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Jonathan Kirk Harris

TitleAssociate Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus

    Collapse Research 
    Collapse research activities and funding
    R21HL110721     (TUDER, RUBIN M)Dec 1, 2011 - Nov 30, 2013
    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. 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. 2018 Nov 15; e1800085. PMID: 30431231.
      View in: PubMed
    2. 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
    3. 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
    4. 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 May 15; 197(10):1308-1318. PMID: 29327941.
      View in: PubMed
    5. 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. 2017 Nov 28; 1-8. PMID: 29157044.
      View in: PubMed
    6. 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
    7. 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
    8. 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
    9. 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 Sep; 140(3):860-862.e1. PMID: 28477847.
      View in: PubMed
    10. 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.
      View in: PubMed
    11. 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
    12. 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
    13. 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; PMCID: PMC4928833.
    14. 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.
      View in: PubMed
    15. 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
    16. 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; PMCID: PMC4673858.
    17. 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; PMCID: PMC4491130.
    18. 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; PMCID: PMC4447451.
    19. 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.
      View in: PubMed
    20. 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
    21. Bayin NS, Modrek AS, Dietrich A, Lebowitz J, Abel T, Song HR, Schober M, Zagzag D, Buchholz CJ, Chao MV, Placantonakis DG. Selective lentiviral gene delivery to CD133-expressing human glioblastoma stem cells. PLoS One. 2014; 9(12):e116114. PMID: 25541984; PMCID: PMC4277468.
    22. 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; PMCID: PMC4354477.
    23. 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.
      View in: PubMed
    24. 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; PMCID: PMC4207766.
    25. 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; PMCID: PMC4203793.
    26. 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.
      View in: PubMed
    27. 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; PMCID: PMC4098084.
    28. 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
    29. 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; PMCID: PMC3863730.
    30. 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; PMCID: PMC3834795.
    31. 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.
      View in: PubMed
    32. 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
    33. 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; PMCID: PMC3639911.
    34. 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; PMCID: PMC3648054.
    35. 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
    36. 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; PMCID: PMC3526174.
    37. 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; PMCID: PMC3427217.
    38. 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; PMCID: PMC4986925.
    39. 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.
      View in: PubMed
    40. 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; PMCID: PMC3189942.
    41. 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
    42. 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; PMCID: PMC3100341.
    43. 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; PMCID: PMC2994853.
    44. 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.
      View in: PubMed
    45. 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; PMCID: PMC2905747.
    46. 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; PMCID: PMC2937349.
    47. 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; PMCID: PMC2893486.
    48. 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.
      View in: PubMed
    49. 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; PMCID: PMC2752528.
    50. 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; PMCID: PMC2663194.
    51. 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; PMCID: PMC2483411.
    52. 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; PMCID: PMC3439997.
    53. 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; PMCID: PMC2154465.
    54. 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; PMCID: PMC2223211.
    55. 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; PMCID: PMC1472358.
    56. 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; PMCID: PMC1370759.
    57. 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; PMCID: PMC348892.
    58. 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; PMCID: PMC430263.
    59. 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; PMCID: PMC1370174.
    60. 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; PMCID: PMC1370080.
    61. 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; PMCID: PMC92031.
    62. 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; PMCID: PMC22142.
    63. 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; PMCID: PMC146312.
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