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Koina: Democratizing machine learning for proteomics research.

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Title: Koina: Democratizing machine learning for proteomics research.
Authors: Lautenbacher L; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany.; Munich Data Science Institute, Technical University of Munich, Garching, Germany., Yang KL; Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA., Kockmann T; Functional Genomics Center Zurich (FGCZ) - University of Zurich | ETH Zurich, Winterthurerstrasse 190, CH-, Zurich, Switzerland., Panse C; Functional Genomics Center Zurich (FGCZ) - University of Zurich | ETH Zurich, Winterthurerstrasse 190, CH-, Zurich, Switzerland.; Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, CH-, Lausanne, Switzerland., Gabriel W; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany., Bold D; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany., Kahl E; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany., Chambers M; Department of Genome Sciences, University of Washington, Seattle, WA, USA., MacLean BX; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Li K; Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA., Yu F; Department of Pathology, University of Michigan, Ann Arbor, MI, USA., Searle BC; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.; Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA.; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA., Wilburn DB; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.; Center for RNA Biology, The Ohio State University, Columbus, OH, US., Shahneh MRZ; Department of Computer Science, University of California Riverside, Riverside, CA, USA., Hong Y; Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, USA., Tang H; Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, USA., Wang M; Department of Computer Science, University of California Riverside, Riverside, CA, USA.; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA., Gabriels R; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium., Bouwmeester R; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium., Devreese R; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium., Angelis J; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany., Sabidó E; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona, Spain., Schmidt TK; MSAID GmbH, Garching, Germany., Nesvizhskii AI; Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. nesvi@med.umich.edu.; Department of Pathology, University of Michigan, Ann Arbor, MI, USA. nesvi@med.umich.edu., Wilhelm M; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany. mathias.wilhelm@tum.de.; Munich Data Science Institute, Technical University of Munich, Garching, Germany. mathias.wilhelm@tum.de.
Source: Nature communications [Nat Commun] 2025 Nov 11; Vol. 16 (1), pp. 9933. Date of Electronic Publication: 2025 Nov 11.
Publication Type: Journal Article
Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
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  Data: <searchLink fieldCode="AU" term="%22Lautenbacher+L%22">Lautenbacher L</searchLink>; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany.; Munich Data Science Institute, Technical University of Munich, Garching, Germany.<br /><searchLink fieldCode="AU" term="%22Yang+KL%22">Yang KL</searchLink>; Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.<br /><searchLink fieldCode="AU" term="%22Kockmann+T%22">Kockmann T</searchLink>; Functional Genomics Center Zurich (FGCZ) - University of Zurich | ETH Zurich, Winterthurerstrasse 190, CH-, Zurich, Switzerland.<br /><searchLink fieldCode="AU" term="%22Panse+C%22">Panse C</searchLink>; Functional Genomics Center Zurich (FGCZ) - University of Zurich | ETH Zurich, Winterthurerstrasse 190, CH-, Zurich, Switzerland.; Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, CH-, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Gabriel+W%22">Gabriel W</searchLink>; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany.<br /><searchLink fieldCode="AU" term="%22Bold+D%22">Bold D</searchLink>; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany.<br /><searchLink fieldCode="AU" term="%22Kahl+E%22">Kahl E</searchLink>; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany.<br /><searchLink fieldCode="AU" term="%22Chambers+M%22">Chambers M</searchLink>; Department of Genome Sciences, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22MacLean+BX%22">MacLean BX</searchLink>; Department of Genome Sciences, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Li+K%22">Li K</searchLink>; Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.<br /><searchLink fieldCode="AU" term="%22Yu+F%22">Yu F</searchLink>; Department of Pathology, University of Michigan, Ann Arbor, MI, USA.<br /><searchLink fieldCode="AU" term="%22Searle+BC%22">Searle BC</searchLink>; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.; Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA.; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.<br /><searchLink fieldCode="AU" term="%22Wilburn+DB%22">Wilburn DB</searchLink>; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.; Center for RNA Biology, The Ohio State University, Columbus, OH, US.<br /><searchLink fieldCode="AU" term="%22Shahneh+MRZ%22">Shahneh MRZ</searchLink>; Department of Computer Science, University of California Riverside, Riverside, CA, USA.<br /><searchLink fieldCode="AU" term="%22Hong+Y%22">Hong Y</searchLink>; Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, USA.<br /><searchLink fieldCode="AU" term="%22Tang+H%22">Tang H</searchLink>; Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, USA.<br /><searchLink fieldCode="AU" term="%22Wang+M%22">Wang M</searchLink>; Department of Computer Science, University of California Riverside, Riverside, CA, USA.; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.<br /><searchLink fieldCode="AU" term="%22Gabriels+R%22">Gabriels R</searchLink>; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.<br /><searchLink fieldCode="AU" term="%22Bouwmeester+R%22">Bouwmeester R</searchLink>; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.<br /><searchLink fieldCode="AU" term="%22Devreese+R%22">Devreese R</searchLink>; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.<br /><searchLink fieldCode="AU" term="%22Angelis+J%22">Angelis J</searchLink>; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany.<br /><searchLink fieldCode="AU" term="%22Sabidó+E%22">Sabidó E</searchLink>; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona, Spain.<br /><searchLink fieldCode="AU" term="%22Schmidt+TK%22">Schmidt TK</searchLink>; MSAID GmbH, Garching, Germany.<br /><searchLink fieldCode="AU" term="%22Nesvizhskii+AI%22">Nesvizhskii AI</searchLink>; Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. nesvi@med.umich.edu.; Department of Pathology, University of Michigan, Ann Arbor, MI, USA. nesvi@med.umich.edu.<br /><searchLink fieldCode="AU" term="%22Wilhelm+M%22">Wilhelm M</searchLink>; Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany. mathias.wilhelm@tum.de.; Munich Data Science Institute, Technical University of Munich, Garching, Germany. mathias.wilhelm@tum.de.
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