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Robert Quinn

TitleAssociate Project Scientist
InstitutionUniversity of California San Diego
DepartmentSchool of Pharmacy and Pharmaceutical Science
Address9500 Gilman Drive #0751
La Jolla CA 92093
Phone858-822-5437
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    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 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. Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn R, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018 May 23. PMID: 29795328.
      View in: PubMed
    2. Hartmann AC, Petras D, Quinn R, Protsyuk I, Archer FI, Ransome E, Williams GJ, Bailey BA, Vermeij MJA, Alexandrov T, Dorrestein PC, Rohwer FL. Meta-mass shift chemical profiling of metabolomes from coral reefs. Proc Natl Acad Sci U S A. 2017 Oct 31; 114(44):11685-11690. PMID: 29078340.
      View in: PubMed
    3. Quinn R. Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease. Am J Respir Crit Care Med. 2017 10 01; 196(7):806-807. PMID: 28628375.
      View in: PubMed
    4. 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 05 08; (123). PMID: 28518116.
      View in: PubMed
    5. 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 08; 139:61-67. PMID: 28385456.
      View in: PubMed
    6. 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
    7. 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
    8. 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. 2017 02; 38(2):143-154. PMID: 27842887.
      View in: PubMed
    9. Petras D, Nothias LF, Quinn R, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook V, Garg N, Hoffner N, Jiang Y, Kapono CA, Koester I, Knight R, Leber CA, Ling TJ, 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 Nov 15; 88(22):10775-10784. PMID: 27732780.
      View in: PubMed
    10. 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; PMCID: PMC5013801.
      View in: PubMed, PubMed Central
    11. 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
    12. Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn R, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016 08 09; 34(8):828-837. PMID: 27504778.
      View in: PubMed
    13. 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 07 07; 535(7610):94-103. PMID: 27383984.
      View in: PubMed
    14. 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.
    15. 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; PMCID: PMC4855392.
      View in: PubMed, PubMed Central
    16. 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
    17. 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. 2016 06; 10(6):1483-98. PMID: 26623545.
      View in: PubMed
    18. 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; PMCID: PMC4611607.
      View in: PubMed, PubMed Central
    19. 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 Mar 17; 9(4):1024-38. PMID: 25514533; PMCID: PMC4817692.
      View in: PubMed, PubMed Central
    20. Quinn R, Alexandrov T. The community ecology of microbial molecules. J Chem Ecol. 2014 Dec; 40(11-12):1161-2. PMID: 25466220; PMCID: PMC4272644.
      View in: PubMed, PubMed Central
    21. 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 Mar 18; 5(2):e00956-13. PMID: 24643867; PMCID: PMC3967525.
      View in: PubMed, PubMed Central
    22. 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
    23. 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 06; 85(15):7014-8. PMID: 23819546; PMCID: PMC3890442.
      View in: PubMed, PubMed Central
    24. 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
    25. 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
    26. 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
    27. 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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