Publications

Selected publications

Metabolome / Microbiome

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.


Mass Spectrometry-based Molecular Networking

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.

Ernst, M.; Nothias-Scaglia, L.-F.; van der Hooft, J.; Silva, R. R.; Haris Saslis-Lagoudakis, C.; Grace, O. M.; Martinez-Swatson, K.; Hassemer, G.; Funez, L.; Simonsen, H. T.; et al. Did a plant-herbivore arms race drive chemical diversity in Euphorbia? bioRxiv, 2018, 323014.


List of publications

The list of publications can be consulted on Google Scholar [here] or on PubMed [click here or see below]