Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
Keywords
Last Name
Institution

Jonathan Kirk Harris

TitleAssociate Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-PEDS
Phone720/777-4943
ORCID ORCID Icon0000-0002-2378-4202 Additional info

    Collapse Research 
    Collapse research activities and funding
    R21HL110721     (TUDER, RUBIN M.)Dec 1, 2011 - Nov 30, 2013
    NIH
    Microbiome in COPD
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Wagner BD, Zemanick ET, Sagel SD, Robertson CE, Stevens MJ, Mayer-Hamblett N, Retsch-Bogart G, Ramsey BW, Harris JK. Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection. BMC Microbiol. 2023 10 27; 23(1):312. PMID: 37891457.
      View in: PubMed
    2. Osborne CM, Langelier C, Kamm J, Williamson K, Ambroggio L, Reeder RW, Locandro C, Kirk Harris J, Wagner BD, Maddux AB, Caldera S, Lyden A, Soesanto V, Sim?es EAF, Leroue MK, Carpenter TC, Hall MW, Zuppa AF, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Notterman DA, DeRisi J, Mourani PM. Viral Detection by Reverse Transcriptase Polymerase Chain Reaction in Upper Respiratory Tract and Metagenomic RNA Sequencing in Lower Respiratory Tract in Critically Ill Children With Suspected Lower Respiratory Tract Infection. Pediatr Crit Care Med. 2024 Jan 01; 25(1):e1-e11. PMID: 37732845.
      View in: PubMed
    3. Harris JK, Wagner BD, Robertson CE, Stevens MJ, Lingard C, Borowitz D, Leung DH, Heltshe SL, Ramsey BW, Zemanick ET. Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen. J Cyst Fibros. 2023 07; 22(4):644-651. PMID: 37137746.
      View in: PubMed
    4. O'Connor JB, Wagner BD, Harris JK, Frank DN, Clabots DE, Laguna TA. Detection and identification of fungi in the lower airway of children with and without cystic fibrosis. Front Microbiol. 2023; 14:1119703. PMID: 36846802.
      View in: PubMed
    5. Leroue MK, Williamson KM, Curtin PC, Sontag MK, Wagner BD, Ambroggio L, Bixby M, Busgang SA, Murphy SE, Peterson LA, Vevang KR, Sipe CJ, Kirk Harris J, Reeder RW, Locandro C, Carpenter TC, Maddux AB, Sim?es EAF, Osborne CM, Robertson CE, Langelier C, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Mourani PM. Tobacco smoke exposure, the lower airways microbiome and outcomes of ventilated children. Pediatr Res. 2023 08; 94(2):660-667. PMID: 36750739.
      View in: PubMed
    6. Furuta GT, Fillon SA, Williamson KM, Robertson CE, Stevens MJ, Aceves SS, Arva NC, Chehade M, Collins MH, Davis CM, Dellon ES, Falk GW, Gonsalves N, Gupta SK, Hirano I, Khoury P, Leung J, Martin LJ, Menard-Katcher P, Mukkada VA, Peterson K, Spergel JM, Wechsler JB, Yang GY, Rothenberg ME, Harris JK. Mucosal Microbiota Associated With Eosinophilic Esophagitis and Eosinophilic Gastritis. J Pediatr Gastroenterol Nutr. 2023 03 01; 76(3):347-354. PMID: 36525669.
      View in: PubMed
    7. Hoppe JE, Wagner BD, Kirk Harris J, Rowe SM, Heltshe SL, DeBoer EM, Sagel SD. Effects of ivacaftor on systemic inflammation and the plasma proteome in people with CF and G551D. J Cyst Fibros. 2022 11; 21(6):950-958. PMID: 35440409.
      View in: PubMed
    8. O'Connor JB, Mottlowitz M, Kruk ME, Mickelson A, Wagner BD, Harris JK, Wendt CH, Laguna TA. Network Analysis to Identify Multi-Omic Correlations in the Lower Airways of Children With Cystic Fibrosis. Front Cell Infect Microbiol. 2022; 12:805170. PMID: 35360097.
      View in: PubMed
    9. Tsitsiklis A, Osborne CM, Kamm J, Williamson K, Kalantar K, Dudas G, Caldera S, Lyden A, Tan M, Neff N, Soesanto V, Harris JK, Ambroggio L, Maddux AB, Carpenter TC, Reeder RW, Locandro C, Sim?es EAF, Leroue MK, Hall MW, Zuppa AF, Carcillo J, Meert KL, Sapru A, Pollack MM, McQuillen PS, Notterman DA, Dean JM, Zinter MS, Wagner BD, DeRisi JL, Mourani PM, Langelier CR. Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics. Lancet Microbe. 2022 04; 3(4):e284-e293. PMID: 35544065.
      View in: PubMed
    10. Broderick DTJ, Waite DW, Marsh RL, Camargo CA, Cardenas P, Chang AB, Cookson WOC, Cuthbertson L, Dai W, Everard ML, Gervaix A, Harris JK, Hasegawa K, Hoffman LR, Hong SJ, Josset L, Kelly MS, Kim BS, Kong Y, Li SC, Mansbach JM, Mejias A, O'Toole GA, Paalanen L, P?rez-Losada M, Pettigrew MM, Pichon M, Ramilo O, Ruokolainen L, Sakwinska O, Seed PC, van der Gast CJ, Wagner BD, Yi H, Zemanick ET, Zheng Y, Pillarisetti N, Taylor MW. Bacterial Signatures of Paediatric Respiratory Disease: An Individual Participant Data Meta-Analysis. Front Microbiol. 2021; 12:711134. PMID: 35002989.
      View in: PubMed
    11. O'Connor JB, Mottlowitz MM, Wagner BD, Boyne KL, Stevens MJ, Robertson CE, Harris JK, Laguna TA. Divergence of bacterial communities in the lower airways of CF patients in early childhood. PLoS One. 2021; 16(10):e0257838. PMID: 34613995.
      View in: PubMed
    12. Williamson KM, Wagner BD, Robertson CE, Stevens MJ, Sontag MK, Mourani PM, Harris JK. Modified PCR protocol to increase sensitivity for determination of bacterial community composition. Microbiome. 2021 04 13; 9(1):90. PMID: 33849648.
      View in: PubMed
    13. Khalaf RT, Furuta GT, Wagner BD, Robertson CE, Andrews R, Stevens MJ, Fillon SA, Zemanick ET, Harris JK. Influence of Acid Blockade on the Aerodigestive Tract Microbiome in Children With Cystic Fibrosis. J Pediatr Gastroenterol Nutr. 2021 04 01; 72(4):520-527. PMID: 33394582.
      View in: PubMed
    14. Mourani PM, Sontag MK, Williamson KM, Harris JK, Reeder R, Locandro C, Carpenter TC, Maddux AB, Ziegler K, Sim?es EAF, Osborne CM, Ambroggio L, Leroue MK, Robertson CE, Langelier C, DeRisi JL, Kamm J, Hall MW, Zuppa AF, Carcillo J, Meert K, Sapru A, Pollack MM, McQuillen P, Notterman DA, Dean JM, Wagner BD. Temporal airway microbiome changes related to ventilator-associated pneumonia in children. Eur Respir J. 2021 03; 57(3). PMID: 33008935.
      View in: PubMed
    15. Stanish LF, Sherwood OA, Lackey G, Osborn S, Robertson CE, Harris JK, Pace N, Ryan JN. Microbial and Biogeochemical Indicators of Methane in Groundwater Aquifers of the Denver Basin, Colorado. Environ Sci Technol. 2021 01 05; 55(1):292-303. PMID: 33296185.
      View in: PubMed
    16. Jewell MP, Saccomano SC, David AA, Harris JK, Zemanick ET, Cash KJ. Nanodiagnostics to monitor biofilm oxygen metabolism for antibiotic susceptibility testing. Analyst. 2020 Jun 07; 145(11):3996-4003. PMID: 32342070.
      View in: PubMed
    17. Harris JK, Wagner BD, Zemanick ET, Robertson CE, Stevens MJ, Heltshe SL, Rowe SM, Sagel SD. Changes in Airway Microbiome and Inflammation with Ivacaftor Treatment in Patients with Cystic Fibrosis and the G551D Mutation. Ann Am Thorac Soc. 2020 02; 17(2):212-220. PMID: 31604026.
      View in: PubMed
    18. Deterding RR, Wagner BD, Harris JK, DeBoer EM. Pulmonary Aptamer Signatures in Children's Interstitial and Diffuse Lung Disease. Am J Respir Crit Care Med. 2019 12 15; 200(12):1496-1504. PMID: 31409098.
      View in: PubMed
    19. Jewell MP, Galyean AA, Kirk Harris J, Zemanick ET, Cash KJ. Luminescent Nanosensors for Ratiometric Monitoring of Three-Dimensional Oxygen Gradients in Laboratory and Clinical Pseudomonas aeruginosa Biofilms. Appl Environ Microbiol. 2019 10 15; 85(20). PMID: 31420335.
      View in: PubMed
    20. DeBoer EM, Wagner BD, Popler J, Harris JK, Zemanick ET, Accurso FJ, Sagel SD, Deterding RR. Novel Application of Aptamer Proteomic Analysis in Cystic Fibrosis Bronchoalveolar Lavage Fluid. Proteomics Clin Appl. 2019 05; 13(3):e1800085. PMID: 30431231.
      View in: PubMed
    21. Hull NM, Rosenblum JS, Robertson CE, Harris JK, Linden KG. Succession of toxicity and microbiota in hydraulic fracturing flowback and produced water in the Denver-Julesburg Basin. Sci Total Environ. 2018 Dec 10; 644:183-192. PMID: 29981518.
      View in: PubMed
    22. Wagner BD, Grunwald GK, Zerbe GO, Mikulich-Gilbertson SK, Robertson CE, Zemanick ET, Harris JK. On the Use of Diversity Measures in Longitudinal Sequencing Studies of Microbial Communities. Front Microbiol. 2018; 9:1037. PMID: 29872428.
      View in: PubMed
    23. Rosen BH, Evans TIA, Moll SR, Gray JS, Liang B, Sun X, Zhang Y, Jensen-Cody CW, Swatek AM, Zhou W, He N, Rotti PG, Tyler SR, Keiser NW, Anderson PJ, Brooks L, Li Y, Pope RM, Rajput M, Hoffman EA, Wang K, Harris JK, Parekh KR, Gibson-Corley KN, Engelhardt JF. Infection Is Not Required for Mucoinflammatory Lung Disease in CFTR-Knockout Ferrets. Am J Respir Crit Care Med. 2018 05 15; 197(10):1308-1318. PMID: 29327941.
      View in: PubMed
    24. Wagner BD, Sontag MK, Harris JK, Miller JI, Morrow L, Robertson CE, Stephens MJ, Poindexter BB, Abman SH, Mourani PM. Prenatal complications are associated with the postnatal airway host response and microbiota in intubated preterm infants. J Matern Fetal Neonatal Med. 2019 May; 32(9):1499-1506. PMID: 29157044.
      View in: PubMed
    25. Zemanick ET, Wagner BD, Robertson CE, Ahrens RC, Chmiel JF, Clancy JP, Gibson RL, Harris WT, Kurland G, Laguna TA, McColley SA, McCoy K, Retsch-Bogart G, Sobush KT, Zeitlin PL, Stevens MJ, Accurso FJ, Sagel SD, Harris JK. Airway microbiota across age and disease spectrum in cystic fibrosis. Eur Respir J. 2017 11; 50(5). PMID: 29146601.
      View in: PubMed
    26. Leroue MK, Harris JK, Burgess KM, Stevens MJ, Miller JI, Sontag MK, Sierra YL, Wagner BD, Mourani PM. Molecular analysis of endotracheal tube biofilms and tracheal aspirates in the pediatric intensive care unit. Adv Pediatr Res. 2017 Dec; 4(3). PMID: 29963643.
      View in: PubMed
    27. Ahn ES, Hauck MJ, Kirk Harris J, Robertson CE, Dailey RA. Bacterial Biofilms in Jones Tubes. Ophthalmic Plast Reconstr Surg. 2017 Jul/Aug; 33(4):279-284. PMID: 27487729.
      View in: PubMed
    28. Williamson KM, Wagner BD, Robertson CE, Johnson EJ, Zemanick ET, Harris JK. Impact of enzymatic digestion on bacterial community composition in CF airway samples. PeerJ. 2017; 5:e3362. PMID: 28584706.
      View in: PubMed
    29. DeBoer EM, Kroehl ME, Wagner BD, Accurso FJ, Harris JK, Lynch DA, Sagel SD, Deterding RR. Proteomic profiling identifies novel circulating markers associated with bronchiectasis in cystic fibrosis. Proteomics Clin Appl. 2017 09; 11(9-10). PMID: 28452194.
      View in: PubMed
    30. Goleva E, Harris JK, Robertson CE, Jackson LP, Martin RJ, Leung DYM. Airway microbiome and responses to corticosteroids in corticosteroid-resistant asthma patients treated with acid suppression medications. J Allergy Clin Immunol. 2017 09; 140(3):860-862.e1. PMID: 28477847.
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    31. Hull NM, Holinger EP, Ross KA, Robertson CE, Harris JK, Stevens MJ, Pace NR. Longitudinal and Source-to-Tap New Orleans, LA, U.S.A. Drinking Water Microbiology. Environ Sci Technol. 2017 04 18; 51(8):4220-4229. PMID: 28296394.
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    32. Wagner BD, Sontag MK, Harris JK, Miller JI, Morrow L, Robertson CE, Stephens M, Poindexter BB, Abman SH, Mourani PM. Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants. PLoS One. 2017; 12(1):e0170120. PMID: 28129336.
      View in: PubMed
    33. Laguna TA, Wagner BD, Williams CB, Stevens MJ, Robertson CE, Welchlin CW, Moen CE, Zemanick ET, Harris JK. Airway Microbiota in Bronchoalveolar Lavage Fluid from Clinically Well Infants with Cystic Fibrosis. PLoS One. 2016; 11(12):e0167649. PMID: 27930727.
      View in: PubMed
    34. Stanish LF, Hull NM, Robertson CE, Harris JK, Stevens MJ, Spear JR, Pace NR. Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA. PLoS One. 2016; 11(6):e0157966. PMID: 27362708.
      View in: PubMed
    35. Fang R, Wagner BD, Harris JK, Fillon SA. Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis. Epidemiol Infect. 2016 08; 144(11):2447-55. PMID: 27049299.
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    36. Johnson EJ, Zemanick ET, Accurso FJ, Wagner BD, Robertson CE, Harris JK. Molecular Identification of Staphylococcus aureus in Airway Samples from Children with Cystic Fibrosis. PLoS One. 2016; 11(1):e0147643. PMID: 26808658.
      View in: PubMed
    37. Handorean A, Robertson CE, Harris JK, Frank D, Hull N, Kotter C, Stevens MJ, Baumgardner D, Pace NR, Hernandez M. Microbial aerosol liberation from soiled textiles isolated during routine residuals handling in a modern health care setting. Microbiome. 2015 Dec 09; 3:72. PMID: 26646166.
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    38. Keiser NW, Birket SE, Evans IA, Tyler SR, Crooke AK, Sun X, Zhou W, Nellis JR, Stroebele EK, Chu KK, Tearney GJ, Stevens MJ, Harris JK, Rowe SM, Engelhardt JF. Defective innate immunity and hyperinflammation in newborn cystic fibrosis transmembrane conductance regulator-knockout ferret lungs. Am J Respir Cell Mol Biol. 2015 Jun; 52(6):683-94. PMID: 25317669.
      View in: PubMed
    39. Harris JK, Fang R, Wagner BD, Choe HN, Kelly CJ, Schroeder S, Moore W, Stevens MJ, Yeckes A, Amsden K, Kagalwalla AF, Zalewski A, Hirano I, Gonsalves N, Henry LN, Masterson JC, Robertson CE, Leung DY, Pace NR, Ackerman SJ, Furuta GT, Fillon SA. Esophageal microbiome in eosinophilic esophagitis. PLoS One. 2015; 10(5):e0128346. PMID: 26020633.
      View in: PubMed
    40. Baron JL, Harris JK, Holinger EP, Duda S, Stevens MJ, Robertson CE, Ross KA, Pace NR, Stout JE. Effect of monochloramine treatment on the microbial ecology of Legionella and associated bacterial populations in a hospital hot water system. Syst Appl Microbiol. 2015 May; 38(3):198-205. PMID: 25840824.
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    41. Ling AL, Robertson CE, Harris JK, Frank DN, Kotter CV, Stevens MJ, Pace NR, Hernandez MT. High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes. PLoS One. 2015; 10(3):e0116400. PMID: 25748024.
      View in: PubMed
    42. Zemanick ET, Wagner BD, Robertson CE, Stevens MJ, Szefler SJ, Accurso FJ, Sagel SD, Harris JK. Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods. Ann Am Thorac Soc. 2015 Feb; 12(2):221-9. PMID: 25474078.
      View in: PubMed
    43. Lim YW, Haynes M, Furlan M, Robertson CE, Harris JK, Rohwer F. Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples. J Vis Exp. 2014 Dec 22; (94). PMID: 25549184.
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    44. Hull NM, Reens AL, Robertson CE, Stanish LF, Harris JK, Stevens MJ, Frank DN, Kotter C, Pace NR. Molecular analysis of single room humidifier bacteriology. Water Res. 2015 Feb 01; 69:318-327. PMID: 25574772.
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    45. Rutebemberwa A, Stevens MJ, Perez MJ, Smith LP, Sanders L, Cosgrove G, Robertson CE, Tuder RM, Harris JK. Novosphingobium and its potential role in chronic obstructive pulmonary diseases: insights from microbiome studies. PLoS One. 2014; 9(10):e111150. PMID: 25340840.
      View in: PubMed
    46. Harris JK, El Kasmi KC, Anderson AL, Devereaux MW, Fillon SA, Robertson CE, Wagner BD, Stevens MJ, Pace NR, Sokol RJ. Specific microbiome changes in a mouse model of parenteral nutrition associated liver injury and intestinal inflammation. PLoS One. 2014; 9(10):e110396. PMID: 25329595.
      View in: PubMed
    47. Ling AL, Robertson CE, Harris JK, Frank DN, Kotter CV, Stevens MJ, Pace NR, Hernandez MT. Carbon dioxide and hydrogen sulfide associations with regional bacterial diversity patterns in microbially induced concrete corrosion. Environ Sci Technol. 2014 Jul 01; 48(13):7357-64. PMID: 24842376.
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    48. Whiteson KL, Bailey B, Bergkessel M, Conrad D, Delhaes L, Felts B, Harris JK, Hunter R, Lim YW, Maughan H, Quinn R, Salamon P, Sullivan J, Wagner BD, Rainey PB. The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography. Am J Respir Crit Care Med. 2014 Jun 01; 189(11):1309-15. PMID: 24702670.
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    49. Holinger EP, Ross KA, Robertson CE, Stevens MJ, Harris JK, Pace NR. Molecular analysis of point-of-use municipal drinking water microbiology. Water Res. 2014 Feb 01; 49:225-35. PMID: 24333849.
      View in: PubMed
    50. Goleva E, Jackson LP, Harris JK, Robertson CE, Sutherland ER, Hall CF, Good JT, Gelfand EW, Martin RJ, Leung DY. The effects of airway microbiome on corticosteroid responsiveness in asthma. Am J Respir Crit Care Med. 2013 Nov 15; 188(10):1193-201. PMID: 24024497.
      View in: PubMed
    51. Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, Tatem B, Feazel LM, Park K, Pace NR, Frank DN. Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. Bioinformatics. 2013 Dec 01; 29(23):3100-1. PMID: 24021386.
      View in: PubMed
    52. Mittal BB, Wang E, Sejpal S, Agulnik M, Mittal A, Harris K. Effect of recombinant human deoxyribonuclease on oropharyngeal secretions in patients with head-and-neck cancers treated with radiochemotherapy. Int J Radiat Oncol Biol Phys. 2013 Oct 01; 87(2):282-9. PMID: 23910712.
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    53. Harris JK, Zemanick ET. Microbes in bronchiectasis: the forest or the trees? Am J Respir Crit Care Med. 2013 May 15; 187(10):1044-5. PMID: 23675713.
      View in: PubMed
    54. Zemanick ET, Harris JK, Wagner BD, Robertson CE, Sagel SD, Stevens MJ, Accurso FJ, Laguna TA. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One. 2013; 8(4):e62917. PMID: 23646159.
      View in: PubMed
    55. Robertson CE, Baumgartner LK, Harris JK, Peterson KL, Stevens MJ, Frank DN, Pace NR. Culture-independent analysis of aerosol microbiology in a metropolitan subway system. Appl Environ Microbiol. 2013 Jun; 79(11):3485-93. PMID: 23542619.
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    56. Fillon SA, Harris JK, Wagner BD, Kelly CJ, Stevens MJ, Moore W, Fang R, Schroeder S, Masterson JC, Robertson CE, Pace NR, Ackerman SJ, Furuta GT. Novel device to sample the esophageal microbiome--the esophageal string test. PLoS One. 2012; 7(9):e42938. PMID: 22957025.
      View in: PubMed
    57. Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J. 2013 Jan; 7(1):50-60. PMID: 22832344.
      View in: PubMed
    58. Keely S, Kelly CJ, Weissmueller T, Burgess A, Wagner BD, Robertson CE, Harris JK, Colgan SP. Activated fluid transport regulates bacterial-epithelial interactions and significantly shifts the murine colonic microbiome. Gut Microbes. 2012 May-Jun; 3(3):250-60. PMID: 22614705.
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    59. El Kasmi KC, Anderson AL, Devereaux MW, Fillon SA, Harris JK, Lovell MA, Finegold MJ, Sokol RJ. Toll-like receptor 4-dependent Kupffer cell activation and liver injury in a novel mouse model of parenteral nutrition and intestinal injury. Hepatology. 2012 May; 55(5):1518-28. PMID: 22120983.
      View in: PubMed
    60. Harris JK, Wagner BD. Bacterial identification and analytic challenges in clinical microbiome studies. J Allergy Clin Immunol. 2012 Feb; 129(2):441-2. PMID: 22284932.
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    61. Mourani PM, Harris JK, Sontag MK, Robertson CE, Abman SH. Molecular identification of bacteria in tracheal aspirate fluid from mechanically ventilated preterm infants. PLoS One. 2011; 6(10):e25959. PMID: 22016793.
      View in: PubMed
    62. Zemanick ET, Sagel SD, Harris JK. The airway microbiome in cystic fibrosis and implications for treatment. Curr Opin Pediatr. 2011 Jun; 23(3):319-24. PMID: 21494150.
      View in: PubMed
    63. Wagner BD, Robertson CE, Harris JK. Application of two-part statistics for comparison of sequence variant counts. PLoS One. 2011; 6(5):e20296. PMID: 21629788.
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    64. Zemanick ET, Wagner BD, Sagel SD, Stevens MJ, Accurso FJ, Harris JK. Reliability of quantitative real-time PCR for bacterial detection in cystic fibrosis airway specimens. PLoS One. 2010 Nov 30; 5(11):e15101. PMID: 21152087.
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    65. Sahl JW, Gary MO, Harris JK, Spear JR. A comparative molecular analysis of water-filled limestone sinkholes in north-eastern Mexico. Environ Microbiol. 2011 Jan; 13(1):226-240. PMID: 20738374.
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    66. Widmann J, Harris JK, Lozupone C, Wolfson A, Knight R. Stable tRNA-based phylogenies using only 76 nucleotides. RNA. 2010 Aug; 16(8):1469-77. PMID: 20558546.
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    67. Zemanick ET, Wagner BD, Harris JK, Wagener JS, Accurso FJ, Sagel SD. Pulmonary exacerbations in cystic fibrosis with negative bacterial cultures. Pediatr Pulmonol. 2010 Jun; 45(6):569-77. PMID: 20503282.
      View in: PubMed
    68. Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, Spear JR. Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing. Appl Environ Microbiol. 2010 Jun; 76(12):3863-8. PMID: 20418443.
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    69. Sahl JW, Fairfield N, Harris JK, Wettergreen D, Stone WC, Spear JR. Novel microbial diversity retrieved by autonomous robotic exploration of the world's deepest vertical phreatic sinkhole. Astrobiology. 2010 Mar; 10(2):201-13. PMID: 20298146.
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    70. Zemanick ET, Harris JK, Conway S, Konstan MW, Marshall B, Quittner AL, Retsch-Bogart G, Saiman L, Accurso FJ. Measuring and improving respiratory outcomes in cystic fibrosis lung disease: opportunities and challenges to therapy. J Cyst Fibros. 2010 Jan; 9(1):1-16. PMID: 19833563.
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    71. Feazel LM, Baumgartner LK, Peterson KL, Frank DN, Harris JK, Pace NR. Opportunistic pathogens enriched in showerhead biofilms. Proc Natl Acad Sci U S A. 2009 Sep 22; 106(38):16393-9. PMID: 19805310.
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    72. Robertson CE, Spear JR, Harris JK, Pace NR. Diversity and stratification of archaea in a hypersaline microbial mat. Appl Environ Microbiol. 2009 Apr; 75(7):1801-10. PMID: 19114531.
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    73. Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P. Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol. 2008; 4:198. PMID: 18523433.
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    74. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods. 2008 Mar; 5(3):235-7. PMID: 18264105.
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    75. Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, Penvari C, Kaess H, Deterding RR, Accurso FJ, Pace NR. Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A. 2007 Dec 18; 104(51):20529-33. PMID: 18077362.
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    76. Feazel LM, Spear JR, Berger AB, Harris JK, Frank DN, Ley RE, Pace NR. Eucaryotic diversity in a hypersaline microbial mat. Appl Environ Microbiol. 2008 Jan; 74(1):329-32. PMID: 17993566.
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    77. Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin ML, Pace NR. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol. 2006 May; 72(5):3685-95. PMID: 16672518.
      View in: PubMed
    78. Robertson CE, Harris JK, Spear JR, Pace NR. Phylogenetic diversity and ecology of environmental Archaea. Curr Opin Microbiol. 2005 Dec; 8(6):638-42. PMID: 16236543.
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    79. Marquez SM, Harris JK, Kelley ST, Brown JW, Dawson SC, Roberts EC, Pace NR. Structural implications of novel diversity in eucaryal RNase P RNA. RNA. 2005 May; 11(5):739-51. PMID: 15811915.
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    80. Harris JK, Kelley ST, Pace NR. New perspective on uncultured bacterial phylogenetic division OP11. Appl Environ Microbiol. 2004 Feb; 70(2):845-9. PMID: 14766563.
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    81. Harris JK, Kelley ST, Spiegelman GB, Pace NR. The genetic core of the universal ancestor. Genome Res. 2003 Mar; 13(3):407-12. PMID: 12618371.
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    82. Kelley ST, Harris JK, Pace NR. Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities. RNA. 2001 Sep; 7(9):1310-6. PMID: 11565752.
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    83. Harris JK, Haas ES, Williams D, Frank DN, Brown JW. New insight into RNase P RNA structure from comparative analysis of the archaeal RNA. RNA. 2001 Feb; 7(2):220-32. PMID: 11233979.
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    84. Dojka MA, Harris JK, Pace NR. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol. 2000 Apr; 66(4):1617-21. PMID: 10742250.
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    85. Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW. RNase P RNAs from some Archaea are catalytically active. Proc Natl Acad Sci U S A. 1999 Jul 06; 96(14):7803-8. PMID: 10393902.
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    86. Haas ES, Banta AB, Harris JK, Pace NR, Brown JW. Structure and evolution of ribonuclease P RNA in Gram-positive bacteria. Nucleic Acids Res. 1996 Dec 01; 24(23):4775-82. PMID: 8972865.
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