Publications

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

C.J.R. Murphy-Barltrop, and J.L. Wadsworth. Modelling Non-Stationarity in Asymptotically Independent Extremes. Computational Statistics and Data Analysis, (199):108025, Elsevier BV, November 2024. [PUMA: imported topic_mathfoundation] 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

C. J. R. Murphy-Barltrop, J. L. Wadsworth, and E. F. Eastoe. Improving Estimation for Asymptotically Independent Bivariate Extremes via Global Estimators for the Angular Dependence Function. Extremes, Aug 13, 2024. [PUMA: imported topic_mathfoundation] URL

Franz Baader, and Filippo De Bortoli. Logics with Concrete Domains: First-Order Properties, Abstract Expressive Power, and (Un)Decidability. SIGAPP Appl. Comput. Rev., (24)3:5–17, Association for Computing Machinery, New York, NY, USA, Oct 8, 2024. [PUMA: imported topic_knowledge] URL

Maik Fröbe, Jan Heinrich Reimer, Sean MacAvaney, Niklas Deckers, Simon Reich, Janek Bevendorff, Benno Stein, Matthias Hagen, and Martin Potthast. The Information Retrieval Experiment Platform (Extended Abstract). Proceedings of the Thirty-ThirdInternational Joint Conference on Artificial Intelligence, 8405–8410, International Joint Conferences on Artificial Intelligence Organization, August 2024. [PUMA: imported topic_language] URL

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

Maik Fröbe, Harrisen Scells, Theresa Elstner, Christopher Akiki, Lukas Gienapp, Jan Heinrich Reimer, Sean MacAvaney, Benno Stein, Matthias Hagen, and Martin Potthast. Resources for Combining Teaching and Research in Information Retrieval Coursework. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, 1115–1125, ACM, July 2024. [PUMA: imported topic_language] URL

Lukas Gienapp, Harrisen Scells, Niklas Deckers, Janek Bevendorff, Shuai Wang, Johannes Kiesel, Shahbaz Syed, Maik Fröbe, Guido Zuccon, Benno Stein, Matthias Hagen, and Martin Potthast. Evaluating Generative Ad Hoc Information Retrieval. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, 1916–1929, ACM, July 2024. [PUMA: imported topic_language] URL

Carsten Lutz, and Quentin Manière. Adding Circumscription to Decidable Fragments of First-Order Logic: A Complexity Rollercoaster. July 2024. [PUMA: imported topic_knowledge]

Nandan Thakur, Luiz Bonifacio, Maik Fröbe, Alexander Bondarenko, Ehsan Kamalloo, Martin Potthast, Matthias Hagen, and Jimmy Lin. Systematic Evaluation of Neural Retrieval Models on the Touché 2020 Argument Retrieval Subset of BEIR. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval, 1420–1430, ACM, July 2024. [PUMA: imported topic_language] 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

E. B. L. Mackay, C. J. R. Murphy-Barltrop, and P. Jonathan. The SPAR Model: A New Paradigm for Multivariate Extremes: Application to Joint Distributions of Metocean Variables. Journal of Offshore Mechanics and Arctic Engineering, (147)1ASME International, July 2024. [PUMA: imported topic_mathfoundation] 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

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

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

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

Shreya Arya, Justin Curry, and Sayan Mukherjee. A Sheaf-Theoretic Construction of Shape Space. Foundations of Computational Mathematics, May 2024. [PUMA: imported topic_mathfoundation]

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

Robert Haase, Christian Tischer, Jean-Karim Heriche, and Nico Scherf. Benchmarking Large Language Models for Bio-Image Analysis Code Generation. Cold Spring Harbor Laboratory, April 2024. [PUMA: imported topic_neuroinspired unit_transfer] URL