Publications

Ulisses Rocha, Jonas Coelho Kasmanas, René Kallies, Joao Pedro Saraiva, Rodolfo Brizola Toscan, Polonca Stefanic, Marcos Fleming Bicalho, Felipe Borim Correa, Merve Nida Bastürk, Efthymios Fousekis, und others. MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy. Molecular Ecology Resources, (24)2:e13904, Wiley Online Library, 2024. [PUMA: imported zno]

Eugenio Llanos, Wilmer Leal, Andrés Bernal, Jürgen Jost, und Peter F. Stadler. Are the chemical families still there? Formal structure of similarity of elements and its thermochemical domain. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, (480)2298The Royal Society, September 2024. [PUMA: Formal chemical families similarity structure zno] URL

Ulisses Nunes da Rocha, Jonas Coelho Kasmanas, René Kallies, Joao Pedro Saraiva, Rodolfo Brizola Toscan, Polonca Stefanic, Marcos Fleming Bicalho, Felipe Borim Correa, Merve Nida Bastürk, Efthymios Fousekis, und others. MuDoGeR: Multi-domain genome recovery from metagenomes made easy. bioRxiv, 2022--06, Cold Spring Harbor Laboratory, 2022. [PUMA: imported zno]

Jörg Fallmann, Robin Goldmann, und Peter F Stadler. MONSDA: Modular Organizer of Nextflow and Snakemake Driven HTS Data Analysis. OSF Preprints, 2022. [PUMA: imported zno]

Sebastian G Gornik, Victor Flores, Franziska Reinhardt, Lieselotte Erber, Dayana E Salas-Leiva, Olga Douvropoulou, Imen Lassadi, Elin Einarsson, Mario Mörl, Anna Git, und others. Mitochondrial genomes in Perkinsus decode conserved frameshifts in all genes. Molecular biology and evolution, (39)10:msac191, Oxford University Press US, 2022. [PUMA: imported zno]

Hossein Batebi, Guillermo Pérez-Hernández, Sabrina N Rahman, Baoliang Lan, Antje Kamprad, Mingyu Shi, David Speck, Johanna KS Tiemann, Ramon Guixà-González, Franziska Reinhardt, und others. Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor. Nature structural & molecular biology, 1--10, Nature Publishing Group US New York, 2024. [PUMA: imported zno]

Hossein Batebi, Guillermo Pérez-Hernández, Jesper Mathiesen, Mingyu Shi, Johanna KS Tiemann, Ramon Guixà-González, Franziska Reinhardt, Peter F Stadler, Patrick Scheerer, Brian Kobilka, und others. Mechanistic insights into G protein association with a G protein-coupled receptor. 2023. [PUMA: imported zno]

Eugenio Llanos Ballestas, Wilmer Leal, Andrés Bernal, Jürgen Jost, und Peter F. Stadler. Are the chemical families still there? exploration of similarity among elements. American Chemical Society (ACS), Oktober 2022. [PUMA: chemical exploration families similarity zno] URL

Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K Beckmann, Ivo L Hofacker, Sarah Von Löhneysen, und Peter F Stadler. Local RNA folding revisited. Journal of Bioinformatics and Computational Biology, (21)04:2350016, World Scientific, 2023. [PUMA: imported zno]

Tim Kolberg, Sarah von Löhneysen, Iuliia Ozerova, Karolin Wellner, Roland K Hartmann, Peter F Stadler, und Mario Mörl. Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA. Nucleic Acids Research, (51)11:e63--e63, Oxford University Press, 2023. [PUMA: imported zno]

Marieke Vromman, Jasper Anckaert, Stefania Bortoluzzi, Alessia Buratin, Chia-Ying Chen, Qinjie Chu, Trees-Juen Chuang, Roozbeh Dehghannasiri, Christoph Dieterich, Xin Dong, und others. Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nature methods, (20)8:1159--1169, Nature Publishing Group US New York, 2023. [PUMA: imported zno]

Thomas Gatter, und Peter F Stadler. Kosteneffektive hybride Genomassemblierung mit LazyB. BIOspektrum, (28)3:283--286, Springer, 2022. [PUMA: imported zno]

Karl Käther, Steffen Lemke, und Peter F. Stadler. Annotation-Free Identification of Potential Synteny Anchors. Bioinformatics and Biomedical Engineering, 217–230, Springer Nature Switzerland, 2023. [PUMA: Anchors Annotation-Free Identification Potential Synteny zno] URL

Marc Hellmuth, Katharina T Huber, Vincent Moulton, Guillaume E Scholz, und Peter F Stadler. Injective split systems. Graphs and Combinatorics, (39)4:65, Springer, 2023. [PUMA: imported zno]

Robson P Bonidia, Anderson P Avila Santos, Breno LS de Almeida, Peter F Stadler, Ulisses Nunes da Rocha, Danilo S Sanches, und André CPLF De Carvalho. Information theory for biological sequence classification: a novel feature extraction technique based on Tsallis entropy. Entropy, (24)10:1398, MDPI, 2022. [PUMA: imported zno]

Leonhard Sidl, Maximilian Faissner, Manuel Uhlir, Cristian A Velandia-Huerto, Maria Waldl, Hua-Ting Yao, Ivo L Hofacker, und Peter F Stadler. A Relation between Natural Selection and Computational Complexity. Oktober 2024. [PUMA: Biological Complexity Computation Computational Developmental Folding Genotype-Phenotype Map Program RNA zno] URL

John Anders, und Peter F. Stadler. RNAcode_Web – Convenient identification of evolutionary conserved protein coding regions. Journal of Integrative Bioinformatics, (20)3Walter de Gruyter GmbH, August 2023. [PUMA: RNAcode_Web coding evolutionary identification protein regions zno] URL

Kyriakos Soulios, Patrick Scheibe, Matthias Bernt, Jörg Hackermüller, und Jana Schor. deepFPlearn+: enhancing toxicity prediction across the chemical universe using graph neural networks. Bioinformatics, (39)12:btad713, Oxford University Press, 2023. [PUMA: imported zno]

Laurin Mordhorst, Maria Morozova, Sebastian Papazoglou, Björn Fricke, Jan Malte Oeschger, Thibault Tabarin, Henriette Rusch, Carsten Jäger, Stefan Geyer, Nikolaus Weiskopf, und others. Towards a representative reference for MRI-based human axon radius assessment using light microscopy. Neuroimage, (249):118906, Elsevier, 2022. [PUMA: imported zno]

Jana Schor, Patrick Scheibe, Matthias Bernt, Wibke Busch, Chih Lai, und Jörg Hackermüller. AI for predicting chemical-effect associations at the chemical universe level—deepFPlearn. Briefings in bioinformatics, (23)5:bbac257, Oxford University Press, 2022. [PUMA: imported zno]