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RPRC Publications

2017 July
Henkle E, Novosad SA, Shafer S, Hedberg K, Siegel SAR, Ku J, Varley C, Prevots DR, Marras TK, Winthrop KL
Long-Term Outcomes in a Population-based Cohort with Respiratory Nontuberculous Mycobacteria Isolation.
Ann Am Thorac Soc. 2017 Jul;14(7):1120-1128. doi: 10.1513/AnnalsATS.201610-801OC. PMID: 28406709

2017 July
Novosad SA, Henkle E, Schafer S, Hedberg K, Ku J, Siegel SAR, Choi D, Slatore CG, Winthrop KL
Mortality after Respiratory Isolation of Nontuberculous Mycobacteria. A Comparison of Patients Who Did and Did Not Meet Disease Criteria.
Ann Am Thorac Soc. 2017 Jul;14(7):1112-1119. doi: 10.1513/AnnalsATS.201610-800OC. PMID: 28387532

2017 June
Khan A, Katanic D, Thakar J
Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes.
BMC Bioinformatics. 2017 Jun 6;18(1):295. doi: 10.1186/s12859-017-1669-x. PMID: 28587632

2017 May
Wong T, Hall J, Boehm D, Barbier M, Damron FH
Development of RNAseq Methodologies To Profile The In Vivo Transcriptome Of Bordetella pertussis During Murine Lung Infection
bioRxiv. 2017 May. doi: https://doi.org/10.1101/140632 

2017 May
Geno KA, Saad JS, Nahm MH
Discovery of Novel Pneumococcal Serotype 35D, a Natural WciG-Deficient Variant of Serotype 35B.
J Clin Microbiol. 2017 May;55(5):1416-1425. doi: 10.1128/JCM.00054-17. PMID: 28202800

2017 Mar
Caserta MT, Qiu X, Tesini B, Wang L, Murphy A, Corbett A, Topham DJ, Falsey AR, Holden-Wiltse J, Walsh EE
Development of a Global Respiratory Severity Score for Respiratory Syncytial Virus Infection in Infants.
J Infect Dis. 2017 Mar 1;215(5):750-756. doi: 10.1093/infdis/jiw624. PMID: 28011907

2017 Mar
Caserta MT, Yang H, Gill SR, Holden-Wiltse J, Pryhuber G
Viral Respiratory Infections in Preterm Infants during and after Hospitalization.
J Pediatr. 2017 Mar;182:53-58.e3. doi: 10.1016/j.jpeds.2016.11.077.  PMID: 28041669

2017 Feb
Burton RL, Antonello J, Cooper D, Goldblatt D, Kim KH, Plikaytis BD, Roalfe L, Wauters D, Williams F, Xie GL, Nahm MH, Akkoyunlu M
Assignment of Opsonic Values to Pneumococcal Reference Serum 007sp for Use in Opsonophagocytic Assays for 13 Serotypes.
Clin Vaccine Immunol. 2017 Feb 6;24(2). pii: e00457-16. doi: 10.1128/CVI.00457-16. PMID: 27974397

2017 Feb
Zhang Y, Topham DJ, Thakar J, Qiu X
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis.
Bioinformatics. 2017 Feb 21. doi: 10.1093/bioinformatics/btx104. PMID: 28334094

2017 Jan
Eby JC, Gray MC, Warfel JM, Merkel TJ, Hewlett EL
Use of a Toxin Neutralization Assay To Characterize the Serologic Response to Adenylate Cyclase Toxin after Infection with Bordetella pertussis.
Clin Vaccine Immunol. 2017 Jan 5;24(1). pii: e00370-16. doi: 10.1128/CVI.00370-16. PMID: 27760780

2016 Dec
Groves AM, Johnston CJ, Misra RS, Williams JP, Finkelstein JN
Effects of IL-4 on pulmonary fibrosis and the accumulation and phenotype of macrophage subpopulations following thoracic irradiation.
Int J Radiat Biol. 2016 Dec;92(12):754-765. PMID: 27539247

2016 Dec
Katanic D, Khan A, Thakar J
PathCellNet: Cell-type specific pathogen-response network explorer.
J Immunol Methods. 2016 Dec;439:15-22. doi: 10.1016/j.jim.2016.09.005. PMID: 27659011

2016 Nov
Li H, Qiu X
Moments of Distance from a Vertex to a Uniformly Distributed Random Point within Arbitrary Triangles
Mathematical Problems in Engineering, vol. 2016, Article ID 8371750

2016 Oct
Misra RS, Bhattacharya S, Huyck HL, Wang JC, Slaunwhite CG, Slaunwhite SL, Wightman TR, Secor-Socha S, Misra SK, Bushnell TP, Reynolds AM, Ryan RM, Quataert SA, Pryhuber GS, Mariani TJ
Flow-based sorting of neonatal lymphocyte populations for transcriptomics analysis.
J Immunol Methods. 2016 Oct;437:13-20. doi: 10.1016/j.jim.2016.07.001. PMID: 27438473

2016 Oct
Sun X, Hu F, Wu S, Qiu X, Linel P, Wu H
Controllability and Stability Analysis of Large Transcriptomic Dynamic Systems for Host Response to Influenza Infection in Human
Infectious Disease Modelling, Volume 1, Issue 1, October 2016. Pages 52–70

2016 Sept
Chu CY, Qiu X, Wang L, Bhattacharya S, Lofthus G, Corbett A, Holden-Wiltse J, Grier A, Tesini B, Gill SR, Falsey AR, Caserta MT, Walsh EE, Mariani TJ.
The Healthy Infant Nasal Transcriptome: A Benchmark Study.
Sci Rep. 2016 Sep 23;6:33994. doi: 10.1038/srep33994. PMID: 27658638

2016 June
Zhang Y, Cao J, Zhang S, Lee AJ, Sun G, Larsen CN, Zhao H, Gu Z, He S, Klem EB, Scheuermann RH
Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak.
Virus Evol. 2016 Jun 15;2(1):vew015. doi: 10.1093/ve/vew015. PMID: 28512577

2016 Apr
Branche AR, Walsh EE, Jadhav N, Karmally R, Baran A, Peterson DR, Falsey AR.
Provider Decisions to Treat Respiratory Illnesses with Antibiotics: Insights from a Randomized Controlled Trial.
PLoS One. 2016 Apr 4;11(4):e0152986. doi: 10.1371/journal.pone.0152986. PMID: 27043012

2016 Apr
Burton RL, Geno KA, Saad JS, Nahm MH.
Pneumococcus with the "6E" cps Locus Produces Serotype 6B Capsular Polysaccharide.
J Clin Microbiol. 2016 Apr;54(4):967-71. doi: 10.1128/JCM.03194-15. Epub 2016 Jan 27. PMID: 26818670

2016 Feb 
Cattelan N,Dubey P,Arnal L,Yantorno OM,Deora R.
Bordetella biofilms: a lifestyle leading to persistent infections.
Pathog Dis. 2016 Feb;74(1):ftv108. doi: 10.1093/femspd/ftv108. Epub 2015 Nov 19. PMID: 26586694

2016 Jan 
Hsiao C,Liu M,Stanton R,McGee M,Qian Y, Scheuermann RH.
Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure
Cytometry A. 2016 Jan;89(1):71-88. doi: 10.1002/cyto.a.22735. Epub 2015 Aug 14. PMID:26274018

2015 Dec
Angela R. Branche, Edward E. Walsh, Roberto Vargas, Barbara Hulbert, Maria A. Formica,  Andrea Baran, Derick R. Peterson, and Ann R. Falsey
Serum Prolactonin Measurement and Viral Testing to Guide Antibiotic Use for Respiratory Infections in Hospitalized Adults: A Randomized Controlled Trial.
J Infect Dis. 2015 Apr 24. pii: jiv252. PMID: 25910632

2015 Dec
Eby JC, Hoffman CL, Gonyar LA, Hewlett EL.
Review of the neutrophil response to Bordetella pertussis infection.
Pathog Dis. 2015 Dec;73(9):ftv081. doi: 10.1093/femspd/ftv081. Epub 2015 Oct 2. PMID: 26432818

2015 Dec
Scheible KM, Emo J, Yang H, Holden-Wiltse J, Straw A, Huyck H, Misra S, Topham DJ, Ryan RM, Reynolds, AM, Mariani TJ and Pryhuber GS
Developmentally determined reduction in CD31 during gestation is associated with CD8+ T cell effector differentiation in preterm infants.
Clin Immunol. 2015 Jul 29. pii: S1521-6616(15)30007-3. doi: 10.1016/j.clim.2015.07.003. PMID: 26232733

2015 Dec
Pryhuber GS
Postnatal Infections and Immunology Affecting Chronic Lung Disease of Prematurity.
Clin Perinatol. 2015 Dec;42(4):697-718. doi: 10.1016/j.clp.2015.08.002. Epub 2015 Oct 1. PMID: 26593074

2015 Oct
Halliley JL, Khurana S, Krammer F, Fitzgerald T, Coyle EM, Chung KY, Baker SF, Yang H, Martínez-Sobrido L, Treanor JJ, Subbarao K, Golding H, Topham DJ, Sangster MY
High-Affinity H7 Head and Stalk Domain-Specific Antibody Responses to an Inactivated Influenza H7N7 Vaccine After Priming With Live Attenuated Influenza Vaccine.
J Infect Dis. 2015 Apr 2. pii: jiv210. PMID: 25838266

2015 Oct
Terajima M, Co MD, Cruz J, Ennis FA
High Antibody-Dependent Cellular Cytotoxicity Antibody Titers to H5N1 and H7N9 Avian Influenza A Viruses in Healthy US Adults and Older Children.
J Infect Dis. 2015 Mar 20. pii: jiv18. PMID: 25795791

2015 Sept
Leddon SA, Richards KA, Treanor JJ, Sant AJ.
Abundance and specificity of influenza reactive circulating memory Tfh and non-Tfh CD4 T cells in healthy adults.
Immunology. 2015 Sep;146(1):157-62. doi: 10.1111/imm.12491. Epub 2015 Jul 14. PMID: 26094691

2015 Aug
Bucukovski J, Latorre-Margalef N, Stallknecht DE, Miller BL
A Multiplex Label-Free Approach to Avian Influenza Surveillance and Serology.
PLoS One. 2015 Aug 4;10(8):e0134484. doi: 10.1371/journal.pone.0134484. eCollection 2015. PMID: 26241048

2015 Aug
Domm W, Misra RS, O'Reilly MA.
Affect of Early-Life Oxygen Exposure on Proper Lung Development and Response to Respiratory Viral Infection.
Front Med (Lausanne). 2015 Aug 10;2:55. doi: 10.3389/fmed.2015.00055. eCollection 2015. PMID: 26322310

2015 July
Richards KA, Nayak J, Chaves FA, DiPiazza A, Knowlden ZA, Alam S, Treanor JJ, Sant AJ
Seasonal Influenza Can Poise Hosts for CD4 T-Cell Immunity to H7N9 Avian Influenza.
J Infect Dis. 2015 Jul 1;212(1):86-94. doi: 10.1093/infdis/jiu662. PMID: 25492919

2015 Jul
Qian Y, Kim H, Purawat S, Wang J, Stanton R, Lee A, Xu W, Altintas I, Sinkovits R, Scheuermann RH
FlowGate: Towards Extensible and Scalable Web-based Flow Cytometry Data Analysis
Proceedings of the 4th Annual XSEDE (Extreme Science and Engineering Discovery Environment) Conference, St. Louis, MO, July 26-30, 2015, ACM Press.

2015 Jul
Geno KA, Gilbert GL, Song JY, Skovsted IC, Klugman KP, Jones C, Konradsen HB, Nahm MH.
Pneumococcal Capsules and Their Types: Past, Present, and Future.
Clin Microbiol Rev. 2015 Jul;28(3):871-99. doi: 10.1128/CMR.00024-15. PMID: 26085553

2015 May
Misra RS, Shah S, Fowell DJ, Wang H, Scheible K, Misra SK, Huyck H, Wyman CP, Ryan RM, Reynolds AM, Mariani TJ, Katzman PJ, Pryhuber GS.
Preterm cord blood CD4T cells exhibit increased IL-6 production in chorioamnionitis and decreased CD4T cells in bronchopulmonary dysplasia.
Hum Immunol. 2015 May;76(5):329-38. doi: 10.1016/j.humimm.2015.03.007. Epub 2015 Mar 20. PMID: 25797206

2015 May
Wu H, Miao H, Xue H, Topham DJ, Zand M
Quantifying Immune Response to Influenza Virus Infection via Multivariate Nonlinear ODE Models with Partially Observed State Variables and Time-Varying Parameters.
Stat Biosci. 2015 May 1;7(1):147-166. PMID: 26085850

2015 May
Henkle E, Hedberg K, Schafer S, Novosad AS, Winthrop KL
Population-based incidence of pulmonary nontuberculous mycobacterial disease in Oregon 2007-2012.
Ann Am Thorac Soc. 2015 May;12(5):642-7. doi: 10.1513/AnnalsATS.201412-559OC. PMID: 25692495

2015 May 
Maitre NL, Ballard RA, Ellenberg JH, Davis SD, Greenberg JM, Hamvas A, Pryhuber GS
Respiratory consequences of prematurity: evolution of a diagnosis and development of a comprehensive approach.
J Perinatol. 2015 May;35(5):313-21. doi: 10.1038/jp.2015.19. PMID: 25811285

2015 May
Lee AJ, Das SR, Wang W, Fitzgerald T, Pickett BE, Aevermann BD, Topham DJ, Falsey AR, Scheuermann RH.
Diversifying selection analysis predicts antigenic evolution of 2009 pandemic H1N1 influenza A virus in humans.
J Virol. 2015 May;89(10):5427-40. doi: 10.1128/JVI.03636-14. PMID: 25741011

2015 Apr
Pryhuber GS, Maitre, NL, Ballard RA, Cifelli D, Davis SD, Ellenberg JH, Greenberg JM, Kemp J, Mariani TJ, Panitch H, Ren C, Shaw P, Taussig LM, Hamvas, A
Prematurity and Respiratory Outcomes Program. Prematurity and Respiratory Outcome Program (PROP): Study Protocol of a Prospective Multicenter Study Of Respiratory Outcomes of Preterm Infants in the United States.
BMC Pediatr. 2015 Apr 10;15:37. doi: 10.1186/s12887-015-0346-3. PMID: 25886363

2015 Mar
Henkle E, Winthrop KL.
Nontuberculous mycobacteria infections in immunosuppressed hosts.
Clin Chest Med. 2015 Mar;36(1):91-9. doi: 10.1016/j.ccm.2014.11.002. PMID: 25676522

2014 Nov
Misra RS.
A Review of the CD4+ T Cell Contribution to Lung Infection, Inflammation and Repair with a Focus on Wheeze and Asthma in the Pediatric Population.
EC Microbiol. 2014;1(1):4-14. PMID:26280024

2014 Oct
Bhattacharya S, Zhou Z, Yee M, Chu CY, Lopez AM, Lunger VA, Solleti SK, Resseguie E, Buczynski B, Mariani TJ, O'Reilly MA
The genome-wide transcriptional response to neonatal hyperoxia identifies Ahr as a key regulator.
Am J Physiol Lung Cell Mol Physiol. 2014 Oct 1;307(7):L516-23. doi: 10.1152/ajplung.00200.2014. PMID: 25150061

2014 Oct
Branche AR, Walsh EE, Formica MA, Falsey AR.
Detection of Respiratory Viruses in Sputum from Adults Using Automated Multiplex Polymerase Chain Reaction (PCR).
J Clin Microbiol. 2014 Oct;52(10):3590-6. doi: 10.1128/JCM.01523-14. PMID: 25056335

2014 Jan 
Brady A, Spencer B, Falsey AR, Nahm MH.
Blood collection tubes influence serum ficolin-5 1 and ficolin-2 levels.
Clin Vaccine Immunol. 2014 Jan;21(1):51-5. doi: 10.1128/CVI.00607-13. PMID:24173025

2014 Jan
Alam S, Knowlden ZA, Sangster MY, Sant AJ
CD4 T cell help is limiting and selective during the primary B cell response to influenza virus infection.
J Virol. 2014 Jan;88(1):314-24. doi: 10.1128/JVI.02077-13. PMID: 24155379

2013 Jul 
Tung J, Sant AJ
Orchestration of CD4 T cell epitope preferences after multipeptide immunization.
J Immunol. 2013 Jul 15;191(2):764-72. doi: 10.4049/jimmunol.1300312. PMID:23772029

2012 Oct 
Leddon SA, Sant AJ.
The Peptide specificity of the endogenous T follicular helper cell repertoire generated after protein immunization.
PLoS One. 7(10):e46952. PMID: 23077537