Publications

2013

Gallagher LA, Ramage E, Patrapuvich R, Weiss E, Brittnacher M, Manoil C. (2013) Sequence-Defined Transposon Mutant Library of Burkholderia thailandensis. Mbio. 2013 Nov 5;4(6). doi:pii: e00604-13. 10.1128/mBio.00604-13. PubMed PMID: 24194535.

Wen H, Miao EA, Ting JP. (2013) Mechanisms of NOD-like receptor-associated inflammasome activation. Immunity. 2013 Sep 19;39(3):432-41. doi: 10.1016/j.immuni.2013.08.037. PubMed PMID: 24054327.

Hagar JA, Powell DA, Aachoui Y, Ernst RK, Miao EA. (2013) Cytoplasmic LPS activates caspase-11: implications in TLR4-independent endotoxic shock. Science. 2013 Sep 13;341(6151):1250-3. doi: 10.1126/science.1240988. PubMed PMID: 24031018.

Ko DC, Urban TJ. (2013) Understanding human variation in infectious disease susceptibility through clinical and cellular GWAS. PLoS Pathog. 2013 Aug;9(8):e1003424. doi: 10.1371/journal.ppat.1003424. Epub 2013 Aug 1. PubMed PMID: 23935492; PubMed Central PMCID: PMC3731241.

Christensen QH, Grove TL, Booker SJ, Greenberg EP. (2013) A high-throughput screen for quorum-sensing inhibitors that target acyl-homoserine lactone synthases. Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):13815-20. doi: 10.1073/pnas.1313098110. Epub 2013 Aug 7. PubMed PMID: 23924613; PubMed Central PMCID: PMC3752275.

Lowery CA, Matamouros S, Niessen S, Zhu J, Scolnick J, Lively JM, Cravatt BF, Miller SI, Kaufmann GF, Janda KD. (2013) A chemical biology approach to interrogate quorum-sensing regulated behaviors at the molecular and cellular level. Chem Biol. 2013 Jul 25;20(7):903-11. doi: 10.1016/j.chembiol.2013.05.009. PubMed PMID: 23890008; PubMed Central PMCID: PMC3736722.

Rayamajhi M, Zhang Y, Miao EA. (2013) Detection of pyroptosis by measuring released lactate dehydrogenase activity. Methods Mol Biol. 2013;1040:85-90. doi: 10.1007/978-1-62703-523-1_7. PubMed PMID: 23852598; PubMed Central PMCID: PMC3756820.

Aachoui Y, Sagulenko V, Miao EA, Stacey KJ. (2013) Inflammasome-mediated pyroptotic and apoptotic cell death, and defense against infection. Curr Opin Microbiol. 2013 Jun;16(3):319-26. doi: 10.1016/j.mib.2013.04.004. Epub 2013 May 23. PubMed PMID: 23707339; PubMed Central PMCID: PMC3742712.

Kolodziejek AM, Caplan AB, Bohach GA, Paszczynski AJ, Minnich SA, Hovde CJ. (2013) Physiological levels of glucose induce membrane vesicle secretion and affect the lipid and protein composition of Yersinia pestis cell surfaces. Appl Environ Microbiol. 2013 Jul;79(14):4509-14. doi: 10.1128/AEM.00675-13. Epub 2013 May 17. PubMed PMID: 23686263; PubMed Central PMCID: PMC3697494.

Russell AB, LeRoux M, Hathazi K, Agnello DM, Ishikawa T, Wiggins PA, Wai SN, Mougous JD. (2013) Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors. Nature. 2013 Apr 25;496(7446):508-12. doi: 10.1038/nature12074. Epub 2013 Apr 3. PubMed PMID: 23552891; PubMed Central PMCID: PMC3652678.

Nguyen EV, Gharib SA, Palazzo SJ, Chow YH, Goodlett DR, Schnapp LM. (2013) Proteomic profiling of bronchoalveolar lavage fluid in critically ill patients with ventilator-associated pneumonia. PLoS One. 2013;8(3):e58782. doi: 10.1371/journal.pone.0058782. Epub 2013 Mar 7. PubMed PMID: 23505561; PubMed Central PMCID: PMC3591362.

Majerczyk C, Kinman L, Han T, Bunt R, Greenberg EP. (2013) Virulence of Burkholderia mallei quorum-sensing mutants. Infect Immun. 2013 May;81(5):1471-8. doi: 10.1128/IAI.00048-13. Epub 2013 Feb 19. PubMed PMID: 23429539; PubMed Central PMCID: PMC3648008.

Aachoui Y, Leaf IA, Hagar JA, Fontana MF, Campos CG, Zak DE, Tan MH, Cotter PA, Vance RE, Aderem A, Miao EA. (2013) Caspase-11 protects against bacteria that escape the vacuole. Science. 2013 Feb 22;339(6122):975-8. doi: 10.1126/science.1230751. Epub 2013 Jan 24. PubMed PMID: 23348507.

Rayamajhi M, Miao EA. (2013) Just say NO to NLRP3. Nat Immunol. 2013 Jan;14(1):12-4. doi: 10.1038/ni.2493. PubMed PMID: 23238751.

West TE, Chantratita N, Chierakul W, Limmathurotsakul D, Wuthiekanun V, Myers ND, Emond MJ, Wurfel MM, Hawn TR, Peacock SJ, Skerrett SJ. (2013) Impaired TLR5 Functionality Is Associated with Survival in Melioidosis. J Immunol. 2013 Apr 1;190(7):3373-9. doi: 10.4049/jimmunol.1202974. Epub 2013 Feb 27. PubMed PMID: 23447684; PubMed Central PMCID: PMC3607401.

2012

Awoniyi M, Miller SI, Wilson CB, Hajjar AM, Smith KD (2012) Homeostatic regulation of Salmonella-induced mucosal inflammation and injury by IL-23. PLoS One. 2012;7(5):e37311. Epub 2012 May 18. PubMed PMID: 22624013; PubMed Central PMCID: PMC3356277.

Brunette RL, Young JM, Whitley DG, Brodsky IE, Malik HS, Stetson DB (2012) Extensive evolutionary and functional diversity among mammalian AIM2-like receptors. J Exp Med. 2012 Oct 22;209(11):1969-83. doi: 10.1084/jem.20121960. Epub 2012 Oct 8. PubMed PMID: 23045604; PubMed Central PMCID: PMC3478938.

Chandler JR, Truong TT, Silva PM, Seyedsayamdost MR, Carr G, Radey M, Jacobs MA, Sims EH, Clardy J, Greenberg EP (2012) Bactobolin resistance is conferred by mutations in the L2 ribosomal protein. MBio. 2012 Dec 18;3(6). doi:pii: e00499-12. 10.1128/mBio.00499-12. PubMed PMID: 23249812; PubMed Central PMCID: PMC3529544.

Chandler JR, Heilmann S, Mittler JE, Greenberg EP. (2012) Acyl-homoserine lactone-dependent eavesdropping promotes competition in a laboratory co-culture model. ISME J. 2012 Dec;6(12):2219-28. doi: 10.1038/ismej.2012.69. Epub 2012 Jul 5. PubMed PMID: 22763647; PubMed Central PMCID: PMC3504959.

Chugani S, Kim BS, Phattarasukol S, Brittnacher MJ, Choi SH, Harwood CS, Greenberg EP. (2012) Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon. Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):E2823-31. doi: 10.1073/pnas.1214128109. Epub 2012 Sep 17. PubMed PMID: 22988113; PubMed Central PMCID: PMC3478653.

Enstrom M, Held K, Ramage B, Brittnacher M, Gallagher L, Manoil C (2012) Genotype-phenotype associations in a nonmodel prokaryote. MBio. 2012 Mar 20;3(2). pii: e00001-12. doi: 10.1128/mBio.00001-12. Print 2012. PubMed PMID: 22434848; PubMed Central PMCID: PMC3312209

Goo E, Majerczyk CD, An JH, Chandler JR, Seo YS, Ham H, Lim JY, Kim H, Lee B, Jang MS, Greenberg EP, Hwang I (2012) Bacterial quorum sensing, cooperativity, and anticipation of stationary-phase stress. Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19775-80. doi: 10.1073/pnas.1218092109. Epub 2012 Nov 12. PubMed PMID: 23150539; PubMed Central PMCID: PMC3511722.

Hajjar AM, Ernst RK, Fortuno ES 3rd, Brasfield AS, Yam CS, Newlon LA, Kollmann TR, Miller SI, Wilson CB. (2012) Humanized TLR4/MD-2 mice reveal LPS recognition differentially impacts susceptibility to Yersinia pestis and Salmonella enterica. PLoS Pathog. 2012 Oct;8(10):e1002963. doi: 10.1371/journal.ppat.1002963. Epub 2012 Oct 11. PubMed PMID: 23071439; PubMed Central PMCID: PMC3469661.

Hayden HS, Lim R, Brittnacher MJ, Sims EH, Ramage ER, Fong C, Wu Z, Crist E, Chang J, Zhou Y, Radey M, Rohmer L, Haugen E, Gillett W, Wuthiekanun V, Peacock SJ, Kaul R, Miller SI, Manoil C, Jacobs MA (2012) Evolution of Burkholderia pseudomallei in Recurrent Melioidosis. PLoS One. 2012;7(5):e36507. Epub 2012 May 15. PubMed PMID: 22615773; PubMed Central PMCID: PMC3352902.

Hocquet D, Llanes C, Thouverez M, Kulasekara HD, Bertrand X, Plésiat P, Mazel D, Miller SI. (2012) Evidence for induction of integron-based antibiotic resistance by the SOS response in a clinical setting. PLoS Pathog. 2012;8(6):e1002778. doi: 10.1371/journal.ppat.1002778. Epub 2012 Jun 14. PubMed PMID: 22719259; PubMed Central PMCID: PMC3375312.

Huang Y, Yoon SH, Heron SR, Masselon CD, Edgar JS, Tureček F, Goodlett DR. (2012) Surface acoustic wave nebulization produces ions with lower internal energy than electrospray ionization. J Am Soc Mass Spectrom. 2012 Jun;23(6):1062-70. doi: 10.1007/s13361-012-0352-8. Epub 2012 Apr 3. PubMed PMID: 22476889.

Icenogle LM, Hengel SM, Coye LH, Streifel A, Collins CM, Goodlett DR, Moseley SL. (2012) Molecular and biological characterization of Streptococcal SpyA-mediated ADP-ribosylation of intermediate filament protein vimentin. J Biol Chem. 2012 Jun 15;287(25):21481-91. doi: 10.1074/jbc.M112.370791. Epub 2012 May 1. PubMed PMID: 22549780; PubMed Central PMCID: PMC3375569.

Jørgensen I, Miao EA (2012) YopM puts caspase-1 on ice. Cell Host Microbe. 2012 Dec 13;12(6):737-8. doi: 10.1016/j.chom.2012.11.006. PubMed PMID: 23245318; PubMed Central PMCID: PMC3590850.

Kanistanon D, Powell DA, Hajjar AM, Pelletier MR, Cohen IE, Way SS, Skerrett SJ, Wang X, Raetz CR, Ernst RK (2012) Role of Francisella lipid A phosphate modification in virulence and long-term protective immune responses. Infect Immun. 2012 Mar;80(3):943-51. Epub 2012 Jan 3. PubMed PMID: 22215738; PubMed Central PMCID: PMC3294632

Karadzic I, Maupin-Furlow J, Humbard M, Prunetti L, Singh P, Goodlett DR. (2012) Chemical cross-linking, mass spectrometry, and in silico modeling of proteasomal 20S core particles of the haloarchaeon Haloferax volcanii. Proteomics. 2012 Jun;12(11):1806-14. doi: 10.1002/pmic.201100260. PubMed PMID: 22623373; PubMed Central PMCID: PMC3517063.

Ko DC, Gamazon ER, Shukla KP, Pfuetzner RA, Whittington D, Holden TD, Brittnacher MJ, Fong C, Radey M, Ogohara C, Stark AL, Akey JM, Dolan ME, Wurfel MM, Miller SI. (2012) Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death. Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):E2343-52. doi: 10.1073/pnas.1206701109. Epub 2012 Jul 25. PubMed PMID: 22837397; PubMed Central PMCID: PMC3435171.

LaRock CN, Cookson BT (2012) The Yersinia virulence effector YopM binds caspase-1 to arrest inflammasome assembly and processing. Cell Host Microbe. 2012 Dec 13;12(6):799-805. doi: 10.1016/j.chom.2012.10.020. PubMed PMID: 23245324.

LaRock DL, Brzovic PS, Levin I, Blanc MP, Miller SI. (2012) A Salmonella typhimurium-translocated glycerophospholipid:cholesterol acyltransferase promotes virulence by binding to the RhoA protein switch regions. J Biol Chem. 2012 Aug 24;287(35):29654-63. doi: 10.1074/jbc.M112.363598. Epub 2012 Jun 27. PubMed PMID: 22740689; PubMed Central PMCID: PMC3436183.

LeRoux M, De Leon JA, Kuwada NJ, Russell AB, Pinto-Santini D, Hood RD, Agnello DM, Robertson SM, Wiggins PA, Mougous JD (2012) Quantitative single-cell characterization of bacterial interactions reveals type VI secretion is a double-edged sword. Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19804-9. doi: 10.1073/pnas.1213963109. Epub 2012 Nov 12. PubMed PMID: 23150540; PubMed Central PMCID: PMC3511723.

Li Y, Powell DA, Shaffer SA, Rasko DA, Pelletier MR, Leszyk JD, Scott AJ, Masoudi A, Goodlett DR, Wang X, Raetz CR, Ernst RK. (2012) LPS remodeling is an evolved survival strategy for bacteria. Proc Natl Acad Sci U S A. 2012 May 29;109(22):8716-21. doi: 10.1073/pnas.1202908109. Epub 2012 May 14. Erratum in: Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13877. PubMed PMID: 22586119; PubMed Central PMCID: PMC3365160.

Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA. (2012) Protein identification using top-down. Mol Cell Proteomics. 2012 Jun;11(6):M111.008524. doi: 10.1074/mcp.M111.008524. Epub 2011 Oct 25. PubMed PMID: 22027200; PubMed Central PMCID: PMC3433905.

Mikacenic C, Reiner AP, Holden TD, Nickerson DA, Wurfel MM. (2012) Variation in the TLR10/TLR1/TLR6 locus is the major genetic determinant of interindividual difference in TLR1/2-mediated responses. Genes Immun. 2012 Nov 15. doi: 10.1038/gene.2012.53. PubMed PMID: 23151486.

Phattarasukol S, Radey MC, Lappala CR, Oda Y, Hirakawa H, Brittnacher MJ, Harwood CS. (2012) Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris by Xpression, an integrated tool for prokaryotic RNA-seq data processing. Appl Environ Microbiol. 2012 Oct;78(19):6812-8. doi: 10.1128/AEM.01418-12. Epub 2012 Jul 13. PubMed PMID: 22798355; PubMed Central PMCID: PMC3457485.

Ramage E, Gallagher L, Manoil C. (2012) Exploiting a natural auxotrophy for genetic selection. Appl Environ Microbiol. 2012 Aug;78(16):5926-8. doi: 10.1128/AEM.00762-12. Epub 2012 Jun 1. PubMed PMID: 22660718; PubMed Central PMCID: PMC3406110.

Russell AB, Singh P, Brittnacher M, Bui NK, Hood RD, Carl MA, Agnello DM, Schwarz S, Goodlett DR, Vollmer W, Mougous JD (2012) A Widespread Bacterial Type VI Secretion Effector Superfamily Identified Using a Heuristic Approach. Cell Host Microbe. 2012 May 17;11(5):538-49. PubMed PMID: 22607806; PubMed Central PMCID: PMC3358704.

Silverman JM, Brunet YR, Cascales E, Mougous JD. (2012) Structure and regulation of the type VI secretion system. Annu Rev Microbiol. 2012;66:453-72. Epub 2012 Jun 28. PubMed PMID: 22746332.

Stetson DB (2012) Endogenous retroelements and autoimmune disease. Curr Opin Immunol. 2012 Dec;24(6):692-7. doi: 10.1016/j.coi.2012.09.007. Epub 2012 Oct 10. PubMed PMID: 23062469.

Svensson K, Sjödin A, Byström M, Granberg M, Brittnacher MJ, Rohmer L, Jacobs MA, Sims-Day EH, Levy R, Zhou Y, Hayden HS, Lim R, Chang J, Guenthener D, Kang A, Haugen E, Gillett W, Kaul R, Forsman M, Larsson P, Johansson A. (2012) Genome Sequence of Francisella tularensis subspecies holarctica Strain FSC200, Isolated from a Child with Tularemia. J Bacteriol. 2012 Dec;194(24):6965-6. doi: 10.1128/JB.01040-12. PubMed PMID: 23209222; PubMed Central PMCID: PMC3510583.

Takaki K, Cosma CL, Troll MA, Ramakrishnan L. (2012) An in vivo platform for rapid high-throughput antitubercular drug discovery. Cell Rep. 2012 Jul 26;2(1):175-84. doi: 10.1016/j.celrep.2012.06.008. Epub 2012 Jul 20. PubMed PMID: 22840407; PubMed Central PMCID: PMC3433401.

Varnum SM, Webb-Robertson BJ, Pounds JG, Moore RJ, Smith RD, Frevert CW, Skerrett SJ, Wunschel D. (2012) Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp. novicida. J Proteome Res. 2012 Jul 6;11(7):3690-703. doi: 10.1021/pr3001767. Epub 2012 Jun 22. PubMed PMID: 22663564; PubMed Central PMCID: PMC3423085.

West TE, Chierakul W, Chantratita N, Limmathurotsakul D, Wuthiekanun V, Emond MJ, Hawn TR, Peacock SJ, Skerrett SJ (2012) Toll-like receptor 4 region genetic variants are associated with susceptibility to melioidosis. Genes Immun. 2012 Jan;13(1):38-46. doi: 10.1038/gene.2011.49. Epub 2011 Jul 21. PubMed PMID: 21776015

West TE, Myers ND, Liggitt HD, Skerrett SJ (2012) Murine pulmonary infection and inflammation induced by inhalation of Burkholderia pseudomallei. Int J Exp Pathol. 2012 Dec;93(6):421-8. doi: 10.1111/j.1365-2613.2012.00842.x. PubMed PMID: 23136994; PubMed Central PMCID: PMC3521898.

Yoon SH, Huang Y, Edgar JS, Ting YS, Heron SR, Kao Y, Li Y, Masselon CD, Ernst RK, Goodlett DR. (2012) Surface acoustic wave nebulization facilitating lipid mass spectrometric analysis. Anal Chem. 2012 Aug 7;84(15):6530-7. doi: 10.1021/ac300807p. Epub 2012 Jul 12. PubMed PMID: 22742654.

2011

Adams KN, Takaki K, Connolly LE, Wiedenhoft H, Winglee K, Humbert O, Edelstein PH, Cosma CL, Ramakrishnan L (2011) Drug tolerance in replicating mycobacteria mediated by a macrophage-induced efflux mechanism. Cell. 2011 Apr 1;145(1):39-53. Epub 2011 Mar 3. Erratum in: Cell. 2011 Apr 1;145(1):159. PubMed PMID: 21376383

Bergsbaken T, Fink SL, den Hartigh AB, Loomis WP, Cookson BT (2011) Coordinated host responses during pyroptosis: caspase-1-dependent lysosome exocytosis and inflammatory cytokine maturation. J Immunol. 2011 Sep 1;187(5):2748-54. Epub 2011 Jul 29. PubMed PMID: 21804020

Bochet P, Rügheimer F, Guina T, Brooks P, Goodlett D, Clote P, Schwikowski B. (2011) Fragmentation-free LC-MS can identify hundreds of proteins. Proteomics. 2011 Jan;11(1):22-32. doi: 10.1002/pmic.200900765. Epub 2010 Dec 6. PubMed PMID: 21182191.

Brittnacher MJ, Fong C, Hayden HS, Jacobs MA, Radey M, Rohmer L. (2011) PGAT: A multi-strain analysis resource for microbial genomes. Bioinformatics. 27(17), 2429. Epub 2011 Jul 15. PMCID: PMC3157930

Carr G, Seyedsayamdost MR, Chandler JR, Greenberg EP, Clardy J (2011) Sources of diversity in bactobolin biosynthesis by Burkholderia thailandensis E264. Org Lett. Jun 17;13(12):3048-51. Epub 2011 May 26. PMCID: PMC3111747

Chu LJ, Yang H, Shih P, Kao Y, Tsai YS, Chen J, Huang G, Weng RR, Ting YS, Fang X, von Haller PD, Goodlett DR, Ng WV (2011) Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses. J Proteome Res. 2011 Jul 1;10(7):3261-73. Epub 2011 Jun 14. PMCID: PMC3168985

Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R (2011) The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Res. 2011 Nov;21(11):1981-94. Epub 2011 Aug 8. PubMed PMID: 21824995; PubMed Central PMCID: PMC3205581

Ferens WA, Hovde CJ (2011) Escherichia coli O157:H7: animal reservoir and sources of human infection. Foodborne Pathog Dis. 2011 Apr;8(4):465-87. Epub 2010 Nov 30. PubMed PMID: 21117940.

Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Karanicolas J, Baker D (2011) Hotspot-centric de novo design of protein binders. J Mol Biol. 2011 Nov 11;413(5):1047-62. Epub 2011 Sep 10. PubMed PMID: 21945116

Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, Wilson IA (2011) Baker D. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science. May 13;332(6031):816-21. PMCID: PMC3164876

Gallagher LA, Shendure J, Manoil C (2011) Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq. MBio. 2011 Jan 18;2(1):e00315-10. PMCID: PMC3023915

Madhusoodanan J, Seo KS, Remortel B, Park JY, Hwang SY, Fox LK, Park YH, Deobald CF, Wang D, Liu S, Daugherty SC, Gill AL, Bohach GA, Gill SR (2011) An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis. J Bacteriol. 2011 Apr;193(8):1854-62. Epub 2011 Feb 11. PubMed PMID: 21317317

MacArthur I, Jones JW, Goodlett DR, Ernst RK, Preston A. (2011) Role of pagL and lpxO in Bordetella bronchiseptica lipid A biosynthesis. J Bacteriol. Sep;193(18):4726-35. Epub 2011 Jul 15. PMCID: PMC3165656

Mealman TD, Bagai I, Singh P, Goodlett DR, Rensing C, Zhou H, Wysocki VH, McEvoy MM (2011) Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry. Biochemistry. 2011 Apr 5;50(13):2559-66. Epub 2011 Mar 8. PMCID: PMC3072847

Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR (2011) Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem. 2011 Mar 15;83(6):2250-7. Epub 2011 Feb 22. PubMed PMID: 21341720

Rohmer L, Hocquet D, Miller SI (2011) Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis. Trends Microbiol. Jul;19(7):341-8. Epub 2011 May 18. Review. PubMed PMCID: PMC3130110

Ting YS, Shaffer SA, Jones JW, Ng WV, Ernst RK, Goodlett DR (2011) Automated lipid a structure assignment from hierarchical tandem mass spectrometry data. J Am Soc Mass Spectrom. 2011 May;22(5):856-66. Epub 2011 Mar 5. PubMed PMID: 21472520

West TE, Chierakul W, Chantratita N, Limmathurotsakul D, Wuthiekanun V, Emond MJ, Hawn TR, Peacock SJ, Skerrett SJ (2011) Toll-like receptor 4 region genetic variants are associated with susceptibility to melioidosis. Genes Immun. 2012 Jan;13(1):38-46. doi: 10.1038/gene.2011.49. Epub 2011 Jul 21. PubMed PMID: 21776015.

2010

Christen M, Kulasekara HD, Christen B, Kulasekara BR, Hoffman LR, Miller SI (2010) Asymmetrical distribution of the second messenger c-di-GMP upon bacterial cell division. Science. 2010 Jun 4;328(5983):1295-7. PubMed PMID: 20522779

Fong C, Ko DC, Wasnick M, Radey M, Miller SI, Brittnacher M (2010) GWAS Analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. Bioinformatics. 2010 Feb 15;26:(4), 560-4. PMCID: PMC2820681

Hengel SM, Icenogle L, Collins C, Goodlett DR (2010) Sequence assignment of ADP-ribosylated peptides is facilitated as peptide length increases. Rapid Commun Mass Spectrom. 2010 Aug 15;24(15):2312-6. PubMed PMID: 20623715

Hood RD, Singh P, Hsu F, Güvener T, Carl MA, Trinidad RR, Silverman JM, Ohlson BB, Hicks KG, Plemel RL, Li M, Schwarz S, Wang WY, Merz AJ, Goodlett DR, Mougous JD (2010) A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe. 2010 Jan 21;7(1):25-37. PubMed PMID: 20114026; PubMed Central PMCID: PMC2831478

Jones JW, Cohen IE, Tureĉek F, Goodlett DR, Ernst RK (2010) Comprehensive structure characterization of lipid A extracted from Yersinia pestis for determination of its phosphorylation configuration. J Am Soc Mass Spectrom. 2010 May;21(5):785-99. Epub 2010 Jan 25. PubMed PMID: 20185334

Kolodziejek AM, Schnider DR, Rohde HN, Wojtowicz AJ, Bohach GA, Minnich SA, Hovde CJ. Outer membrane protein X (Ail) contributes to Yersinia pestis virulence in pneumonic plague and its activity is dependent on the lipopolysaccharide core length. Infect Immun. 2010 Dec;78(12):5233-43. Epub 2010 Sep 13. PubMed PMID: 20837715; PubMed Central PMCID: PMC2981323.

Lim JY, Hong JB, Sheng H, Shringi S, Kaul R, Besser TE, Hovde CJ (2010) Phenotypic diversity of Escherichia coli O157:H7 strains associated with the plasmid O157. J Microbiol. 2010 Jun;48(3):347-57. Epub 2010 Jun 23. PubMed PMID: 20571953; PubMed Central PMCID: PMC2951829

Lim JY, Yoon J, Hovde CJ (2010) A brief overview of Escherichia coli O157:H7 and its plasmid O157. J Microbiol Biotechnol. 2010 Jan;20(1):5-14. Review. PubMed PMID: 20134227

McIlwain S, Draghicescu P, Singh P, Goodlett DR, Noble WS (2010) Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs. J Proteome Res. 2010 May 7;9(5):2488-95. PubMed PMID: 20349954; PubMed Central PMCID: PMC2866041

McMillan DG, Velasquez I, Nunn BL, Goodlett DR, Hunter KA, Lamont I, Sander SG, Cook GM (2010) Acquisition of iron by alkaliphilic bacillus species. Appl Environ Microbiol. 2010 Oct;76(20):6955-61. Epub 2010 Aug 27. PubMed PMID: 20802068; PubMed Central PMCID: PMC2953014

Miao EA, Leaf IA, Treuting PM, Mao DP, Dors M, Sarkar A, Warren SE, Wewers MD, Aderem A. Caspase-1-induced pyroptosis is an innate immune effector mechanism against intracellular bacteria. Nat Immunol. 2010 Dec;11(12):1136-42. Epub 2010 Nov 7. PubMed PMID: 21057511.

Miao EA, Mao DP, Yudkovsky N, Bonneau R, Lorang CG, Warren SE, Leaf IA, Aderem A (2010) Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome. Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):3076-80. Epub 2010 Feb 1. PubMed PMID: 20133635; Pub Proteome Res. 2010 May 7;9(5):2508-15. PubMed PMID: 20302351; PubMed Central PMCID: PMC2884221

Panchaud A, Singh P, Shaffer SA, Goodlett DR (2010) xComb: a cross-linked peptide database approach to protein-protein interaction analysis. J Proteome Res. 2010 May 7;9(5):2508-15. PubMed PMID: 20302351; PubMed Central PMCID: PMC2884221

Park JY, Fox LK, Seo KS, McGuire MA, Park YH, Rurangirwa FR, Sischo WM, Bohach GA. Comparison of phenotypic and genotypic methods for the species identification of coagulase-negative staphylococcal isolates from bovine intramammary infections. Vet Microbiol. 2011 Jan 10;147(1-2):142-8. Epub 2010 Jul 1. PubMed PMID: 20667671.

Park JY, Fox LK, Seo KS, McGuire MA, Park YH, Rurangirwa FR, Sischo WM, Bohach GA. Detection of classical and newly described staphylococcal superantigen genes in coagulase-negative staphylococci isolated from bovine intramammary infections. Vet Microbiol. 2011 Jan 10;147(1-2):149-54. Epub 2010 Jul 1. PubMed PMID: 20667668.

Parra MC, Shaffer SA, Hajjar AM, Gallis BM, Hager A, Goodlett DR, Guina T, Miller S, Collins CM (2010) Identification, cloning, expression, and purification of Francisella lpp3: an immunogenic lipoprotein. Microbiol Res. 2010 Sep 20;165(7):531-45. Epub 2009 Dec 14. PubMed PMID: 20006480

Sanowar S, Singh P, Pfuetzner RA, André I, Zheng H, Spreter T, Strynadka NC, Gonen T, Baker D, Goodlett DR, Miller SI (2010) Interactions of the transmembrane polymeric rings of the Salmonella enterica serovar Typhimurium type III secretion system. MBio. 2010 Aug 3;1(3). pii: e00158-10. PubMed PMID: 20824104; PubMed Central PMCID: PMC2932509.

Seo KS, Park JY, Terman DS, Bohach GA (2010) A quantitative real time PCR method to analyze T cell receptor Vbeta subgroup expansion by staphylococcal superantigens. J Transl Med. 2010 Jan 13;8:2. PubMed PMID: 20070903; PubMed Central PMCID: PMC2841588

Seyedsayamdost MR, Chandler JR, Blodgett JA, Lima PS, Duerkop BA, Oinuma K, Greenberg EP, Clardy J (2010) Quorum-sensing-regulated bactobolin production by Burkholderia thailandensis E264. Org Lett. 2010 Feb 19;12(4):716-9. PubMed PMID: 20095633; PubMed Central PMCID: PMC2821070

Schwarz S, Hood RD, Mougous JD. What is type VI secretion doing in all those bugs? Trends Microbiol. 2010 Dec;18(12):531-7. Epub 2010 Oct 18. PubMed PMID: 20961764; PubMed Central PMCID: PMC2991376.

Schwarz S, West TE, Boyer F, Chiang WC, Carl MA, Hood RD, Rohmer L, Tolker-Nielsen T, Skerrett SJ, Mougous JD. Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions. PLoS Pathog. 2010 Aug 26;6(8). pii: e1001068. PubMed PMID: 20865170; PubMed Central PMCID: PMC2928800.

Schwarz S, West TE, Boyer F, Chiang WC, Carl MA, Hood RD, Rohmer L, Tolker-Nielsen T, Skerrett SJ, Mougous JD (2010) Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions. PLoS Pathog. 2010 Aug 26;6(8). pii: e1001068. PubMed PMID: 20865170; PubMed Central PMCID: PMC2928800

Yoon JW, Park MK, Hovde CJ, Cho SH, Kim JC, Park MS, Kim W (2010) Characterization of BNT2, an intrinsically curved DNA of Escherichia coli O157:H7. Biochem Biophys Res Commun. 2010 Jan 22;391(4):1792-7. Epub 2010 Jan 5. PubMed PMID: 20051226; PubMed Central PMCID: PMC2814767

2009

Annest A, Bumgarner RE, Raftery AE, Yeung KY. (2009) Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data. BMC Bioinformatics. 2009 Feb 26;10:72. PMCID: PMC2657791.

Kalhorn TF, Kiavand A, Cohen IE, Nelson AK, Ernst RK. (2009) A sensitive liquid chromatography/mass spectrometry-based assay for quantitation of amino-containing moieties in lipid A. Rapid Commun Mass Spectrom. 2009 Feb;23(3):433-42. PMCID: PMC2716696.

Ko DC, Shukla KP, Fong C, Wasnick M, Brittnacher MJ, Wurfel MM, Holden TD, O\'Keefe GE, Van Yserloo B, Akey JM, Miller SI. (2009) A genome-wide in vitro bacterial-infection screen reveals human variation in the host response associated with inflammatory disease. Am J Hum Genet. 2009 Aug;85(2):214-27. PMCID:PMC2725265

Kraemer PS, Mitchell A, Pelletier MR, Gallagher LA, Wasnick M, Rohmer L, Brittnacher MJ, Manoil C, Skerett SJ, Salama NR. (2009) Genome-wide screen in Francisella novicida for genes required for pulmonary and systemic infection in mice. Infect Immun. 2009 Jan;77(1):232-44. Epub 2008 Oct 27. PMCID: PMC2612238.

Nickerson EK, West TE, Day NP, Peacock SJ. (2009) Staphylococcus aureus disease and drug resistance in resource-limited countries in south and east Asia. Lancet Infect Dis. 2009 Feb;9(2):130-5.

Nickerson EK, Hongsuwan M, Limmathurotsakul D, Wuthiekanun V, Shah KR, Srisomang P, Mahavanakul W, Wacharaprechasgul T, Fowler VG, West TE, Teerawatanasuk N, Becher H, White NJ, Chierakul W, Day NP, Peacock SJ. (2009) Staphylococcus aureus bacteraemia in a tropical setting: patient outcome and impact of antibiotic resistance. PLoS One. 2009;4(1):e4308. Epub 2009 Jan 30. PMCID: PMC2628727.

Webb-Robertson BJ, McCue LA, Beagley N, McDermott JE, Wunschel DS, Varnum SM, Hu JZ, Isern NG, Buchko GW, Mcateer K, Pounds JG, Skerrett SJ, Liggitt D, Frevert CW. (2009) A Bayesian integration model of high-throughput proteomics and metabolomics data for improved early detection of microbial infections. Pac Symp Biocomput. 2009:451-63.

Wunschel D, Webb-Robertson BJ, Frevert CW, Skerrett S, Beagley N, Willse A, Colburn H, Antolick K. (2009) Differentiation of gram-negative bacterial aerosol exposure using detected markers in bronchial-alveolar lavage fluid. PLoS One. 2009 Sep 16;4(9):e7047. PMCID: PMC2737641.

2008

Airhart, C. L., H. N. Rohde, G. A. Bohach, C. J. Hovde, C. F. Deobald, S. S. Lee, and S. A. Minnich. (2008) Induction of innate immunity by lipid A mimetics increases survival from pneumonic plague. Microbiology 154:2131-8.

Airhart CL, Rohde HN, Hovde CJ, Bohach GA, Deobald CF, Lee SS, Minnich SA. (2008) Lipid A mimetics are potent adjuvants for an intranasal pneumonic plague vaccine. Vaccine. 2008 Aug 21.

Cheng AC, West TE, Limmathurotsakul D, Peacock SJ. (2008) Strategies to reduce mortality from bacterial sepsis in adults in developing countries. PLoS Med. 2008 Aug 19;5(8):e175.

Chu VT, Gottardo R, Raftery AE, Bumgarner RE, Yeung KY. (2008) MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis. Genome Biol. 2008;9(7):R118.

Fong, C., Rohmer, L., Radey, M., Wasnick, M. and Brittnacher, M.J. (2008) PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes. BMC Bioinformatics, 9, 170. PMCID: PMC2358893

Duerkop, B. A., J. P. Herman, R. L. Ulrich, M. E. Churchill, and E. P. Greenberg. (2008) The Burkholderia mallei BmaR3-BmaI3 quorum-sensing system produces and responds to N-3-hydroxy-octanoyl homoserine lactone. J Bacteriol 190:5137-41.

Hayden HS, Gillett W, Saenphimmachak C, Lim R, Zhou Y, Jacobs MA, Chang J, Rohmer L, D\'Argenio DA, Palmieri A, Levy R, Haugen E, Wong GK, Brittnacher MJ, Burns JL, Miller SI, Olson MV, and Kaul R. (2008) Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients. Genomics. 2008 Jun;91(6):530-7.

Haraga, A., Ohlson, M.B. and Miller, S.I. (2008) Salmonellae interplay with host cells. Nat Rev Microbiol, 6, 53-66.

Haraga, A., West, T.E., Brittnacher, M.J., Skerrett, S.J., Miller, S.I. (2008) Burkholderia thailandensis as a model system for the study of the virulence-associated type III secretion system of Burkholderia pseudomallei. Infect Immun. 2008 Nov; 76(11):5402-11.

Jones JW, Shaffer SA, Ernst RK, Goodlett DR, Turecek F. (2008) Determination of pyrophosphorylated forms of lipid A in Gram-negative bacteria using a multivaried mass spectrometric approach. Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12742-7.

Kanistanon, D., Hajjar, A.M., Pelletier, M.R., Gallagher, L.A., Kalhorn, T., Shaffer, S.A., Goodlett, D.R., Rohmer, L., Brittnacher, M.J., Skerrett, S.J. and Ernst, R.K. (2008) A Francisella mutant in lipid A carbohydrate modification elicits protective immunity. PLoS Pathog, 4, e24.

Kline T, Jackson SR, Deng W, Verlinde CL, Miller SI. Design and synthesis of bis-carbamate analogs of cyclic bis-(3'-5')-diguanylic acid (c-di-GMP) and the acyclic dimer PGPG. Nucleosides Nucleotides Nucleic Acids. 2008 Dec;27(12):1282-300. PubMed PMID: 19003573.

Kline, T., Trent, M.S., Stead, C.M., Lee, M.S., Sousa, M.C., Felise, H.B., Nguyen, H.V. and Miller, S.I. (2008) Synthesis of and evaluation of lipid A modification by 4-substituted 4-deoxy arabinose analogs as potential inhibitors of bacterial polymyxin resistance. Bioorg Med Chem Lett, 18, 1507-1510.

Lembo, A., M. Pelletier, R. Iyer, M. Timko, J. C. Dudda, T. E. West, C. B. Wilson, A. M. Hajjar, and S. J. Skerrett. (2008) Administration of a synthetic TLR4 agonist protects mice from pneumonic tularemia. J Immunol 180:7574-81.

Mattmann, M. E., G. D. Geske, G. A. Worzalla, J. R. Chandler, K. J. Sappington, E. P. Greenberg, and H. E. Blackwell. (2008) Synthetic ligands that activate and inhibit a quorum-sensing regulator in Pseudomonas aeruginosa. Bioorg Med Chem Lett 18:3072-5.

Ohlson MB, Huang Z, Alto NM, Blanc MP, Dixon JE, Chai J, Miller SI. (2008) Structure and function of Salmonella SifA indicate that its interactions with SKIP, SseJ, and RhoA family GTPases induce endosomal tubulation. Cell Host Microbe. 2008 Nov 13;4(5):434-46. PMCID: PMC2658612.

Rohmer, L., Guina, T., Chen, J., Gallis, B., Taylor, G.K., Shaffer, S.A., Miller, S.I., Brittnacher, M.J. and Goodlett, D.R. (2008) Determination and Comparison of the Francisella tularensis subsp.novicida U112 Proteome to Other Bacterial Proteomes. J Proteome Res.

Scherl, A., Shaffer, S.A., Taylor, G.K., Kulasekara, H.D., Miller, S.I. and Goodlett, D.R. (2008) Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides. Anal Chem, 80, 1182-1191.

Scherl, A., S. A. Shaffer, G. K. Taylor, P. Hernandez, R. D. Appel, P. A. Binz, and D. R. Goodlett. (2008) On the benefits of acquiring peptide fragment ions at high measured mass accuracy. J Am Soc Mass Spectrom 19:891-901.

Scherl, A., Y. S. Tsai, S. A. Shaffer, and D. R. Goodlett. (2008) Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses. Proteomics 8:2791-7.

Sheng, H., J. Y. Lim, M. K. Watkins, S. A. Minnich, and C. J. Hovde. (2008) Characterization of an Escherichia coli O157:H7 O-antigen deletion mutant and effect of the deletion on bacterial persistence in the mouse intestine and colonization at the bovine terminal rectal mucosa. Appl Environ Microbiol 74:5015-22.

Thiede, H., N. S. Close, J. Koepsell, A. Baer, and J. S. Duchin. (2008) Completeness of reporting of rabies postexposure prophylaxis in King County, Washington. J Public Health Manag Pract 14:448-53.

Thongdee, M., L. A. Gallagher, M. Schell, T. Dharakul, S. Songsivilai, and C. Manoil. (2008) Targeted mutagenesis of Burkholderia thailandensis and Burkholderia pseudomallei through natural transformation of PCR fragments. Appl Environ Microbiol 74:2985-9.

West TE, Pelletier MR, Majure MC, Lembo A, Hajjar AM, Skerrett SJ. (2008) Inhalation of Francisella novicida Delta mglA causes replicative infection that elicits innate and adaptive responses but is not protective against invasive pneumonic tularemia. Microbes Infect. 2008 Jun;10(7):773-80.

West TE, Ernst RK, Jansson-Hutson MJ, Skerrett SJ. (2008) Activation of Toll-like receptors by Burkholderia pseudomallei. BMC Immunol. 2008 Aug 8;9:46.

Wurfel MM, Gordon AC, Holden TD, Radella F, Strout J, Kajikawa O, Ruzinski JT, Rona G, Black RA, Stratton S, Jarvik GP, Hajjar AM, Nickerson DA, Rieder M, Sevransky J, Maloney JP, Moss M, Martin G, Shanholtz C, Garcia JG, Gao L, Brower R, Barnes KC, Walley KR, Russell JA, Martin TR. (2008) Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis. Am J Respir Crit Care Med. 2008 Oct 1;178(7):710-20.

Zarivach, R., W. Deng, M. Vuckovic, H. B. Felise, H. V. Nguyen, S. I. Miller, B. B. Finlay, and N. C. Strynadka. (2008) Structural analysis of the essential self-cleaving type III secretion proteins EscU and SpaS. Nature 453:124-7.

2007

Cobbold, R.N., Hancock, D.D., Rice, D.H., Berg, J., Stilborn, R., Hovde, C.J. and Besser, T.E. (2007) Rectoanal junction colonization of feedlot cattle by Escherichia coli O157:H7 and its association with supershedders and excretion dynamics. Appl Environ Microbiol, 73, 1563-1568.

Duerkop, B.A., Ulrich, R.L. and Greenberg, E.P. (2007) Octanoyl-homoserine lactone is the cognate signal for Burkholderia mallei BmaR1-BmaI1 quorum sensing. J Bacteriol, 189, 5034-5040.

Ferens, W.A., Halver, M., Gustin, K.E., Ott, T. and Hovde, C.J. (2007) Differential sensitivity of viruses to the antiviral activity of Shiga toxin 1 A subunit. Virus Res, 125, 104-108.

Ferens, W.A. and Hovde, C.J. (2007) The non-toxic A subunit of Shiga toxin type 1 prevents replication of bovine immunodeficiency virus in infected cells. Virus Res, 125, 29-41.

Foss, E.J., Radulovic, D., Shaffer, S.A., Ruderfer, D.M., Bedalov, A., Goodlett, D.R. and Kruglyak, L. (2007) Genetic basis of proteome variation in yeast. Nat Genet, 39, 1369-1375.

Gallagher, L., Turner, C., Ramage, E. and Manoil, C. (2007) Creating recombination-activated genes and sequence-defined mutant libraries using transposons. Methods Enzymol, 421, 126-140.

Gallagher, L.A., Ramage, E., Jacobs, M.A., Kaul, R., Brittnacher, M. and Manoil, C. (2007) A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate. Proc Natl Acad Sci U S A, 104, 1009-1014. PMCID: PMC1783355

Guina, T., Radulovic, D., Bahrami, A.J., Bolton, D.L., Rohmer, L., Jones-Isaac, K.A., Chen, J., Gallagher, L.A., Gallis, B., Ryu, S., Taylor, G.K., Brittnacher, M.J., Manoil, C. and Goodlett, D.R. (2007) MglA regulates Francisella tularensis subsp. novicida (Francisella novicida) response to starvation and oxidative stress. J Bacteriol, 189, 6580-6586. PMCID: PMC2045168

Gunn, J.S. and Ernst, R.K. (2007) The structure and function of Francisella lipopolysaccharide. Ann N Y Acad Sci, 1105, 202-218.

Jones, J.W., Sasaki, T., Goodlett, D.R. and Turecek, F. (2007) Electron capture in spin-trap capped peptides. An experimental example of ergodic dissociation in peptide cation-radicals. J Am Soc Mass Spectrom, 18, 432-444.

Kolodziejek, A.M., Sinclair, D.J., Seo, K.S., Schnider, D.R., Deobald, C.F., Rohde, H.N., Viall, A.K., Minnich, S.S., Hovde, C.J., Minnich, S.A. and Bohach, G.A. (2007) Phenotypic characterization of OmpX, an Ail homologue of Yersinia pestis KIM. Microbiology, 153, 2941-2951.

Kwon, N.H., Beaux, M.F., 2nd, Ebert, C., Wang, L., Lassiter, B.E., Park, Y.H., McIlroy, D.N., Hovde, C.J. and Bohach, G.A. (2007) Nanowire-based delivery of Escherichia coli O157 shiga toxin 1 A subunit into human and bovine cells. Nano Lett, 7, 2718-2723.

Li, J. and Hovde, C.J. (2007) Expression profiles of bovine genes in the rectoanal junction mucosa during colonization with Escherichia coli O157:H7. Appl Environ Microbiol, 73, 2380-2385.

Lim, J.Y., Li, J., Sheng, H., Besser, T.E., Potter, K. and Hovde, C.J. (2007) Escherichia coli O157:H7 colonization at the rectoanal junction of long-duration culture-positive cattle. Appl Environ Microbiol, 73, 1380-1382.

Lim, J.Y., Sheng, H., Seo, K.S., Park, Y.H. and Hovde, C.J. (2007) Characterization of an Escherichia coli O157:H7 plasmid O157 deletion mutant and its survival and persistence in cattle. Appl Environ Microbiol, 73, 2037-2047.

Minnich, S.A. and Rohde, H.N. (2007) A rationale for repression and/or loss of motility by pathogenic Yersinia in the mammalian host. Adv Exp Med Biol, 603, 298-310.

Prakash, A., Piening, B., Whiteaker, J., Zhang, H., Shaffer, S.A., Martin, D., Hohmann, L., Cooke, K., Olson, J.M., Hansen, S., Flory, M.R., Lee, H., Watts, J., Goodlett, D.R., Aebersold, R., Paulovich, A. and Schwikowski, B. (2007) Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics, 6, 1741-1748.

Rohmer, L., Fong, C., Abmayr, S., Wasnick, M., Larson Freeman, T.J., Radey, M., Guina, T., Svensson, K., Hayden, H.S., Jacobs, M., Gallagher, L.A., Manoil, C., Ernst, R.K., Drees, B., Buckley, D., Haugen, E., Bovee, D., Zhou, Y., Chang, J., Levy, R., Lim, R., Gillett, W., Guenthener, D., Kang, A., Shaffer, S.A., Taylor, G., Chen, J., Gallis, B., D\'Argenio, D.A., Forsman, M., Olson, M.V., Goodlett, D.R., Kaul, R., Miller, S.I. and Brittnacher, M.J. (2007) Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains. Genome Biol, 8, R102.

Seo, K.S., Lee, S.U., Park, Y.H., Davis, W.C., Fox, L.K. and Bohach, G.A. (2007) Long-term staphylococcal enterotoxin C1 exposure induces soluble factor-mediated immunosuppression by bovine CD4+ and CD8+ T cells. Infect Immun, 75, 260-269.

Shaffer, S.A., Harvey, M.D., Goodlett, D.R. and Ernst, R.K. (2007) Structural heterogeneity and environmentally regulated remodeling of Francisella tularensis subspecies novicida lipid A characterized by tandem mass spectrometry. J Am Soc Mass Spectrom, 18, 1080-1092.

Wang, H., Kennedy, D.S., Nugent, K.D., Taylor, G.K. and Goodlett, D.R. (2007) A Qit-q-Tof mass spectrometer for two-dimensional tandem mass spectrometry. Rapid Commun Mass Spectrom, 21, 3223-3226.

2006

Anderson, N.R., Tarczy-Hornoch, P. and Bumgarner, R.E. (2006) On the persistence of supplementary resources in biomedical publications. BMC Bioinformatics, 7, 260.

Bylund, J., Burgess, L.A., Cescutti, P., Ernst, R.K. and Speert, D.P. (2006) Exopolysaccharides from Burkholderia cenocepacia inhibit neutrophil chemotaxis and scavenge reactive oxygen species. J Biol Chem, 281, 2526-2532.

Davis, M.A., Rice, D.H., Sheng, H., Hancock, D.D., Besser, T.E., Cobbold, R. and Hovde, C.J. (2006) Comparison of cultures from rectoanal-junction mucosal swabs and feces for detection of Escherichia coli O157 in dairy heifers. Appl Environ Microbiol, 72, 3766-3770.

Davis, M.A., Sheng, H., Newman, J., Hancock, D.D. and Hovde, C.J. (2006) Comparison of a waterless hand-hygiene preparation and soap-and-water hand washing to reduce coliforms on hands in animal exhibit settings. Epidemiol Infect, 134, 1024-1028.

Dobbin, H.S., Hovde, C.J., Williams, C.J. and Minnich, S.A. (2006) The Escherichia coli O157 flagellar regulatory gene flhC and not the flagellin gene fliC impacts colonization of cattle. Infect Immun, 74, 2894-2905.

Ferens, W.A., Cobbold, R. and Hovde, C.J. (2006) Intestinal Shiga toxin-producing Escherichia coli bacteria mitigate bovine leukemia virus infection in experimentally infected sheep. Infect Immun, 74, 2906-2916.

Gao, Q., Doneanu, C.E., Shaffer, S.A., Adman, E.T., Goodlett, D.R. and Nelson, S.D. (2006) Identification of the interactions between cytochrome P450 2E1 and cytochrome b5 by mass spectrometry and site-directed mutagenesis. J Biol Chem, 281, 20404-20417.

Gao, Q., Xue, S., Doneanu, C.E., Shaffer, S.A., Goodlett, D.R. and Nelson, S.D. (2006) Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry. Anal Chem, 78, 2145-2149.

Gottardo, R., Raftery, A.E., Yeung, K.Y. and Bumgarner, R.E. (2006) Bayesian robust inference for differential gene expression in microarrays with multiple samples. Biometrics, 62, 10-18.

Hager, A.J., Bolton, D.L., Pelletier, M.R., Brittnacher, M.J., Gallagher, L.A., Kaul, R., Skerrett, S.J., Miller, S.I. and Guina, T. (2006) Type IV pili-mediated secretion modulates Francisella virulence. Mol Microbiol, 62, 227-237.

Hajjar, A.M., Harvey, M.D., Shaffer, S.A., Goodlett, D.R., Sjostedt, A., Edebro, H., Forsman, M., Bystrom, M., Pelletier, M., Wilson, C.B., Miller, S.I., Skerrett, S.J. and Ernst, R.K. (2006) Lack of in vitro and in vivo recognition of Francisella tularensis subspecies lipopolysaccharide by Toll-like receptors. Infect Immun, 74, 6730-6738.

Kudva, I.T., Krastins, B., Sheng, H., Griffin, R.W., Sarracino, D.A., Tarr, P.I., Hovde, C.J., Calderwood, S.B. and John, M. (2006) Proteomics-based expression library screening (PELS): a novel method for rapidly defining microbial immunoproteomes. Mol Cell Proteomics, 5, 1514-1519.

Nunn, B.L., Shaffer, S.A., Scherl, A., Gallis, B., Wu, M., Miller, S.I. and Goodlett, D.R. (2006) Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO. Brief Funct Genomic Proteomic, 5, 154-168.

Park, Y.H., Lee, S.U., Ferens, W.A., Samuels, S., Davis, W.C., Fox, L.K., Ahn, J.S., Seo, K.S., Chang, B.S., Hwang, S.Y. and Bohach, G.A. (2006) Unique features of bovine lymphocytes exposed to a staphylococcal enterotoxin. J Vet Sci, 7, 233-239.

Rebeil, R., Ernst, R.K., Jarrett, C.O., Adams, K.N., Miller, S.I. and Hinnebusch, B.J. (2006) Characterization of late acyltransferase genes of Yersinia pestis and their role in temperature-dependent lipid A variation. J Bacteriol, 188, 1381-1388.

Rohmer, L., Brittnacher, M., Svensson, K., Buckley, D., Haugen, E., Zhou, Y., Chang, J., Levy, R., Hayden, H., Forsman, M., Olson, M., Johansson, A., Kaul, R. and Miller, S.I. (2006) Potential source of Francisella tularensis live vaccine strain attenuation determined by genome comparison. Infect Immun, 74, 6895-6906. PMCID: PMC1698093

Salama, N.R. and Manoil, C. (2006) Seeking completeness in bacterial mutant hunts. Curr Opin Microbiol, 9, 307-311.

Schnapp, L.M., Donohoe, S., Chen, J., Sunde, D.A., Kelly, P.M., Ruzinski, J., Martin, T. and Goodlett, D.R. (2006) Mining the acute respiratory distress syndrome proteome: identification of the insulin-like growth factor (IGF)/IGF-binding protein-3 pathway in acute lung injury. Am J Pathol, 169, 86-95.

Sheng, H., Knecht, H.J., Kudva, I.T. and Hovde, C.J. (2006) Application of bacteriophages to control intestinal Escherichia coli O157:H7 levels in ruminants. Appl Environ Microbiol, 72, 5359-5366.

Sheng, H., Lim, J.Y., Knecht, H.J., Li, J. and Hovde, C.J. (2006) Role of Escherichia coli O157:H7 virulence factors in colonization at the bovine terminal rectal mucosa. Infect Immun, 74, 4685-4693.

2005

Davis, M.A., Cloud-Hansen, K.A., Carpenter, J. and Hovde, C.J. (2005) Escherichia coli O157:H7 in environments of culture-positive cattle. Appl Environ Microbiol, 71, 6816-6822.

Jin, Z., Bohach, G.A., Shiloach, J., Norris, S.E., Freedberg, D.I., Deobald, C., Coxon, B., Robbins, J.B. and Schneerson, R. (2005) Conjugates of group A and W135 capsular polysaccharides of neisseria meningitidis bound to recombinant Staphylococcus aureus enterotoxin C1: preparation, physicochemical characterization, and immunological properties in mice. Infect Immun, 73, 7887-7893.

Li, Q., Fraley, C., Bumgarner, R.E., Yeung, K.Y. and Raftery, A.E. (2005) Donuts, scratches and blanks: robust model-based segmentation of microarray images. Bioinformatics, 21, 2875-2882.

Sheng, H., Davis, M.A., Knecht, H.J., Hancock, D.D., Van Donkersgoed, J. and Hovde, C.J. (2005) Characterization of a shiga toxin-, intimin-, and enterotoxin hemolysin-producing Escherichia coli ONT:H25 strain commonly isolated from healthy cattle. J Clin Microbiol, 43, 3213-3220.

Smyth, D.S., Hartigan, P.J., Meaney, W.J., Fitzgerald, J.R., Deobald, C.F., Bohach, G.A. and Smyth, C.J. (2005) Superantigen genes encoded by the egc cluster and SaPIbov are predominant among Staphylococcus aureus isolates from cows, goats, sheep, rabbits and poultry. J Med Microbiol, 54, 401-411.

Wurfel, M.M., Park, W.Y., Radella, F., Ruzinski, J., Sandstrom, A., Strout, J., Bumgarner, R.E. and Martin, T.R. (2005) Identification of high and low responders to lipopolysaccharide in normal subjects: an unbiased approach to identify modulators of innate immunity. J Immunol, 175, 2570-2578.

Yeung, K.Y., Bumgarner, R.E. and Raftery, A.E. (2005) Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics, 21, 2394-2402.

Yoon, J.W., Lim, J.Y., Park, Y.H. and Hovde, C.J. (2005) Involvement of the Escherichia coli O157:H7(pO157) ecf operon and lipid A myristoyl transferase activity in bacterial survival in the bovine gastrointestinal tract and bacterial persistence in farm water troughs. Infect Immun, 73, 2367-2378.

2004

Lina, G., Bohach, G.A., Nair, S.P., Hiramatsu, K., Jouvin-Marche, E. and Mariuzza, R. (2004) Standard nomenclature for the superantigens expressed by Staphylococcus. J Infect Dis, 189, 2334-2336.

Medvedovic, M., Yeung, K.Y. and Bumgarner, R.E. (2004) Bayesian mixture model based clustering of replicated microarray data. Bioinformatics, 20, 1222-1232.

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