Collecting reliable clades using the Greedy Strict Consensus Merger

Autor: Markus Fleischauer, Sebastian Böcker

Publikováno v: PeerJ, Vol 4, p e2172 (2016)

Supertree methods combine a set of phylogenetic trees into a single supertree. Similar to supermatrix methods, these methods provide a way to reconstruct larger parts of the Tree of Life, potentially evading the computational complexity of phylogenet

Externí odkaz: https://doaj.org/article/213dfeba5b3c4b71952f84115050667a

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

Autor: Markus Fleischauer, Daniel Petras, Martin Hoffmann, William H. Gerwick, Pieter C. Dorrestein, Juho Rousu, Kai Dührkop, Marcus Ludwig, Sebastian Böcker, Louis-Félix Nothias, Raphael Reher

Publikováno v: Nature Biotechnology. 39:462-471

Metabolomics using nontargeted tandem mass spectrometry can detect thousands of molecules in a biological sample. However, structural molecule annotation is limited to structures present in libraries or databases, restricting analysis and interpretat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::aa19706337d285f094ed8addf277de3a
https://doi.org/10.1038/s41587-020-0740-8

Feature-based molecular networking in the GNPS analysis environment

Autor: Robert A. Quinn, Mélissa Nothias-Esposito, Oriane Moyne, Neha Garg, Fernando Vargas, Hiroshi Tsugawa, Zdeněk Kameník, Bindesh Shrestha, Julia M. Gauglitz, Sven W. Meyer, Tam Dang, Pieter C. Dorrestein, Michael Witting, Abinesh Sarvepalli, Madeleine Ernst, Alexey Gurevich, Giorgis Isaac, Nikolas Kessler, Zheng Zhang, Robin Schmid, Marcus Ludwig, Ngoc Hung Nguyen, Johannes Rainer, Mingxun Wang, Theodore Alexandrov, Laura-Isobel McCall, Ivan Protsyuk, Audrey Le Gouellec, Pierre-Marie Allard, Sebastian Böcker, Alan K. Jarmusch, Ricardo Silva, Heiko Neuweger, Irina Koester, Ansgar Korf, Oliver Kohlbacher, Anupriya Tripathi, Daniel Petras, Kai Dührkop, Simon Rogers, Julien Paolini, Alexander A. Aksenov, Markus Fleischauer, Oliver Alka, Fabian Aicheler, Steffen Neumann, Kelly C. Weldon, Louis-Félix Nothias, Mustafa Morsy, Christian Martin H, Hosein Mohimani, Vanessa V. Phelan, Nuno Bandeira, Jonathan McSayles, Xavier Cachet, Justin J. J. van der Hooft, Kyo Bin Kang, Florian Zubeil, Tomáš Pluskal, Aiko Barsch, Heejung Yang, Andrés Mauricio Caraballo-Rodríguez

Publikováno v: Nature methods, vol 17, iss 9
Nature methods
Nature Methods
Nature Methods, Nature Publishing Group, 2020, 17 (9), pp.905-908. ⟨10.1038/s41592-020-0933-6⟩
Nat. Methods 17, 905–908 (2020)
Nature Methods 17 (2020) 9
Nature Methods, 17(9), 905-908

Feature-based molecular networking allows the generation of molecular networks for mass spectrometry data that can recognize isomers, incorporate relative quantification and integrate ion mobility data.Molecular networking has become a key method to

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6a31c0489fe436e78d33f542d30efe91
https://doi.org/10.1038/s41592-020-0933-6

High-confidence structural annotation of metabolites absent from spectral libraries

Autor: Louis-Félix Nothias, Sebastian Böcker, Marcus Ludwig, Emily C. Gentry, Kai Dührkop, Pieter C. Dorrestein, Martin Hoffmann, Michael Witting, Markus Fleischauer

Publikováno v: Nat. Biotechnol. 40, 411–421 (2021)
Nature Biotechnology

Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but, typically, only a small fraction of spectra can be matched. Previous in silico methods search in structure databases but cannot distinguish between correct

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::41aa492dd92bcea93e7c6e958630ff85
https://mediatum.ub.tum.de/1638482

Classes for the masses: Systematic classification of unknowns using fragmentation spectra

Autor: Markus Fleischauer, Sebastian Böcker, Martin Hoffmann, Pieter C. Dorrestein, Louis-Félix Nothias, Juho Rousu, Kai Dührkop, Marcus Ludwig

Metabolomics experiments can employ non-targeted tandem mass spectrometry to detect hundreds to thousands of molecules in a biological sample. Structural annotation of molecules is typically carried out by searching their fragmentation spectra in spe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f567ce9a69239b9637a8a0f58251d687