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    Robert Quinn

    TitleAssociate Project Scientist
    SchoolUniversity of California, San Diego
    DepartmentSchool of Pharmacy and Pharmaceutical Science
    Address9500 Gilman Drive #0751
    CA La Jolla 92093
    Phone858-822-5437
    vCardDownload vCard

      Collapse Biography 
      Collapse Awards and Honors
      Vertex Pharmaceuticals2015 - 2016CF Research Innovation Award
      Cystic Fibrosis Research Inc.2012 - 2015Elizabeth Nash Memorial Fellowship

      Collapse Overview 
      Collapse Overview
      My research focus is the structure and function of microbiomes in health and disease. I have studied complex communities of microbes on everything from corals and lobsters to lungs and guts. My belief is that we can learn from classic ecological principles how to best understand the dynamics of the human microbiome. Using metagenomics, metabolomics and transcriptomics methods I study how the core function and chemical environment of a microbial community changes in times of disease. My principle focus has been the human disease cystic fibrosis (CF). A complex community of opportunistic pathogens live in the lungs of CF patients and contribute to their eventual death from the disease. I have focused my work on exacerbations of CF, where I have shown that a change in the core physiology of the microbiome is associated with acute disease in patients.


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      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Quinn R. Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease. Am J Respir Crit Care Med. 2017 Jun 19. PMID: 28628375.
        View in: PubMed
      2. Comstock WJ, Huh E, Weekes R, Watson C, Xu T, Dorrestein PC, Quinn R. The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections. J Vis Exp. 2017 May 08; (123). PMID: 28518116.
        View in: PubMed
      3. Quinn R, Hazra S, Smolowitz R, Chistoserdov AY. Real-time PCR assay for Aquimarina macrocephali subsp. homaria and its distribution in shell disease lesions of Homarus americanus, Milne-Edwards, 1837, and environmental samples. J Microbiol Methods. 2017 Aug; 139:61-67. PMID: 28385456.
        View in: PubMed
      4. Morton JT, Sanders J, Quinn R, McDonald D, Gonzalez A, Vázquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R. Balance Trees Reveal Microbial Niche Differentiation. mSystems. 2017 Jan-Feb; 2(1). PMID: 28144630.
        View in: PubMed
      5. Quinn R, Whiteson K, Lim YW, Zhao J, Conrad D, LiPuma JJ, Rohwer F, Widder S. Ecological networking of cystic fibrosis lung infections. NPJ Biofilms Microbiomes. 2016; 2:4. PMID: 28649398.
        View in: PubMed
      6. Quinn R, Nothias LF, Vining O, Meehan M, Esquenazi E, Dorrestein PC. Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy. Trends Pharmacol Sci. 2016 Nov 11. PMID: 27842887.
        View in: PubMed
      7. Petras D, Nothias LF, Quinn R, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook VY, Garg N, Hoffner N, Jiang Y, Kapono CA, Koester I, Knight R, Leber CA, Ling T, Luzzatto-Knaan T, McCall LI, McGrath AP, Meehan MJ, Merritt JK, Mills RH, Morton J, Podvin S, Protsyuk I, Purdy T, Satterfield K, Searles S, Shah S, Shires S, Steffen D, White M, Todoric J, Tuttle R, Wojnicz A, Sapp V, Vargas F, Yang J, Zhang C, Dorrestein PC. Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats. Anal Chem. 2016 Oct 12. PMID: 27732780.
        View in: PubMed
      8. Quinn R, Vermeij MJ, Hartmann AC, d'Auriac IG, Benler S, Haas A, Quistad SD, Lim YW, Little M, Sandin S, Smith JE, Dorrestein PC, Rohwer F. Correction to 'Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence'. Proc Biol Sci. 2016 Aug 31; 283(1837). PMID: 27559065.
        View in: PubMed
      9. Quinn R, Lim YW, Mak TD, Whiteson K, Furlan M, Conrad D, Rohwer F, Dorrestein P. Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease. PeerJ. 2016; 4:e2174. PMID: 27602256; PMCID: PMC4991883.
        View in: PubMed, PubMed Central
      10. Gilbert JA, Quinn R, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 2016 Jul 7; 535(7610):94-103. PMID: 27383984.
        View in: PubMed
      11. Robert A. Quinn, Jose A. Navas-Molina, Embriette R. Hyde, Se Jin Song, Yoshiki Vázquez-Baeza, Greg Humphrey, James Gaffney, Jeremiah J. Minich, Alexey V. Melnik, Jakob Herschend, Jeff DeReus, Austin Durant, Rachel J. Dutton, Mahdieh Khosroheidari, Clifford Green, Ricardo da Silva, Pieter C. Dorrestein, Rob Knight. From Sample to Multi-Omics Conclusions in Under 48 Hours. mSystems. 2016; DOI: 10.1128/mSystems.00038-16.
      12. Quinn R, Vermeij MJ, Hartmann AC, Galtier d'Auriac I, Benler S, Haas A, Quistad SD, Lim YW, Little M, Sandin S, Smith JE, Dorrestein PC, Rohwer F. Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence. Proc Biol Sci. 2016 Apr 27; 283(1829). PMID: 27122568.
        View in: PubMed
      13. Quinn R, Navas-Molina JA, Hyde ER, Song SJ, Vázquez-Baeza Y, Humphrey G, Gaffney J, Minich JJ, Melnik AV, Herschend J, DeReus J, Durant A, Dutton RJ, Khosroheidari M, Green C, da Silva R, Dorrestein PC, Knight R. From Sample to Multi-Omics Conclusions in under 48 Hours. mSystems. 2016 Mar-Apr; 1(2). PMID: 27822524.
        View in: PubMed
      14. Quinn R, Phelan VV, Whiteson KL, Garg N, Bailey BA, Lim YW, Conrad DJ, Dorrestein PC, Rohwer FL. Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome. ISME J. 2015 Dec 1. PMID: 26623545.
        View in: PubMed
      15. da Silva RR, Dorrestein PC, Quinn R. Illuminating the dark matter in metabolomics. Proc Natl Acad Sci U S A. 2015 Oct 13; 112(41):12549-50. PMID: 26430243.
        View in: PubMed
      16. Quinn R, Whiteson K, Lim YW, Salamon P, Bailey B, Mienardi S, Sanchez SE, Blake D, Conrad D, Rohwer F. A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. ISME J. 2015; 9:1024-38. PMID: 25514533.
        View in: PubMed
      17. Quinn R, Alexandrov T. The community ecology of microbial molecules. J Chem Ecol. 2014 Dec; 40(11-12):1161-2. PMID: 25466220.
        View in: PubMed
      18. Quinn R, Lim YW, Maughan H, Conrad D, Rohwer F, Whiteson KL. Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. MBio. 2014; 5(2):e00956-13. PMID: 24643867.
        View in: PubMed
      19. Smolowitz R, Quinn R, Cawthorn RJ, Summerfield RL, Chistoserdov AY. Pathology of two forms of shell disease of the American lobster Homarus americanus Milne Edwards in Atlantic Canada. J Fish Dis. 2014 Jun; 37(6):577-81. PMID: 23952709.
        View in: PubMed
      20. Hsu CC, ElNaggar MS, Peng Y, Fang J, Sanchez LM, Mascuch SJ, Møller KA, Alazzeh EK, Pikula J, Quinn R, Zeng Y, Wolfe BE, Dutton RJ, Gerwick L, Zhang L, Liu X, Månsson M, Dorrestein PC. Real-time metabolomics on living microorganisms using ambient electrospray ionization flow-probe. Anal Chem. 2013 Aug 6; 85(15):7014-8. PMID: 23819546.
        View in: PubMed
      21. Quinn R, Cawthorn RJ, Summerfield RL, Smolowitz R, Chistoserdov AY. Bacterial communities associated with lesions of two forms of shell disease in the American lobster (Homarus americanus, Milne Edwards) from Atlantic Canada. Can J Microbiol. 2013 Jun; 59(6):380-90. PMID: 23750952.
        View in: PubMed
      22. Quinn R, Smolowitz R, Chistoserdov AY. Culture-independent analysis of bacterial communities in hemolymph of American lobsters with epizootic shell disease. Dis Aquat Organ. 2013 Mar 26; 103(2):141-8. PMID: 23548364.
        View in: PubMed
      23. Quinn R, Metzler A, Tlusty M, Smolowitz RM, Leberg P, Chistoserdov AY. Lesion bacterial communities in American lobsters with diet-induced shell disease. Dis Aquat Organ. 2012 Apr 26; 98(3):221-33. PMID: 22535872.
        View in: PubMed
      24. Quinn R, Stevenson RM. Denaturing gradient gel electrophoresis for nonlethal detection of Aeromonas salmonicida in salmonid mucus and its potential for other bacterial fish pathogens. Can J Microbiol. 2012 May; 58(5):563-71. PMID: 22506865.
        View in: PubMed
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