Publications

Brinda Vallat, Benjamin M. Webb, John D. Westbrook, Thomas D. Goddard, Christian A. Hanke, Andrea Graziadei, Ezra Peisach, Arthur Zalevsky, Jared Sagendorf, Hongsuda Tangmunarunkit, Serban Voinea, Monica Sekharan, Jian Yu, Alexander A.M.J.J. Bonvin, Frank DiMaio, Gerhard Hummer, Jens Meiler, Emad Tajkhorshid, Thomas E. Ferrin, Catherine L. Lawson, Alexander Leitner, Juri Rappsilber, Claus A.M. Seidel, Cy M. Jeffries, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar, Torsten Schwede, Jill Trewhella, Carl Kesselman, Helen M. Berman, and Andrej Sali. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. Journal of Molecular Biology, 168546, March 2024. [PUMA: imported xack] URL

Nico Domschke, Bruno Schmidt, Thomas Gatter, Richard Golnik, Paul Eisenhuth, Fabian Liessmann, Jens Meiler, and Peter F Stadler. Crossover Operators for Molecular Graphs with an Application to Virtual Drug Screening. American Chemical Society (ACS), September 2024. [PUMA: Crossover Drug Graphs Molecular Operators Screening Virtual Xack Yaff] URL

Marcos E González Laffitte, Klaus Weinbauer, Tieu-Long Phan, Nora Beier, Nico Domschke, Christoph Flamm, Thomas Gatter, Daniel Merkle, and Peter F Stadler. Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions. Symmetry, 9:1217, Multidisciplinary Digital Publishing Institute, 2024. [PUMA: RYaff Xack imported]

Ameera Vaheeda Shanavas, Manoj Changat, and Peter F Stadler. On the Cut-Vertex and the Interval Transit Functions of Hypergraphs. Graphs and Combinatorics, (41)1:1--26, Springer, 2025. [PUMA: imported xack]

Iuliia Ozerova, Jörg Fallmann, Mario Mörl, Matthias Bernt, Sonja J Prohaska, and Peter F Stadler. Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution. In Selene Fernandez-Valverde (Eds.), Genome Biology and Evolution, (16)11Oxford University Press (OUP), October 2024. [PUMA: Aberrant Animal Appear Evolution Frequently Genes Mitochondrial tRNA xack] URL

Stefan Müller, Christoph Flamm, and Peter F. Stadler. What makes a reaction network “chemical”?. Journal of Cheminformatics, (14)1Springer Science and Business Media LLC, September 2022. [PUMA: network reaction xack] URL

Zachary P Adams, and Sayan Mukherjee. Meta-Posterior Consistency for the Bayesian Inference of Metastable System. 2024. [PUMA: Bayesian_Inference Consistency Meta-Posterior Metastable_System Xack imported] URL

Alex Ivliev, Lukas Gerlach, Simon Meusel, Jakob Steinberg, and Markus Krötzsch. Nemo: A Scalable and Versatile Datalog Engine. In Mario Alviano, and Matthias Lanzinger (Eds.), Proceedings of the 5th International Workshop on the Resurgence of Datalog in Academia and Industry (Datalog-2.0 2024), (3801):43-47, CEUR-WS.org, November 2024. [PUMA: Datalog_Engine Nemo Scalable Versatile Xack imported]

Maja Schneider. Distributed, Privacy-Aware Location Data Aggregation. 2024. [PUMA: Aggregation Data Distributed Location Privacy-Aware Xack] URL

Erik Daniel, and Florian Tschorsch. Poster: On Integrating Sphinx in IPFS. Proceedings of the 2024 ACM on Internet Measurement Conference, 753–754, Association for Computing Machinery, New York, NY, USA, Nov 4, 2024. [PUMA: imported xack] URL

Ali Al-Fatlawi, Md. Ballal Hossen, Ferras El-Hendi, and Michael Schroeder. Protein secondary structure and remote homology detection. bioRxiv, Cold Spring Harbor Laboratory, 2024. [PUMA: imported xack] URL

Trina De, Vardan Andriasyan, and Artur Yakimovich. PyPlaque: an Open-source Python Package for Phenotypic Analysis of Virus Plaque Assays. bioRxiv, Cold Spring Harbor Laboratory, 2024. [PUMA: imported xack] URL

Daniil Kosakin, Sergei Obiedkov, Ivan Smirnov, Ekaterina Rakhilina, Anastasia Vyrenkova, and Ekaterina Zalivina. Russian Learner Corpus: Towards Error-Cause Annotation for L2 Russian. In Nicoletta Calzolari, Min-Yen Kan, Veronique Hoste, Alessandro Lenci, Sakriani Sakti, and Nianwen Xue (Eds.), Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), 14240--14258, ELRA and ICCL, Torino, Italia, May 2024. [PUMA: imported xack] URL

Quentin Manière, and Marcin Przybylko. Spectra of Cardinality Queries over Description Logic Knowledge Bases (Extended Abstract). In Laura Giordano, Jean Christoph Jung, and Ana Ozaki (Eds.), Proceedings of the 37th International Workshop on Description Logics (DL 2024), Bergen, Norway, June 18-21, 2024, (3739)CEUR-WS.org, 2024. [PUMA: imported xack] URL

Lorenzo Titone, Nikola Milosevic, and Lars Meyer. The ARC Toolbox: Artificial Languages with Rhythmicity Control. bioRxiv, Cold Spring Harbor Laboratory, 2024. [PUMA: imported xack] URL

Ali Al-Fatlawi, Md. Ballal Hossen, Stella de Paula Lopes, A. Francis Stewart, and Michael Schroeder. The Rad52 superfamily as seen by AlphaFold. bioRxiv, Cold Spring Harbor Laboratory, 2024. [PUMA: imported xack] URL

Changsong Deng, Xiang Li, Rene L. Schilling, and Lihu Xu. Total variation distance between SDEs with stable noise and Brownian motion with applications to Poisson PDEs. 2024. [PUMA: imported xack] URL

Franz Baader, and Oliver Fernández Gil. Unification in the Description Logic \$\$\backslashmathcal \ELH\\_\\backslashmathcal \R\^+\\$\$Without the Top Concept Modulo Cycle-Restricted Ontologies. In Christoph Benzmüller, Marijn J.H. Heule, and Renate A. Schmidt (Eds.), Automated Reasoning, 279--297, Springer Nature Switzerland, Cham, 2024. [PUMA: imported xack]

Jan Köhler, Elisabeth Varga, Stephanie Spahr, Jörn Gessner, Kerstin Stelzer, Gunnar Brandt, Miguel D. Mahecha, Guido Kraemer, Martin Pusch, Christian Wolter, Michael T. Monaghan, Matthias Stöck, and Tobias Goldhammer. Unpredicted ecosystem response to compound human impacts in a European river. Scientific Reports, (14)1:16445, Jul 16, 2024. [PUMA: imported xack] URL

Neeratyoy Mallik, Maciej Janowski, Johannes Hog, Herilalaina Rakotoarison, Aaron Klein, Josif Grabocka, and Frank Hutter. Warmstarting for Scaling Language Models. 2024. [PUMA: imported xack] URL