Recent Publications

Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. “Learning representations of microbe-metabolite interactions.” Nat Methods. (2019) Nov 4. doi: 10.1038/s41592-019-0616-3

Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. “Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.” Genome Biol. (2019) Oct 31;20(1):226. doi: 10.1186/s13059-019-1834-9

Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N. “Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.” mSystems. (2019) Sep 24;4:(5). doi: 10.1128/mSystems.00375-19

Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC. “Niche partitioning of a pathogenic microbiome driven by chemical gradients.” Sci Adv. (2018) Sep 26;4(9):eaau1908. doi: 10.1126/sciadv.aau1908

Raghuvanshi R, Grayson AG, Schena I, Amanze O, Suwintono K, Quinn RA. “Microbial Transformations of Organically Fermented Foods.” Metabolites. (2019) Aug 10;9:(8). doi: 10.3390/metabo9080165

Cobián Güemes AG, Lim YW, Quinn RA, Conrad DJ, Benler S, Maughan H, Edwards R, Brettin T, Cantú VA, Cuevas D, Hamidi R, Dorrestein P, Rohwer F. “Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.” MBio. (2019) Apr 16;10:(2). doi: 10.1128/mBio.00431-19

Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC. “Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome.” Microbiome. (2019) Feb 13;7(1):23. doi: 10.1186/s40168-019-0636-3

Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC. “Niche partitioning of a pathogenic microbiome driven by chemical gradients.” Sci Adv. (2018) Sep;4(9):eaau1908. doi: 10.1126/sciadv.aau1908

Galtier d'Auriac I, Quinn RA, Maughan H, Nothias LF, Little M, Kapono CA, Cobian A, Reyes BT, Green K, Quistad SD, Leray M, Smith JE, Dorrestein PC, Rohwer F, Deheyn DD, Hartmann AC. “Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism.” Proc Biol Sci. (2018) Aug 15;285:(1884). doi: 10.1098/rspb.2018.1307

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 RA, 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. doi: 10.1038/s41579-018-0029-9

Hartmann AC, Petras D, Quinn RA, 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. doi: 10.1073/pnas.1710248114

Quinn RA. “Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease.” Am J Respir Crit Care Med. (2017) Oct 1;196(7):806-807. doi: 10.1164/rccm.201704-0671ED

Quinn RA, 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. doi: 10.1038/s41522-016-0002-1

Comstock WJ, Huh E, Weekes R, Watson C, Xu T, Dorrestein PC, Quinn RA. “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 8;. doi: 10.3791/55532

Morton JT, Sanders J, Quinn RA, 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). doi: 10.1128/mSystems.00162-16

Quinn RA, 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) Feb;38(2):143-154. doi: 10.1016/j.tips.2016.10.011

Petras D, Nothias LF, Quinn RA, 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. doi: 10.1021/acs.analchem.6b03456

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 RA, 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) Aug 9;34(8):828-837. doi: 10.1038/nbt.3597

Gilbert JA, Quinn RA, 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. doi: 10.1038/nature18850

Quinn RA, 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) Jun;10(6):1483-98. doi: 10.1038/ismej.2015.207

Quinn RA, 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). doi: 10.1098/rspb.2016.0469

Quinn RA, 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). doi: 10.1128/mSystems.00038-16

Quinn RA, 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. doi: 10.7717/peerj.2174

da Silva RR, Dorrestein PC, Quinn RA. “Illuminating the dark matter in metabolomics.” Proc Natl Acad Sci U S A. (2015) Oct 13;112(41):12549-50. doi: 10.1073/pnas.1516878112

Quinn RA, 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):1052. doi: 10.1038/ismej.2014.266

Quinn RA, Alexandrov T. “The community ecology of microbial molecules.” J Chem Ecol. (2014) Dec;40(11-12):1161-2. doi: 10.1007/s10886-014-0528-8

Smolowitz R, Quinn RA, 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. doi: 10.1111/jfd.12136

Quinn RA, 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. doi: 10.1128/mBio.00956-13

Hsu CC, ElNaggar MS, Peng Y, Fang J, Sanchez LM, Mascuch SJ, Møller KA, Alazzeh EK, Pikula J, Quinn RA, 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. doi: 10.1021/ac401613x

Quinn RA, 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. doi: 10.1139/cjm-2012-0679

Quinn RA, 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. doi: 10.3354/dao02565

Quinn RA, 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. doi: 10.3354/dao02446

Quinn RA, 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. doi: 10.1139/w2012-024