Publications

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: myown topic_lifescience single-cell transcriptomics melanoma Yaff] URL

Xiaohan Kuang, zhaoqian su, Yunchao Liu, Xiaobo Lin, Jesse Spencer Smith, Tyler Derr, Yinghao Wu, and Jens Meiler. SuperWater: Predicting Water Molecule Positions on Protein Structures by Generative AI. Cold Spring Harbor Laboratory, November 2024. [PUMA: imported topic_lifescience] 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] URL

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: discovery; small GPR56; GPR64; GPR97; adhesion ep ADGRG2; ADGRG3; ligands; ADGRG1; structure GPCRs; drug ADGRG6; ADGRG7; ADGRG5; GPR128; molecules; GPR126; GPR114; topic_lifescience area_bigdata]

Chaithra Umesh, Manjunath Mahendra, Saptarshi Bej, Olaf Wolkenhauer, and Markus Wolfien. Challenges and applications in generative AI for clinical tabular data in physiology. Pflügers Archiv : European journal of physiology, Springer, Berlin u. a., Oct 17, 2024. [PUMA: FIS_scads imported topic_lifescience]

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

Johannes Pahlke, and Ivo Sbalzarini. Proven Distributed Memory Parallelization of Particle Methods. ACM Trans. Parallel Comput., Association for Computing Machinery, New York, NY, USA, Sep 18, 2024. [PUMA: meshfree definition, software algorithmics, bounds, simulation distributed engineering methods, scalability formal algorithms, topic_lifescience particle memory, parallelization,] URL

Katja Hoffmann, Yuan Peng, Tobias Schlosser, Gabriel Stolze, Holger Langner, Marcel Susky, Trixy Meyer, Marc Ritter, Danny Kowerko, Vinodh Kakkassery, Markus Wolfien, and Martin Sedlmayr. Towards Standardizing Ophthalmic Data for Seamless Interoperability in Eye Care. Studies in health technology and informatics, (317):139--145, IOS Press, Amsterdam u. a., Aug 30, 2024. [PUMA: FIS_scads Learning, Health Diseases/therapy, Germany, Interoperability/standards, Information Electronic Machine Humans, Eye Records/standards, topic_lifescience Ophthalmology Seven/standards, Level]

Waldemar Hahn, Najia Ahmadi, Katja Hoffmann, Jan-Niklas Eckardt, Martin Sedlmayr, and Markus Wolfien. Synthetic Data Generation in Hematology - Paving the Way for OMOP and FHIR Integration. Studies in health technology and informatics, (316):1472--1476, IOS Press, Amsterdam u. a., Aug 22, 2024. [PUMA: FIS_scads Health Leukemia, Hematology, Information Electronic Care Humans, Acute, Assessment, Outcome topic_lifescience Interoperability, Records, Myeloid,]

Najia Ahmadi, Michele Zoch, Oya Guengoeze, Carlo Facchinello, Antonia Mondorf, Katharina Stratmann, Khader Musleh, Hans-Peter Erasmus, Jana Tchertov, Richard Gebler, Jannik Schaaf, Lena S Frischen, Azadeh Nasirian, Jiabin Dai, Elisa Henke, Douglas Tremblay, Andrew Srisuwananukorn, Martin Bornhäuser, Christoph Röllig, Jan-Niklas Eckardt, Jan Moritz Middeke, Markus Wolfien, and Martin Sedlmayr. How to customize common data models for rare diseases: an OMOP-based implementation and lessons learned. Orphanet journal of rare diseases, (19)1BioMed Central, London, Aug 14, 2024. [PUMA: FIS_scads Humans, Rare topic_lifescience Diseases]

Christopher W. Moth, Jonathan H. Sheehan, Abdullah Al Mamun, R. Michael Sivley, Alican Gulsevin, David Rinker, John A. Capra, and Jens Meiler. VUStruct: a compute pipeline for high throughput and personalized structural biology. Cold Spring Harbor Laboratory, August 2024. [PUMA: imported topic_lifescience] URL

Jan Ewald, Ziyang He, Wassili Dimitriew, and Stefan Schuster. Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells. npj Systems Biology and Applications, (10)1Springer Science and Business Media LLC, July 2024. [PUMA: imported topic_lifescience] URL

Joseph DeCorte, Benjamin Brown, and Jens Meiler. Interpretable deep-learning pKa prediction for small molecule drugs via atomic sensitivity analysis. American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] 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] URL

Caleb A. H. Jones, Benjamin P. Brown, Daniel C. Schultz, Julie Engers, Valerie M. Kramlinger, Jens Meiler, and Craig W. Lindsley. Computer-Aided Design and Biological Evaluation of Diazaspirocyclic D4R Antagonists. ACS Chemical Neuroscience, (15)12:2396–2407, American Chemical Society (ACS), June 2024. [PUMA: imported topic_lifescience] URL

Suse Seidemann, Florian Salomon, Karl B Hoffmann, Thomas Kurth, Ivo F Sbalzarini, Robert Haase, and Marius Ader. Automated quantification of photoreceptor outer segments in developing and degenerating retinas on microscopy images across scales. FRONTIERS IN MOLECULAR NEUROSCIENCE, (17 (2024))Frontiers Media S.A., May 24, 2024. [PUMA: FIS_scads imported topic_lifescience unit_transfer]

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] URL

Palina Pliushcheuskaya, Sandeep Kesh, Emma Kaufmann, Sophie Wucherpfennig, Frank Schwede, Georg Künze, and Vasilica Nache. Similar Binding Modes of cGMP Analogues Limit Selectivity in Modulating Retinal CNG Channels via the Cyclic Nucleotide-Binding Domain. ACS Chemical Neuroscience, (15)8:1652–1668, American Chemical Society (ACS), April 2024. [PUMA: imported topic_lifescience] URL

Amankeldi A Salybekov, Markus Wolfien, Waldemar Hahn, Sumi Hidaka, and Shuzo Kobayashi. Artificial Intelligence Reporting Guidelines' Adherence in Nephrology for Improved Research and Clinical Outcomes. Biomedicines, (12)3MDPI, Basel, Mar 7, 2024. [PUMA: FIS_scads imported topic_lifescience]

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] URL