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Identification of molecular targets of psychoactive kavalactones using iBodies

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology (opens in new window)

Author(s): Téo Hebra, Helena Smrčková, Büsra Elkatmis, Martin Převorovský, Tomáš Pluskal
Published in: ACS Synthetic Biology, Issue 13, 2024, Page(s) 558-567, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.3c00529

Reproducible mass spectrometry data processing and compound annotation in MZmine 3 (opens in new window)

Author(s): Tito Damiani, Steffen Heuckeroth, Aleksandr Smirnov, Olena Mokshyna, Corinna Brungs, Ansgar Korf, Joshua Smith, Paolo Stincone, Nicola Dreolin, Louis-Félix Nothias, Tuulia Hyötyläinen, Matej Orešič, Uwe Karst, Pieter Dorrestein, Daniel Petras, Xiuxia Du, Justin van der Hooft, Robin Schmid, Tomáš Pluskal
Published in: Nature Protocols, Issue 19, 2024, Page(s) 2597–2641, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.26434/chemrxiv-2023-98n6q-v2

Integrative analysis of multimodal mass spectrometry data in MZmine 3 (opens in new window)

Author(s): Robin Schmid, Steffen Heuckeroth, Ansgar Korf, Aleksandr Smirnov, Owen Myers, Thomas S. Dyrlund, Roman Bushuiev, Kevin J. Murray, Nils Hoffmann, Miaoshan Lu, Abinesh Sarvepalli, Zheng Zhang, Markus Fleischauer, Kai Dührkop, Mark Wesner, Shawn J. Hoogstra, Edward Rudt, Olena Mokshyna, Corinna Brungs, Kirill Ponomarov, Lana Mutabdžija, Tito Damiani, Chris J. Pudney, Mark Earll, Patrick O. Helmer,
Published in: Nature Biotechnology, Issue 41, 2024, Page(s) 447-449, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-01690-2

Emergence of molecular structures from repository-scale self-supervised learning on tandem mass spectra (opens in new window)

Author(s): Roman Bushuiev, Anton Bushuiev, Raman Samusevich, Corinna Brungs, Josef Sivic, Tomáš Pluskal
Published in: Nature Biotechnology, Issue in press, 2024, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.26434/chemrxiv-2023-kss3r-v2

Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data (opens in new window)

Author(s): Abzer K. Pakkir Shah, Axel Walter, Filip Ottosson, Francesco Russo, Marcelo Navarro-Diaz, Judith Boldt, Jarmo-Charles J. Kalinski, Eftychia Eva Kontou, James Elofson, Alexandros Polyzois, Carolina González-Marín, Shane Farrell, Marie R. Aggerbeck, Thapanee Pruksatrakul, Nathan Chan, Yunshu Wang, Magdalena Pöchhacker, Corinna Brungs, Beatriz Cámara, Andrés Mauricio Caraballo-Rodríguez, Andres
Published in: Nature Protocols, Issue 20, 2025, Page(s) 92-162, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-024-01046-3

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation (opens in new window)

Author(s): Timothy R. Fallon, Tereza Čalounová, Martin Mokrejš, Jing-Ke Weng, Tomáš Pluskal
Published in: BMC Bioinformatics, Issue 24, 2023, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-023-05254-8

Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum (opens in new window)

Author(s): Tito Damiani, Joshua Smith, Téo Hebra, Milana Perković, Marijo Čičak, Alžběta Kadlecová, Vlastimil Rybka, Martin Dračínský, Tomáš Pluskal
Published in: The Plant Journal, Issue in press, 2025, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.70086

Studying Plant Specialized Metabolites Using Computational Metabolomics Strategies (opens in new window)

Author(s): Lana Mutabdžija, Akhona Myoli, Niek F. de Jonge, Tito Damiani, Robin Schmid, Justin J. J. van der Hooft, Fidele Tugizimana, Tomáš Pluskal
Published in: Methods in Molecular Biology, Plant Functional Genomics, 2025, Page(s) 97-136, ISBN 978-1-0716-3781-4
Publisher: Springer US
DOI: 10.1007/978-1-0716-3782-1_7

MassSpecGym: A benchmark for the discovery and identification of molecules (opens in new window)

Author(s): Roman Bushuiev, Anton Bushuiev, Niek de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David Wishart, Liping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus Mak, Soha Hassoun, Florian Huber, Justin J.J. van der Hooft, Michael Stravs, S
Published in: Advances in Neural Information Processing Systems (NeurIPS), Issue 37, 2024, ISBN 978-3-319-45173-2
Publisher: NeurIPS
DOI: 10.48550/arxiv.2410.23326

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