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RPRC Publications

2019 February
Tesini BL, Kanagaiah P, Wang J, Hahn M, Halliley JL, Chaves FA, Nguyen PQT, Nogales A, DeDiego ML, Anderson CS, Ellebedy AH, Strohmeier S, Krammer F, Yang H, Bandyopadhyay S, Ahmed R, Treanor JJ, Martinez-Sobrido L, Golding H, Khurana S, Zand MS, Topham DJ, Sangster MY
Broad hemagglutinin-specific memory B cell expansion by seasonal influenza virus infection reflects early-life imprinting and adaptation to the infecting virus.
J Virol. 2019 Feb 6. pii: JVI.00169-19. doi: 10.1128/JVI.00169-19. PMID: 30728266

2018 October
Grier A, McDavid A, Wang B, Qiu X, Java J, Bandyopadhyay S, Yang H, Holden-Wiltse J, Kessler HA, Gill AL, Huyck H, Falsey AR, Topham DJ, Scheible KM, Caserta MT, Pryhuber GS, Gill SR
Neonatal gut and respiratory microbiota: coordinated development through time and space.
Microbiome. 2018 Oct 26;6(1):193. doi: 10.1186/s40168-018-0566-5. PMID: 30367675

2018 July
Roumanes D, Falsey AR, Quataert S, Secor-Socha S, Lee FE, Yang H, Bandyopadhyay S, Holden-Wiltse J, Topham DJ, Walsh EE
T-Cell Responses in Adults During Natural Respiratory Syncytial Virus Infection.
J Infect Dis. 2018 Jul 2;218(3):418-428. PMID: 29920599

2018 July
Wu, L., Qiu, X., Yuan, Y.X., and Wu, H
Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach
Journal of American Statistical Association

2018 July
Branche AR, Yang H, Java J, Holden-Wiltse J, Topham DJ, Peasley M, Frost MR, Nahm MH, Falsey AR
Effect of prior vaccination on carriage rates of Streptococcus pneumoniae in older adults: A longitudinal surveillance study.
Vaccine. 2018 Jul 5;36(29):4304-4310. doi: 10.1016/j.vaccine.2018.05.107. PMID: 29871816

2018 June
Branche AR, Yang H, Java J, Wiltse-Holden J, Topham DJ, Peasley M, Frost MR, Nahm MH, Falsey AR
Effect of prior vaccination on carriage rates of Streptococcus pneumoniae in older adults: A longitudinal surveillance study
Vaccine. 2018 June 2

2018 June
Lee AJ, Chang I, Burel JG, Lindestam Arlehamn CS, Mandava A, Weiskopf D, Peters B, Sette A, Scheuermann RH, Qian Y
DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data.
Cytometry A. 2018 Jun;93(6):597-610. doi: 10.1002/cyto.a.23371. PMID: 29665244

2018 April
Burton RL, Kim HW, Lee S, Kim H, Seok JH, Lee SH, Balloch A, Licciardi P, Marimla R, Bae S, Nahm MH, Kim KH
Creation, characterization, and assignment of opsonic values for a new pneumococcal OPA calibration serum panel (Ewha QC sera panel A) for 13 serotypes.
Medicine (Baltimore). 2018 Apr;97(17):e0567. PMID: 29703046

2018 Mar
Jennings-Gee J, Quataert S, Ganguly T, D'Agostino R Jr, Deora R, Dubey P
The adjuvant Bordetella Colonization Factor A attenuates alum-induced Th2 responses and enhances Bordetella pertussis clearance from mouse lungs.
Infect Immun. 2018 Mar 12. pii: IAI.00935-17. doi: 10.1128/IAI.00935-17. PMID: 29531137

2018 Mar
Walsh EE, Wang L, Falsey AR, Qiu X, Corbett A, Holden-Wiltse J, Mariani TJ, Topham DJ, Caserta MT
Virus-specific aNtibody, Viral Load and Disease Severity in Respiratory Syncytial Virus Infection.
J Infect Dis. 2018 Mar 13. doi: 10.1093/infdis/jiy106. PMID: 29546402

2018 Feb
Scheible KM, Emo J, Laniewski N, Baran AM, Peterson DR, Holden-Wiltse J, Bandyopadhyay S, Straw AG, Huyck H, Ashton JM, Tripi KS, Arul K, Werner E, Scalise T, Maffett D, Caserta M, Ryan RM, Reynolds AM, Ren CL, Topham DJ, Mariani TJ, Pryhuber GS
T cell developmental arrest in former premature infants increases risk of respiratory morbidity later in infancy.
JCI Insight. 2018 Feb 22;3(4). pii: 96724. doi: 10.1172/jci.insight.96724. PMID: 29467329

2018 Jan
Grier A, McDavid A, Wang B, Qui X, Java J, Bandyopadhyay S, Holden-Wiltse J, Kessler HA, Gill AL, Huyck H, Falsey AR, Topham DJ, Scheible KM, Caserta MT, Pryhuber GS, Gill SR
Neonate gut and respiratory microbiota: coordinated development through time and space
bioRxiv. 2018 Jan. doi:

2018 Jan
Jackson LA, El Sahly HM, George S, Winokur P, Edwards K, Brady RC, Rouphael N, Keitel WA, Mulligan MJ, Burton RL, Nakamura A, Ferreria J, Nahm MH
Randomized clinical trial of a single versus a double dose of 13-valent pneumococcal conjugate vaccine in adults 55 through 74 years of age previously vaccinated with 23-valent pneumococcal polysaccharide vaccine.
 2018 Jan 29;36(5):606-614. doi: 10.1016/j.vaccine.2017.12.061. PMID: 29279281

2017 Dec
Grier A, Qiu X, Bandyopadhyay S, Holden-Wiltse J, Kessler HA, Gill AL, Hamilton B, Huyck H, Misra S, Mariani TJ, Ryan RM, Scholer L, Scheible KM, Lee YH, Caserta MT, Pryhuber GS, Gill SR
Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth.
Microbiome. 2017 Dec 11;5(1):158. doi: 10.1186/s40168-017-0377-0. PMID: 29228972

2017 Dec
Liu Y, Zhang J, Qiu X
Super-delta: a new differential gene expression analysis procedure with robust data normalization.
BMC Bioinformatics. 2017 Dec 21;18(1):582. doi: 10.1186/s12859-017-1992-2. PMID: 29268715

2017 Dec
Wu, L., Qiu, X., Yuan, Y.X., and Wu, H.
Parameter Estimation and Variable Selection for Big systems of High-Dimensional Linear ordinary Differential Equations: A Matrix-Based Approach.
Journal of American Statistical Association, in press.

2017 Nov
Mariani TJ, Qiu X, Chu C, Wang L, Thakar J, Holden-Wiltse J, Corbett A, Topham DJ, Falsey AR, Caserta MT, Walsh EE
Association of Dynamic Changes in the CD4 T-Cell Transcriptome With Disease Severity During Primary Respiratory Syncytial Virus Infection in Young Infants.
J Infect Dis. 2017 Nov 15;216(8):1027-1037. doi: 10.1093/infdis/jix400. PMID: 28962005

2017 Nov
Chen I, Kelkar YD, Gu Y, Zhou J, Qiu X, Wu H
High-dimensional linear state space models for dynamic microbial interaction networks.
PLoS One. 2017 Nov 15;12(11):e0187822. doi: 10.1371/journal.pone.0187822. PMID: 29141044

2017 Nov
Dorji D, Mooi F, Yantorno O, Deora R, Graham RM, Mukkur TK
Bordetella Pertussis virulence factors in the continuing evolution of whooping cough vaccines for improved performance.
Med Microbiol Immunol. 2017 Nov 21. doi: 10.1007/s00430-017-0524-z. PMID: 29164393

2017 Nov
Anderson CS, Ortega S, Chaves FA, Clark AM, Yang H, Topham DJ, DeDiego ML
Natural and directed antigenic drift of the H1 influenza virus hemagglutinin stalk domain.
Sci Rep. 2017 Nov 6;7(1):14614. doi: 10.1038/s41598-017-14931-7. PMID: 29097696

2017 Oct
Henkle E, Hedberg K, Schafer SD, Winthrop KL.
Surveillance of Extrapulmonary Nontuberculous Mycobacteria Infections, Oregon, USA, 2007-2012.
Emerg Infect Dis. 2017 Oct;23(10):1627-1630. doi: 10.3201/eid2310.170845. PMID: 28930014

2017 Sept
Geno KA, Bush CA, Wang M, Jin C, Nahm MH, Yang J
WciG O-Acetyltransferase Functionality Differentiates Pneumococcal Serotypes 35C and 42.
J Clin Microbiol. 2017 Sep;55(9):2775-2784. doi: 10.1128/JCM.00822-17. PMID: 28659323

2017 Sept
Gregoire SA, Byam J, Pavelka MS
galK-based suicide vector mediated allelic exchange in Mycobacterium abscessus.
Microbiology. 2017 Sep 21. doi: 10.1099/mic.0.000528. PMID: 28933689

2017 July
Bhattacharya S, Rosenberg AF, Peterson DR, Grzesik K, Baran AM, Ashton JM, Gill SR, Corbett AM, Holden-Wiltse J, Topham DJ, Walsh EE, Mariani TJ, Falsey AR
Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness.
Sci Rep. 2017 Jul 26;7(1):6548. doi: 10.1038/s41598-017-06738-3. PMID: 28747714

2017 July
Pedersen NW, Chandran PA, Qian Y, Rebhahn J, Petersen NV, Hoff MD, White S, Lee AJ, Stanton R, Halgreen C, Jakobsen K, Mosmann T, Gouttefangeas C, Chan C, Scheuermann RH, Hadrup SR
Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells.
Front Immunol. 2017 Jul 26;8:858. doi: 10.3389/fimmu.2017.00858. PMID: 28798746

2017 July
Nicholson TL, Brockmeier SL, Sukumar N, Paharik AE, Lister JL, Horswill AR, Kehrli ME Jr, Loving CL, Shore SM, Deora R
The Bordetella Bps Polysaccharide Is Required for Biofilm Formation and Enhances Survival in the Lower Respiratory Tract of Swine.
Infect Immun. 2017 Jul 19;85(8). pii: e00261-17. doi: 10.1128/IAI.00261-17. PMID: 28559403

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, J. Hall, D. Boehm, M. Barbier, F. H. Damron
Development of RNAseq methodologies to profile the in-vivo transcriptome of Bordetella pertussis during murine lung infection.
bioRxiv. 2017 May. doi: 

2017 May
Yang H, Holden-Wiltse J, Topham DJ, Treanor J
Maximum Likelihood Estimation of Titer via a Power Family of Four-Parameter Logistic Model.
J Biopharm Stat. 2017 May 25:1-9. doi: 10.1080/10543406.2017.1333996. PMID: 28541821

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: 

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
Carbonetti NH, Wirsing von König CH, Lan R, Jacob-Dubuisson F, Cotter PA, Deora R, Merkel TJ, van Els CA, Locht C, Hozbor D, Rodriguez ME
Highlights of the 11th International Bordetella Symposium: from Basic Biology to Vaccine Development.
Clin Vaccine Immunol. 2016 Nov 4;23(11):842-850. PMID: 27655886

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
Billroth-MacLurg AC, Ford J, Rosenberg A, Miller J, Fowell DJ
Regulatory T Cell Numbers in Inflamed Skin Are Controlled by Local Inflammatory Cues That Upregulate CD25 and Facilitate Antigen-Driven Local Proliferation.
J Immunol. 2016 Sep 15;197(6):2208-18. doi: 10.4049/jimmunol.1502575. PMID: 27511734

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
Knowlden ZA, Sant AJ
CD4 T cell epitope specificity determines follicular versus non-follicular helper differentiation in the polyclonal response to influenza infection or vaccination.
Sci Rep. 2016 Jun 22;6:28287. doi: 10.1038/srep28287. PMID: 27329272

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 May
Wright PF, Hoen AG, Ilyushina NA, Brown EP, Ackerman ME, Wieland-Alter W, Connor RI, Jegaskanda S, Rosenberg-Hasson Y, Haynes BC, Luke CJ, Subbarao K, Treanor JJ
Correlates of Immunity to Influenza as Determined by Challenge of Children with Live, Attenuated Influenza Vaccine.
Open Forum Infect Dis. 2016 May 23;3(2):ofw108. doi: 10.1093/ofid/ofw108. PMID: 27419180

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 Mar
Misra RS
The Microbiome, Antibiotics, and Health of the Pediatric Population.
EC Microbiol. 2016 Mar;3(1):388-390. PMID: 27390782

2016 Mar
Liu B, Qiu X, Zhu T, Tian W, Hu R, Ekholm S, Schifitto G, Zhong J.
Improved spatial regression analysis of diffusion tensor imaging for lesion detection during longitudinal progression of multiple sclerosis in individual subjects.
Phys Med Biol. 2016 Mar 21;61(6):2497-513. doi: 10.1088/0031-9155/61/6/2497. PMID: 26948513

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
Fodil M, Teixeira VH, Chaudru V, Hilliquin P, Bombardieri S, Balsa A, Westhovens R, Barrera P, Alves H, Migliorin P, Bardin T, Cornelis F, Boudjema A, Petit-Teixeira E.
Relationship between SNPs and expression level for candidate genes in rheumatoid arthritis.
Scand J Rheumatol. 2015;44(1):2-7. doi: 10.3109/03009742.2014.918175. PMID: 25221852

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
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 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