28.  Santana-Souza L, Irie Y, Eda S.  2022.  PLoS One.  Black queen hypothesis, partial privatization, and quorum sensing evolution.  17(11):e0278449.

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27.  Singh S, Almuhanna Y, Alshahrani MY, Lowman D, Rice PJ, Gell C, Ma Z, Graves B, Jackson D, Lee K, Kelkar R, Koranteng J, Muntaka S, Mitchell D, da Silva AC, Hussain F, Yilmaz G, Mastrotto F, Irie Y, Williams P, Williams D, Cámara M, & Martinez-Pomares L.  2021.  npj Biofilms and Microbiomes.  Carbohydrates from Pseudomonas aeruginosa biofilms interact with immune C-type lectins and interfere with their receptor function.  7(1):87.

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26.  Irie Y, La Mensa A, Murina V, Hauryliuk V, Tenson T, & Shingler V.  2020.  Frontiers in Microbiology.  Hfq-assisted RsmA regulation is central to Pseudomonas aeruginosa biofilm polysaccharide PEL expression.  11:482585.

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25.  Harrison JJ, Almblad H, Irie Y, Wolter DJ, Eggleston HC, Randall TE, Kitzman JO, Stackhouse B, Emerson JC, McNamara S, Larsen TJ, Shendure J, Hoffman LR, Wozniak DJ, & Parsek MR.  2020.  PLOS Genetics.  Elevated exopolysaccharide levels in Pseudomonas aeruginosa flagellar mutants have implications for biofilm growth and chronic infections.  16(6):e1008848.

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24.  Andersen PI, Ianevski A, Lysvand H, Vitkauskiene A, Oksenych V, Bjørås M, Telling K, Lutsar I, Dumpis U, Irie Y, Tenson T, Kantele A, & Kainov DE.  2020.  International Journal of Infectious Diseases.  Discovery and development of safe-in-man broad-spectrum antiviral agents.  93:268-276.

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23.  Wirebrand L, Madhushani AWK, Irie Y, & Shingler V.  2018.  Environmental Microbiology.  Multiple Hfq-Crc target sites are required to impose catabolite repression on (methyl)phenol metabolism in Pseudomonas putida CF600.  20(1):186-199.

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22.  Borlee BR, Borlee GI, Martin KH, Irie Y.  2017.  Methods in Molecular Biology.  Cyclic di-GMP-responsive transcriptional reporter bioassays in Pseudomonas aeruginosa.  1657:99-110.

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21.  Irie Y, Roberts AEL, Kragh KN, Gordon VD, Hutchison J, Allen RJ, Melaugh G, Bjarnsholt T, West SA, Diggle SP.  2017.  mBio.  The Pseudomonas aeruginosa PSL polysaccharide is a social but noncheatable trait in biofilms.  8(3):e00374-17.

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20. Murakami K, Ono T, Noma Y, Minase I, Amoh T, Irie Y, Hirota K, & Miyake Y.  2017.  Journal of Infection and Chemotherapy.  Explorative gene analysis of antiobiotic tolerance-related genes in adherent and biofilm cells of Pseudomonas aeruginosa.  23(5):271-277.

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19. Amoh T, Murakami K, Kariyama R, Hori K, Irie Y, Vidučić D, Hirota K, Igarashi J, Suga H, Kumon H, & Miyake Y.  2017.  The Journal of Medical Investigation.  A Pseudomonas aeruginosa quorum-sensing autoinducer analog enhances the activity of antibiotics against resistant strains.  64(1.2):101-109.

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18. Kovach K, Davis-Fields M, Irie Y, Jain K, Doowar S, Vuong K, Dhamani N, Mohanty K, Touhami A, Gordon VD.  2017.  npj Biofilms and Microbiomes.  Evolutionary adaptations of biofilms infecting cystic fibrosis lungs promote mechanical toughness by adjusting polysaccharide production.  3:1.

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17.  Kragh KN, Hutchison JB, Melaugh G, Rodesney C, Roberts AEL, Irie Y, Jensen PØ, Diggle SP, Allen RJ, Gordon VD, Bjarnsholt T.  2016.  mBio.  The role of multicellular aggregates in biofilm formation.  7(2):e00237-16.

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16.  Melaugh G, Hutchison J, Kragh K, Irie Y, Roberts A, Bjarnsholt T, Diggle SP, Gordon VD, & Allen R.  2016.  PLOS ONE.  Shaping the growth behaviour of biofilms initiated from bacterial aggregates.  11(3):e0149683.

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15.  Park JH, Jo Y, Jang SY, Kwon HN, Irie Y, Parsek MR, Kim MH, & Choi SH.  2015.  PLOS Pathogens.  The cabABC operon essential for biofilm and rugose colony development in Vibrio vulnificus.  11(9):e1005192.

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14.  Hmelo LR, Borlee BR, Almblad H, Love ME, Randall TE, Tseng BS, Lin C, Irie Y, Storek KM, Yang JJ, Siehnel RJ, Howell PL, Singh PK, Tolker-Nielsen T, Parsek MR, Schweizer HP, & Harrison JJ.  2015.  Nature Protocols.  Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange.  10(11):1820-1841.

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13.  Irie Y & Parsek MR.  2014.  Methods in Molecular Biology.  LC/MS/MS-based quantitative assay for the secondary messenger molecule, c-di-GMP.  1149:271-279.

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12.  Hutchison J, Rodesney C, Kaushik K, Le H, Hurwitz D, Irie Y, & Gordon VD.  2014.  Langmuir.  Single-cell control of initial spatial structure in biofilm development using laser trapping.  30(15):4522-4530.

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11.  Jones CJ, Newsom D, Kelly B, Irie Y, Jennings LK, Xu B, Limoli DH, Harrison JJ, Parsek MR, White P, & Wozniak DJ.  2014.  PLOS Pathogens.  ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa.  10(3):e1003984.

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10.  Irie Y, Borlee BR, O’Connor JR, Hill PJ, Harwood CS, Wozniak DJ, & Parsek MR.  2012.  Proceedings of the National Academy of Sciences U. S. A.  Self-produced exopolysaccharide is a signal that stimulates biofilm formation in Pseudomonas aeruginosa.  109(50):20632-20636.

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9.  Rybtke MT, Borlee BR, Murakami K, Irie Y, Hentzer M, Nielsen TE, Givskov M, Parsek MR, & Tolker-Nielsen T.  2012.  Applied and Environmental Microbiology.  A fluorescence-based reporter for gauging cyclic di-GMP levels in Pseudomonas aeruginosa.  78(15):5060-5069.

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8.  Colvin KM, Irie Y, Tart CS, Urbano R, Whitney JC, Ryder C, Howell PL, Wozniak DJ, & Parsek MR.  2012.  Environmental Microbiology.  The Pel and Psl polysaccharides provide Pseudomonas aeruginosa structural redundancy within the biofilm matrix.  14(8):1913-1928.

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7.  Irie Y, Starkey M, Edwards AN, Wozniak DJ, Romeo T, & Parsek MR.  2010.  Molecular Microbiology.  Pseudomonas aeruginosa biofilm matrix polysaccharide Psl is regulated transcriptionally by RpoS and post-transcriptionally by RsmA.  78(1):158-172.

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6.  Peterson SB, Irie Y, Borlee BR, Murakami K, Harrison JJ, Colvin KM, & Parsek MR.  Different methods for culturing biofilms in vitro.  In: Bjarnsholt T, Høiby N, Moser C, & Jensen PØ (eds) Biofilm Infections.  Springer.  ISBN: 978-1-4419-6083-2.

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5.  Irie Y & Parsek MR.  2008.  Current Topics in Microbiology and Immunology.  Quorum sensing and microbial biofilms.  322:67-84.

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4.  Irie Y & Yuk MH.  2007.  FEMS Microbiology Letters.  In vivo colonization profile study of Bordetella bronchiseptica in the nasal cavity.  275(2):191-198.

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3.  Irie Y, Preston A, & Yuk MH.  2006.  Journal of Bacteriology.  Expression of the primary carbohydrate component of the Bordetella bronchiseptica biofilm matrix is dependent on growth phase but independent of Bvg regulation.  188(18):6680-6687.

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2.  Irie Y, O’Toole GA, & Yuk MH.  2005.  FEMS Microbiology Letters.  Pseudomonas aeruginosa rhamnolipids disperse Bordetella bronchiseptica biofilms.  250(2):237-243.

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1.  Irie Y, Mattoo S, & Yuk MH.  2004.  Journal of Bacteriology.  The Bvg control system regulates biofilm formation in Bordetella bronchiseptica.  186(17):5692-5698.