Jonathan K. Harris, Ph.D. - Publications

University of California, Berkeley, Berkeley, CA 
RNA, Microbial Ecosystems

68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Jewell MP, Saccomano SC, David AA, Harris JK, Zemanick ET, Cash KJ. Nanodiagnostics to monitor biofilm oxygen metabolism for antibiotic susceptibility testing. The Analyst. PMID 32342070 DOI: 10.1039/d0an00479k  0.4
2019 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. Annals of the American Thoracic Society. PMID 31604026 DOI: 10.1513/AnnalsATS.201907-493OC  0.72
2019 Jewell MP, Galyean AA, Harris JK, Zemanick ET, Cash KJ. Luminescent nanosensors for ratiometric monitoring of three-dimensional oxygen gradients in lab and clinical biofilms. Applied and Environmental Microbiology. PMID 31420335 DOI: 10.1128/AEM.01116-19  0.4
2019 Deterding RR, Wagner BD, Harris JK, DeBoer EM. Pulmonary Aptamer Signatures in Children's Interstitial and Diffuse Lung Diseases. American Journal of Respiratory and Critical Care Medicine. PMID 31409098 DOI: 10.1164/rccm.201903-0547OC  0.68
2018 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. Clinical Applications. e1800085. PMID 30431231 DOI: 10.1002/prca.201800085  0.68
2018 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. The Science of the Total Environment. 644: 183-192. PMID 29981518 DOI: 10.1016/j.scitotenv.2018.06.067  0.72
2018 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. Frontiers in Microbiology. 9: 1037. PMID 29872428 DOI: 10.3389/fmicb.2018.01037  0.72
2017 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. Advances in Pediatric Research. 4. PMID 29963643 DOI: 10.12715/apr.2017.4.14  0.72
2017 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. The Journal of Maternal-Fetal & Neonatal Medicine : the Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians. 1-211. PMID 29157044 DOI: 10.1080/14767058.2017.1407310  0.72
2017 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, ... ... Harris JK, et al. Airway microbiota across age and disease spectrum in cystic fibrosis. The European Respiratory Journal. 50. PMID 29146601 DOI: 10.1183/13993003.00832-2017  0.72
2017 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. 5: e3362. PMID 28584706 DOI: 10.7717/peerj.3362  0.72
2017 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. The Journal of Allergy and Clinical Immunology. PMID 28477847 DOI: 10.1016/j.jaci.2017.03.011  0.72
2017 DeBoer EM, Kroehl M, Wagner BD, Accurso F, Harris JK, Lynch DA, Sagel SD, Deterding RR. Proteomic profiling identifies novel circulating markers associated with bronchiectasis in cystic fibrosis. Proteomics. Clinical Applications. PMID 28452194 DOI: 10.1002/prca.201600147  0.68
2017 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. 12: e0170120. PMID 28129336 DOI: 10.1371/journal.pone.0170120  0.72
2016 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. 11: e0167649. PMID 27930727 DOI: 10.1371/journal.pone.0167649  0.72
2016 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. 11: e0157966. PMID 27362708 DOI: 10.1371/journal.pone.0157966  1
2016 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. 11: e0147643. PMID 26808658 DOI: 10.1371/journal.pone.0147643  1
2016 FANG R, WAGNER BD, HARRIS JK, FILLON SA. Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis Epidemiology and Infection. 1-9. DOI: 10.1017/S0950268816000662  1
2015 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. 3: 72. PMID 26646166 DOI: 10.1186/s40168-015-0132-3  1
2015 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, et al. Esophageal microbiome in eosinophilic esophagitis. Plos One. 10: e0128346. PMID 26020633 DOI: 10.1371/journal.pone.0128346  1
2015 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. Systematic and Applied Microbiology. 38: 198-205. PMID 25840824 DOI: 10.1016/j.syapm.2015.02.006  1
2015 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. 10: e0116400. PMID 25748024 DOI: 10.1371/journal.pone.0116400  1
2015 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 Research. 69: 318-27. PMID 25574772 DOI: 10.1016/j.watres.2014.11.024  1
2015 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. Annals of the American Thoracic Society. 12: 221-9. PMID 25474078 DOI: 10.1513/AnnalsATS.201407-310OC  1
2015 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. American Journal of Respiratory Cell and Molecular Biology. 52: 683-94. PMID 25317669 DOI: 10.1165/rcmb.2014-0250OC  1
2014 Lim YW, Haynes M, Furlan M, Robertson CE, Harris JK, Rohwer F. Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples. Journal of Visualized Experiments : Jove. PMID 25549184 DOI: 10.3791/52117  1
2014 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. 9: e111150. PMID 25340840 DOI: 10.1371/journal.pone.0111150  1
2014 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. 9: e110396. PMID 25329595 DOI: 10.1371/journal.pone.0110396  1
2014 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. Environmental Science & Technology. 48: 7357-64. PMID 24842376 DOI: 10.1021/es500763e  1
2014 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. American Journal of Respiratory and Critical Care Medicine. 189: 1309-15. PMID 24702670 DOI: 10.1164/rccm.201312-2129PP  1
2014 Holinger EP, Ross KA, Robertson CE, Stevens MJ, Harris JK, Pace NR. Molecular analysis of point-of-use municipal drinking water microbiology. Water Research. 49: 225-35. PMID 24333849 DOI: 10.1016/j.watres.2013.11.027  1
2013 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. American Journal of Respiratory and Critical Care Medicine. 188: 1193-201. PMID 24024497 DOI: 10.1164/rccm.201304-0775OC  1
2013 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 (Oxford, England). 29: 3100-1. PMID 24021386 DOI: 10.1093/bioinformatics/btt526  1
2013 Harris JK, Zemanick ET. Microbes in bronchiectasis: the forest or the trees? American Journal of Respiratory and Critical Care Medicine. 187: 1044-5. PMID 23675713 DOI: 10.1164/rccm.201302-0240ED  1
2013 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. 8: e62917. PMID 23646159 DOI: 10.1371/journal.pone.0062917  1
2013 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. Applied and Environmental Microbiology. 79: 3485-93. PMID 23542619 DOI: 10.1128/AEM.00331-13  1
2013 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. The Isme Journal. 7: 50-60. PMID 22832344 DOI: 10.1038/ismej.2012.79  1
2013 Zemanick ET, Harris JK. The human airway microbiome The Human Microbiota: How Microbial Communities Affect Health and Disease. 119-134. DOI: 10.1002/9781118409855.ch6  1
2012 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. 7: e42938. PMID 22957025 DOI: 10.1371/journal.pone.0042938  1
2012 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. 3: 250-60. PMID 22614705 DOI: 10.4161/gmic.20529  1
2012 Harris JK, Wagner BD. Bacterial identification and analytic challenges in clinical microbiome studies. The Journal of Allergy and Clinical Immunology. 129: 441-2. PMID 22284932 DOI: 10.1016/j.jaci.2011.12.969  1
2012 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 (Baltimore, Md.). 55: 1518-28. PMID 22120983 DOI: 10.1002/hep.25500  1
2011 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. 6: e25959. PMID 22016793 DOI: 10.1371/journal.pone.0025959  1
2011 Wagner BD, Robertson CE, Harris JK. Application of two-part statistics for comparison of sequence variant counts. Plos One. 6: e20296. PMID 21629788 DOI: 10.1371/journal.pone.0020296  1
2011 Zemanick ET, Sagel SD, Harris JK. The airway microbiome in cystic fibrosis and implications for treatment. Current Opinion in Pediatrics. 23: 319-24. PMID 21494150 DOI: 10.1097/MOP.0b013e32834604f2  1
2011 Sahl JW, Gary MO, Harris JK, Spear JR. A comparative molecular analysis of water-filled limestone sinkholes in north-eastern Mexico. Environmental Microbiology. 13: 226-40. PMID 20738374 DOI: 10.1111/j.1462-2920.2010.02324.x  1
2010 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. 5: e15101. PMID 21152087 DOI: 10.1371/journal.pone.0015101  0.72
2010 Widmann J, Harris JK, Lozupone C, Wolfson A, Knight R. Stable tRNA-based phylogenies using only 76 nucleotides. Rna (New York, N.Y.). 16: 1469-77. PMID 20558546 DOI: 10.1261/rna.726010  1
2010 Zemanick ET, Wagner BD, Harris JK, Wagener JS, Accurso FJ, Sagel SD. Pulmonary exacerbations in cystic fibrosis with negative bacterial cultures. Pediatric Pulmonology. 45: 569-77. PMID 20503282 DOI: 10.1002/ppul.21221  1
2010 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. Applied and Environmental Microbiology. 76: 3863-8. PMID 20418443 DOI: 10.1128/AEM.02585-09  1
2010 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. 10: 201-13. PMID 20298146 DOI: 10.1089/ast.2009.0378  1
2010 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. Journal of Cystic Fibrosis : Official Journal of the European Cystic Fibrosis Society. 9: 1-16. PMID 19833563 DOI: 10.1016/j.jcf.2009.09.003  1
2009 Feazel LM, Baumgartner LK, Peterson KL, Frank DN, Harris JK, Pace NR. Opportunistic pathogens enriched in showerhead biofilms. Proceedings of the National Academy of Sciences of the United States of America. 106: 16393-9. PMID 19805310 DOI: 10.1073/pnas.0908446106  1
2009 Robertson CE, Spear JR, Harris JK, Pace NR. Diversity and stratification of archaea in a hypersaline microbial mat. Applied and Environmental Microbiology. 75: 1801-10. PMID 19114531 DOI: 10.1128/AEM.01811-08  1
2008 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. Molecular Systems Biology. 4: 198. PMID 18523433 DOI: 10.1038/msb.2008.35  1
2008 Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods. 5: 235-7. PMID 18264105 DOI: 10.1038/nmeth.1184  1
2008 Feazel LM, Spear JR, Berger AB, Harris JK, Frank DN, Ley RE, Pace NR. Eucaryotic diversity in a hypersaline microbial mat. Applied and Environmental Microbiology. 74: 329-32. PMID 17993566 DOI: 10.1128/AEM.01448-07  1
2007 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. Proceedings of the National Academy of Sciences of the United States of America. 104: 20529-33. PMID 18077362 DOI: 10.1073/pnas.0709804104  1
2006 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. Applied and Environmental Microbiology. 72: 3685-95. PMID 16672518 DOI: 10.1128/AEM.72.5.3685-3695.2006  1
2005 Robertson CE, Harris JK, Spear JR, Pace NR. Phylogenetic diversity and ecology of environmental Archaea. Current Opinion in Microbiology. 8: 638-42. PMID 16236543 DOI: 10.1016/j.mib.2005.10.003  1
2005 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 (New York, N.Y.). 11: 739-51. PMID 15811915 DOI: 10.1261/rna.7211705  1
2004 Harris JK, Kelley ST, Pace NR. New perspective on uncultured bacterial phylogenetic division OP11. Applied and Environmental Microbiology. 70: 845-9. PMID 14766563 DOI: 10.1128/AEM.70.2.845-849.2004  1
2003 Harris JK, Kelley ST, Spiegelman GB, Pace NR. The genetic core of the universal ancestor. Genome Research. 13: 407-12. PMID 12618371 DOI: 10.1101/gr.652803  1
2001 Kelley ST, Harris JK, Pace NR. Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities. Rna (New York, N.Y.). 7: 1310-6. PMID 11565752 DOI: 10.1017/S1355838201010573  1
2001 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 (New York, N.Y.). 7: 220-32. PMID 11233979 DOI: 10.1017/S1355838201001777  1
2000 Dojka MA, Harris JK, Pace NR. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Applied and Environmental Microbiology. 66: 1617-21. PMID 10742250 DOI: 10.1128/AEM.66.4.1617-1621.2000  1
1999 Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW. RNase P RNAs from some Archaea are catalytically active. Proceedings of the National Academy of Sciences of the United States of America. 96: 7803-8. PMID 10393902 DOI: 10.1073/pnas.96.14.7803  1
1996 Haas ES, Banta AB, Harris JK, Pace NR, Brown JW. Structure and evolution of ribonuclease P RNA in Gram-positive bacteria. Nucleic Acids Research. 24: 4775-82. PMID 8972865  1
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