; small structure topic_lifescience xack yaff]

Chiara Molinari, Leonardo Solaini, Francesca Rebuzzi, Gianluca Tedaldi, Davide Angeli, Elisabetta Petracci, Dusan Prascevic, Jan Ewald, Erhard Rahm, Matteo Canale, and others. Genomic events stratifying prognosis of early gastric cancer. Gastric Cancer, 1--12, Springer, 2024. [PUMA: area_bigdata ep imported topic_lifescience xack yaff]

Moritz Ertelt, Vikram Khipple Mulligan, Jack B. Maguire, Sergey Lyskov, Rocco Moretti, Torben Schiffner, Jens Meiler, and Clara T. Schoeder. Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. In Joanna Slusky (Eds.), PLOS Computational Biology, (20)3:e1011939, Public Library of Science (PLoS), March 2024. [PUMA: imported topic_lifescience xack yaff] URL

Shan Jiang, Zhaoqian Su, Nathaniel Bloodworth, Yunchao Liu, Cristina Martina, David G. Harrison, and Jens Meiler. Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA0201. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience xack yaff] URL

Moritz Ertelt, Rocco Moretti, Jens Meiler, and Clara T. Schoeder. Self-supervised machine learning methods for protein design improve sampling, but not the identification of high-fitness variants. Cold Spring Harbor Laboratory, June 2024. [PUMA: imported topic_lifescience xack yaff] URL

Abibe Useini, Inken Kaja Schwerin, Georg Künze, and Norbert Sträter. Structural Studies on the Binding Mode of Bisphenols to PPARγ. Biomolecules, (14)6:640, MDPI AG, May 2024. [PUMA: imported topic_lifescience xack yaff] URL

Kortney Melancon, Palina Pliushcheuskaya, Jens Meiler, and Georg Künze. Targeting ion channels with ultra-large library screening for hit discovery. Frontiers in Molecular Neuroscience, (16)Frontiers Media SA, January 2024. [PUMA: imported topic_lifescience xack yaff] URL

Moritz Ertelt, Jens Meiler, and Clara T Schoeder. Combining Rosetta Sequence Design with Protein Language Model Predictions Using Evolutionary Scale Modeling (ESM) as Restraint. ACS Synthetic Biology, (13)4:1085--1092, ACS Publications, 2024. [PUMA: ESM combining design protein rosetta sequence topic_lifescience xack yaff]

Michelle Philipp, Christopher W Moth, Nikola Ristic, Johanna K S Tiemann, Florian Seufert, Aleksandra Panfilova, Jens Meiler, Peter W Hildebrand, Amelie Stein, Daniel Wiegreffe, and others. MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts. Nucleic Acids Research, gkae301, Oxford University Press, 2024. [PUMA: 3d mutation mutationexplorer proteins topic_lifescience webserver xack yaff]

Martin Bentler, Romain Hardet, Moritz Ertelt, Daniela Rudolf, Dorota Kaniowska, Andreas Schneider, Florian WR Vondran, Clara T Schoeder, Marion Delphin, Julie Lucifora, and others. Modifying immune responses to adeno-associated virus vectors by capsid engineering. Molecular Therapy-Methods & Clinical Development, (30):576--592, Elsevier, 2023. [PUMA: adeno_virus capsid_engineering immune modifying responses topic_lifescience xack yaff]