Publications

Before platelets: the production of platelet activating factor during growth and stress in a basal marine organism

Galtier d'Auriac, I., Quinn, R.A., Maughan, H., Nothias, L-F., Little, M., Kapono, C., Cobian, A., Reyes, B.T., Green, K., Quistad, S.D., Leray, M., Smith, J.E., Dorrestein, P.C., Rohwer, F., Deheyn, D.D., and Aaron C. Hartmann. 2018. Before platelets: the production of platelet activating factor during growth and stress in a basal marine organism. Proceedings of the Royal Society B. 285:4. DOI: 10.1098/rspb.2018.1307

2017

Meta-mass shift chemical (MeMSChem) profiling of metabolomes on coral reefs

Hartmann, A.C., Petras, D., Quinn, R.A., Protsyuk, I., Archer, F.I., Ransome, E.J., Williams, G.J., Bailey, B.A., Vermeij, M.J.A., Alexandrov, T., Dorrestein, P.C., and F. Rohwer. 2017. Meta-mass shift chemical (MeMSChem) profiling of metabolomes on coral reefs. PNAS. doi:10.1073/pnas.1710248114.

Integrating microbiome and metabolome data to understand infectious airway disease

Quinn, R.A.* 2017. Integrating microbiome and metabolome data to understand infectious airway disease. American Journal of Respiratory and Critical Care Medicine. doi.org/10.1164/rccm.201704-0671ED, *corresponding author

The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections

Comstock, W. J., Huh, E., Weekes, R., Watson, C., Xu, T., Dorrestein, P. C., and R.A. Quinn*. 2017. The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections. Journal of Visualized Experiments. (123), e55532, doi.org/10.3791/55532. *corresponding author

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

Quinn, R.A., Hazra, A.Y., Smolowitz, R. and A.Y. Chistoserdov. 2017. 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. Journal of Microbiological Methods. 139:61-67. doi.org/10.1016/j.mimet.2017.04.001

Balance trees provide useful insights into community structure

Morton, J. T., Sanders, J., Quinn, R.A., McDonald, D., Gonzalez, A., Vasquez-Baeza, Y., Navas-Molina, J. A., Hyde, E. R., Song, S. J., Metcalf, J. L., Lladser, M., Dorrestein, P. and R. Knight. 2016. Balance trees provide useful insights into community structure. mSystems. 10.1128/mSystems.00162-16. doi.org/10.1128/mSystems.00162-16

2016

Ecological Networking of Cystic Fibrosis Lung Infections

Quinn, R.A., Whiteson, K., Lim, Y.W., Zhao, J., Conrad, D., LiPuma, J., Rohwer, F. and S. Widder. 2016. Ecological Networking of Cystic Fibrosis Lung Infections. Nature Biofilms and Microbiomes. 2(1):4. doi.org/10.1038/s41522-016-0002-1.

The chemistry associated with built human habitats and transport

Petras, D., Notias, L-F., Quinn, R.A.*, Alexandrov, T., Bandiera, N., Bouslimani, A., Castro-Falcon, G., Chen, L., Dang, T., Dorrestein, P., et al. 2016. The chemistry associated with built human habitats and transport. Analytical Chemistry. 88(22): 10775-10784 *Denotes co-first author.

Mass spectral molecular networking as a pharmaceutical, pharmacological and clinical tool

Quinn, R.A., Nothias, L-F., Vining, O., Meehan, M., Esquenazi, E. and P. Dorrestein. 2016. Mass spectral molecular networking as a pharmaceutical, pharmacological and clinical tool. Trends in Pharmacological Sciences. doi.org/10.1016/j.tips.2016.10.011

Metabolomics of Pulmonary Exacerbations Reveals the Personalized Nature of Cystic Fibrosis Disease

Quinn, R.A., Lim, Y.W., Whiteson, K., Furlan, M., Conrad, D., Rohwer, F. and P. Dorrestein. 2016. Metabolomics of Pulmonary Exacerbations Reveals the Personalized Nature of Cystic Fibrosis Disease. PeerJ. doi.org/10.7717/peerj.2174 Article highlighted here: http://cysticfibrosisnewstoday.com/2016/09/26/

Sharing and community curation of natural products data with Global Natural Products Social molecular networking

Wang, M., Carver, J., Phelan, V., Sanchez, L., Garg, N., Peng, Y., Nguyen, D., Watrous, D., Kapono, C., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A., Meehan, M., Liu, W., Cruesemann, M., Boudreau, P., Esquenazi, E., Sandoval-Calderón, M., Kersten, R., Laura Pace, Quinn, R.A., et. al… W., Moore, B., Dorrestein, P., and Bandiera, N. 2016. Sharing and community curation of natural products data with Global Natural Products Social molecular networking. Nature Biotechnology. 34:828-837. doi.org/10.1038/nbt.3597

Microbiome-wide association studies link dynamic microbial consortia to disease

Gilbert, J., Quinn, R.A., Debelius, J., Xu, Z.Z., Morton, J., Garg, N., Jansson, J., Dorrestein, P. C., and R. Knight. 2016. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 535:94-103. doi.org/10.1038/nature18850.

Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defense

Quinn, R.A., Vermeij, M.A., Hartmann, A.C., Galtier d’Auriac, I., Benler, S., Haas, A., Quistad, S.D., Lim, Y.W., Little, M., Sandin, S., Smith, J.E., Dorrestein, P.C., and F. Rohwer. 2016. Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defense. Proceedings of the Royal Society B. 283:20160469. doi.org/10.1098/rspb.2016.0469 Article highlighted: here1, here2

From sample to multiomics conclusions in under 48 hours

Quinn, R.A., Navas-Molina, J., Hyde, E., Song, S. J., Vazquez-Baeza, Y., Humphrey, G., Gaffney, J., Minich, J. J., Melnik, A. V., Herschend, J., DeReus, J., Durant, A., Dutton, R., Khosroheidari, M., Green, C., da Silva, R., Dorrestein, P.C., and R. Knight. 2016. From sample to multiomics conclusions in under 48 hours. mSystems. 1(2):e00038-16. doi:10.1128/mSystems.00038-16. Article highlighted: here1

Changes in microbial ecology: building predictive understanding of community function and dynamics

Widder, S., Allen, R., Pfeiffer, T., Thomas, C. P., Wiuf, C., Sloan, W. T., Cordero, O., Brown, S., Momeni, B., Shou, W., Kettle, H., Flint, H.J., Haas, A., Laroche, B., Kreft, J., Quinn, R.A., Rainey, P., Isaac Newton Institute Fellows. 2016. Changes in microbial ecology: building predictive understanding of community function and dynamics. ISME J. 10(11):2557-2568. doi.org/10.1038/ismej.2016.45

2015

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome

Quinn, R.A., Phelan, V. P., Whiteson, K., Garg, N., Bailey, B., Lim, Y.W., Conrad, D., Dorrestein, P.C., and F. Rohwer. 2015. Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome. ISME J. 10(6):1483-1498. doi.org/10.1038/ismej.2015.207

Illuminating the dark matter in metabolomics

da Silva, R., Dorrestein, P., and R.A. Quinn. 2015. Illuminating the dark matter in metabolomics. Proceedings of the National Academy of Sciences. 112(41): 12549-12550. doi.org/10.1073/pnas.1516878112

2014

A Winogradsky-based culture system reveals an association between microbial fermentation and cystic fibrosis exacerbation

Quinn, R.A., Whiteson, K., Lim, Y.W., Salamon, P., Bailey, B., Meinardi, S., Sanchez, S., Blake, D., Conrad, D., and F. Rohwer. 2014. A Winogradsky-based culture system reveals an association between microbial fermentation and cystic fibrosis exacerbation. ISME J. 9(4):1024-1038.

The community ecology of microbial molecules

Quinn, R.A. and T. Alexandrov. 2014. The community ecology of microbial molecules. Journal of Chemical Ecology. 40(11):1161-1162.

Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung

Quinn, R.A., Lim, Y.W., Maughan, H., Conrad, D., Rohwer, F and K. L. Whiteson. 2014. Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. mBio. 5(2):e00956-13. doi:10.1128/mBio.00956-13 Article Highlighted in: Molloy, S. 2014. A metabolic milieu. Nat. Rev. Microbiol. 12:315.

The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis patients: parallels from island biogeography

Whiteson, K., Bailey, B., Bergkessel, M., Conrad, D., Delhaes, L., Felts, B., Harris, J.K., Hunter, R., Lim, Y.W., Maughan, H., Quinn, R.A., Salamon, P., Sullivan, J., Wagner, B., and P.B. Rainey. 2014. The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis patients: parallels from island biogeography. American Journal of Respiratory and Critical Care Medicine. 189(11):1309-1315.

Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation

Whiteson, K., Meinardi, S., Lim, Y.W., Schmieder, R., Maughan, H., Quinn, R.A., Black, D., Conrad, D., and F. Rohwer. 2014. Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation. ISME J. 8:1247-1258.

Pathology of two forms of shell disease in the American lobster (Homarus americanus, Milne Edwards) in Atlantic Canada

Smolowitz, R., Quinn, R.A., Cawthorn, R.J., Summerfield, R.L. and A. Y. Chistoserdov. 2014. Pathology of two forms of shell disease in the American lobster (Homarus americanus, Milne Edwards) in Atlantic Canada. Journal of Fish Diseases. 37:577-581.