Publications
List of publications
Selected publications
Metabolome / Microbiome
Quinn R. A., et al. Global chemical effects of the microbiome include new bile-acid conjugations. Nature 2020, 579, 123–129. DOI:10.1038/s41586-020-2047-9.
Quinn, R. A.; Comstock, W.; Zhang, T.; Morton, J. T.; da Silva, R.; Tran, A.; Aksenov, A.; Nothias, L.-F.; Wangpraseurt, D.; Melnik, A. V.; et al. Niche partitioning of a pathogenic microbiome driven by chemical gradients. Sci Adv 2018, 4 (9), eaau1908 DOI: 10.1126/sciadv.aau1908.
Garg, N.; Wang, M.; Hyde, E.; da Silva, R. R.; Melnik, A. V.; Protsyuk, I.; Bouslimani, A.; Lim, Y. W.; Wong, R.; Humphrey, G.; et al. Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. Cell Host Microbe 2017, 22 (5), 705–716.e4 DOI: 10.1016/j.chom.2017.10.001.
Gilbert, J. A.; Quinn, R. A.; Debelius, J.; Xu, Z. Z.; Morton, J.; Garg, N.; Jansson, J. K.; Dorrestein, P. C.; Knight, R. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 2016, 535 (7610), 94–103 DOI: 10.1038/nature18850.
Global Natural Products Social molecular networking (GNPS)
Nothias Louis-Felix, Petras Daniel, Schmid Robin, et al., Feature-based molecular networking in the GNPS analysis environment. Nature Methods 17, (2020): 905–908. DOI:10.1038/s41592-020-0933-6
Jarmusch Alan, et al., ReDU: a framework to find and reanalyze public mass spectrometry data. Nature Methods, 17 (2020) 901–904.
Wang Mingxun, et al., Mass spectrometry searches using MASST. Nature Biotechnology, 38 (2020) 23–26.
Wang Mingxun, et al., Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology 34.8 (2016): 828-837.
Mass Spectrometry-based Molecular Networking
Nothias Louis-Felix, Petras Daniel, Schmid Robin, et al., Feature-based molecular networking in the GNPS analysis environment. Nature Methods 17, (2020): 905–908. DOI:10.1038/s41592-020-0933-6
Wang, M.; Carver, J. J.; Phelan, V. V.; Sanchez, L. M.; Garg, N.; Peng, Y.; Nguyen, D. D.; Watrous, J.; Kapono, C. A.; Luzzatto-Knaan, T.; et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat. Biotechnol. 2016, 34 (8), 828–837 DOI: 10.1038/nbt.3597.
Quinn, R. A.; Nothias, L.-F.; Vining, O.; Meehan, M.; Esquenazi, E.; Dorrestein, P. C. Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy. Trends Pharmacol. Sci. 2017, 38 (2), 143–154 DOI: 10.1016/j.tips.2016.10.011.
Yang, J. Y.; Sanchez, L. M.; Rath, C. M.; Liu, X.; Boudreau, P. D.; Bruns, N.; Glukhov, E.; Wodtke, A.; de Felicio, R.; Fenner, A.; et al. Molecular networking as a dereplication strategy. J. Nat. Prod. 2013, 76 (9), 1686–1699 DOI: 10.1021/np400413s.
Nothias, L.-F.; Nothias-Esposito, M.; da Silva, R.; Wang, M.; Protsyuk, I.; Zhang, Z.; Sarvepalli, A.; Leyssen, P.; Touboul, D.; Costa, J.; et al. Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation. J. Nat. Prod. 2018 DOI: 10.1021/acs.jnatprod.7b00737.
Imaging Mass Spectrometry
Watrous, J.; Roach, P.; Alexandrov, T.; Heath, B. S.; Yang, J. Y.; Kersten, R. D.; van der Voort, M.; Pogliano, K.; Gross, H.; Raaijmakers, J. M.; et al. Mass spectral molecular networking of living microbial colonies. Proc. Natl. Acad. Sci. U. S. A. 2012, 109 (26), E1743–E1752 DOI: 10.1073/pnas.1203689109.
Moree, W. J.; Phelan, V. V.; Wu, C.-H.; Bandeira, N.; Cornett, D. S.; Duggan, B. M.; Dorrestein, P. C. Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 2012, 109 (34), 13811–13816 DOI: 10.1073/pnas.1206855109.
Watrous, J. D.; Dorrestein, P. C. Imaging mass spectrometry in microbiology. Nat. Rev. Microbiol. 2011, 9 (9), 683–694 DOI: 10.1038/nrmicro2634.
3D Molecular Cartography
Bouslimani, A.; Porto, C.; Rath, C. M.; Wang, M.; Guo, Y.; Gonzalez, A.; Berg-Lyon, D.; Ackermann, G.; Christensen, G. J. M.; Nakatsuji, T.; et al. Molecular cartography of the human skin surface in 3D. Proc. Natl. Acad. Sci. U. S. A. 2015, 112 (17), 2120–2129 DOI: 10.1073/pnas.1424409112.
Protsyuk, I.; Melnik, A. V.; Nothias, L.-F.; Rappez, L.; Phapale, P.; Aksenov, A. A.; Bouslimani, A.; Ryazanov, S.; Dorrestein, P. C.; Alexandrov, T. 3D molecular cartography using LC-MS facilitated by Optimus and ’ili software. Nat. Protoc. 2018, 13 (1), 134–154 DOI: 10.1038/nprot.2017.122.
Bouslimani, A.; Melnik, A. V.; Xu, Z.; Amir, A.; da Silva, R. R.; Wang, M.; Bandeira, N.; Alexandrov, T.; Knight, R.; Dorrestein, P. C. Lifestyle chemistries from phones for individual profiling. Proc. Natl. Acad. Sci. U. S. A. 2016, 113 (48), E7645–E7654 DOI: 10.1073/pnas.1610019113.
Petras, D.; Nothias, L.-F.; Quinn, R. A.; Alexandrov, T.; Bandeira, N.; Bouslimani, A.; Castro-Falcón, G.; Chen, L.; Dang, T.; Floros, D. J.; et al. Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats. Anal. Chem. 2016, 88 (22), 10775–10784 DOI: 10.1021/acs.analchem.6b03456.
Computational Annotation of Tandem Mass Spectrometry Data
da Silva, R. R.; Wang, M.; Nothias, L.-F.; van der Hooft, J. J. J.; Caraballo-Rodríguez, A. M.; Fox, E.; Balunas, M. J.; Klassen, J. L.; Lopes, N. P.; Dorrestein, P. C. Propagating annotations of molecular networks using in silico fragmentation. PLoS Comput. Biol. 2018, 14 (4), e1006089 DOI: 10.1371/journal.pcbi.1006089.
Mohimani, H.; Gurevich, A.; Mikheenko, A.; Garg, N.; Nothias, L.-F.; Ninomiya, A.; Takada, K.; Dorrestein, P. C.; Pevzner, P. A. Dereplication of peptidic natural products through database search of mass spectra. Nat. Chem. Biol. 2016, No. 1, 30–37 DOI: 10.1038/nchembio.2219.