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Results: 1 to 20 of 82

1.

flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.

Malek M, Taghiyar MJ, Chong L, Finak G, Gottardo R, Brinkman RR.

Bioinformatics. 2014 Oct 16. pii: btu677. [Epub ahead of print]

PMID:
25378466
[PubMed - as supplied by publisher]
2.

Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial.

Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Bose M, Arroyo MA, O'Connell RJ, deSouza MS, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, McLellan JS, Georgiev IS, Kirys T, Kwong PD, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB.

AIDS Res Hum Retroviruses. 2014 Oct;30 Suppl 1:A25-6. doi: 10.1089/aid.2014.5036.abstract. No abstract available.

PMID:
25357702
[PubMed - in process]
3.

Integrated Systems Biology Analysis Reveals Contrasting Role for Innate Immune Response Genes in Conferring Risk of Infection in RV144 Trial.

Filali-Mouhim A, Fourati S, Lefebvre F, Thomas R, Gottardo R, Frahm N, De Rosa S, Wilkinson P, Stafova P, Sabnis A, Kaewkungwal J, Pitisuttithum P, Nitayanphan S, Rerks-Ngarm S, Michael N, Kim J, Robb ML, O'Connell RJ, McElrath MJ, Cameron M, Sekaly R.

AIDS Res Hum Retroviruses. 2014 Oct;30 Suppl 1:A15-6. doi: 10.1089/aid.2014.5017a.abstract. No abstract available.

PMID:
25357419
[PubMed - in process]
4.

The inner foreskin of healthy males at risk of HIV infection harbors epithelial CD4+ CCR5+ cells and has features of an inflamed epidermal barrier.

Lemos MP, Lama JR, Karuna ST, Fong Y, Montano SM, Ganoza C, Gottardo R, Sanchez J, McElrath MJ.

PLoS One. 2014 Sep 30;9(9):e108954. doi: 10.1371/journal.pone.0108954. eCollection 2014.

PMID:
25268493
[PubMed - in process]
Free PMC Article
5.

OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.

Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, Kalams SA, De Rosa SC, Gottardo R.

PLoS Comput Biol. 2014 Aug 28;10(8):e1003806. doi: 10.1371/journal.pcbi.1003806. eCollection 2014 Aug.

PMID:
25167361
[PubMed - in process]
Free PMC Article
6.

FCGR2C polymorphisms associate with HIV-1 vaccine protection in RV144 trial.

Li SS, Gilbert PB, Tomaras GD, Kijak G, Ferrari G, Thomas R, Pyo CW, Zolla-Pazner S, Montefiori D, Liao HX, Nabel G, Pinter A, Evans DT, Gottardo R, Dai JY, Janes H, Morris D, Fong Y, Edlefsen PT, Li F, Frahm N, Alpert MD, Prentice H, Rerks-Ngarm S, Pitisuttithum P, Kaewkungwal J, Nitayaphan S, Robb ML, O'Connell RJ, Haynes BF, Michael NL, Kim JH, McElrath MJ, Geraghty DE.

J Clin Invest. 2014 Sep 2;124(9):3879-90. doi: 10.1172/JCI75539. Epub 2014 Aug 8.

PMID:
25105367
[PubMed - in process]
Free PMC Article
7.

Modeling bi-modality improves characterization of cell cycle on gene expression in single cells.

McDavid A, Dennis L, Danaher P, Finak G, Krouse M, Wang A, Webster P, Beechem J, Gottardo R.

PLoS Comput Biol. 2014 Jul 17;10(7):e1003696. doi: 10.1371/journal.pcbi.1003696. eCollection 2014 Jul.

PMID:
25032992
[PubMed - in process]
Free PMC Article
8.

Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions.

Vojtech L, Woo S, Hughes S, Levy C, Ballweber L, Sauteraud RP, Strobl J, Westerberg K, Gottardo R, Tewari M, Hladik F.

Nucleic Acids Res. 2014;42(11):7290-304. doi: 10.1093/nar/gku347. Epub 2014 May 16.

PMID:
24838567
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial.

Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, Kijak GH, Edlefsen PT, Frahm N, Larsen BB, Tovanabutra S, Sanders-Buell E, deCamp AC, Magaret CA, Ahmed H, Goodridge JP, Chen L, Konopa P, Nariya S, Stoddard JN, Wong K, Zhao H, Deng W, Maust BS, Bose M, Howell S, Bates A, Lazzaro M, O'Sullivan A, Lei E, Bradfield A, Ibitamuno G, Assawadarachai V, O'Connell RJ, deSouza MS, Nitayaphan S, Rerks-Ngarm S, Robb ML, Sidney J, Sette A, Zolla-Pazner S, Montefiori D, McElrath MJ, Mullins JI, Kim JH, Gilbert PB, Hertz T.

J Virol. 2014 Aug;88(15):8242-55. doi: 10.1128/JVI.01164-14. Epub 2014 May 14.

PMID:
24829343
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium.

Brusic V, Gottardo R, Kleinstein SH, Davis MM; HIPC steering committee.

Nat Biotechnol. 2014 Feb;32(2):146-8. doi: 10.1038/nbt.2777. Epub 2014 Jan 19. No abstract available.

PMID:
24441472
[PubMed - indexed for MEDLINE]
11.

High-throughput flow cytometry data normalization for clinical trials.

Finak G, Jiang W, Krouse K, Wei C, Sanz I, Phippard D, Asare A, De Rosa SC, Self S, Gottardo R.

Cytometry A. 2014 Mar;85(3):277-86. doi: 10.1002/cyto.a.22433. Epub 2013 Dec 31.

PMID:
24382714
[PubMed - indexed for MEDLINE]
12.

Global panel of HIV-1 Env reference strains for standardized assessments of vaccine-elicited neutralizing antibodies.

deCamp A, Hraber P, Bailer RT, Seaman MS, Ochsenbauer C, Kappes J, Gottardo R, Edlefsen P, Self S, Tang H, Greene K, Gao H, Daniell X, Sarzotti-Kelsoe M, Gorny MK, Zolla-Pazner S, LaBranche CC, Mascola JR, Korber BT, Montefiori DC.

J Virol. 2014 Mar;88(5):2489-507. doi: 10.1128/JVI.02853-13. Epub 2013 Dec 18.

PMID:
24352443
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Immunological and virological mechanisms of vaccine-mediated protection against SIV and HIV.

Roederer M, Keele BF, Schmidt SD, Mason RD, Welles HC, Fischer W, Labranche C, Foulds KE, Louder MK, Yang ZY, Todd JP, Buzby AP, Mach LV, Shen L, Seaton KE, Ward BM, Bailer RT, Gottardo R, Gu W, Ferrari G, Alam SM, Denny TN, Montefiori DC, Tomaras GD, Korber BT, Nason MC, Seder RA, Koup RA, Letvin NL, Rao SS, Nabel GJ, Mascola JR.

Nature. 2014 Jan 23;505(7484):502-8. doi: 10.1038/nature12893. Epub 2013 Dec 18.

PMID:
24352234
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Dextromethorphan/levomethorphan issues in a case of opiate overdose.

Bortolotti F, Bertaso A, Gottardo R, Musile G, Tagliaro F.

Drug Test Anal. 2013 Sep-Oct;5(9-10):781-4. doi: 10.1002/dta.1577. No abstract available.

PMID:
24142584
[PubMed - indexed for MEDLINE]
15.

Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial.

Gottardo R, Bailer RT, Korber BT, Gnanakaran S, Phillips J, Shen X, Tomaras GD, Turk E, Imholte G, Eckler L, Wenschuh H, Zerweck J, Greene K, Gao H, Berman PW, Francis D, Sinangil F, Lee C, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Tartaglia J, Robb ML, Michael NL, Kim JH, Zolla-Pazner S, Haynes BF, Mascola JR, Self S, Gilbert P, Montefiori DC.

PLoS One. 2013 Sep 26;8(9):e75665. doi: 10.1371/journal.pone.0075665. eCollection 2013.

PMID:
24086607
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.

Imholte GC, Scott-Boyer MP, Labbe A, Deschepper CF, Gottardo R.

Bioinformatics. 2013 Nov 1;29(21):2797-8. doi: 10.1093/bioinformatics/btt485. Epub 2013 Aug 19.

PMID:
23958729
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Mixture models for single-cell assays with applications to vaccine studies.

Finak G, McDavid A, Chattopadhyay P, Dominguez M, De Rosa S, Roederer M, Gottardo R.

Biostatistics. 2014 Jan;15(1):87-101. doi: 10.1093/biostatistics/kxt024. Epub 2013 Jul 24.

PMID:
23887981
[PubMed - indexed for MEDLINE]
18.

Screening for synthetic cannabinoids in hair by using LC-QTOF MS: a new and powerful approach to study the penetration of these new psychoactive substances in the population.

Gottardo R, Sorio D, Musile G, Trapani E, Seri C, Serpelloni G, Tagliaro F.

Med Sci Law. 2014 Jan;54(1):22-7. doi: 10.1177/0025802413477396. Epub 2013 Jul 10.

PMID:
23842479
[PubMed - indexed for MEDLINE]
19.

PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.

Woo S, Zhang X, Sauteraud R, Robert F, Gottardo R.

Bioinformatics. 2013 Aug 15;29(16):2049-50. doi: 10.1093/bioinformatics/btt348. Epub 2013 Jun 20.

PMID:
23786769
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling.

Imholte GC, Sauteraud R, Korber B, Bailer RT, Turk ET, Shen X, Tomaras GD, Mascola JR, Koup RA, Montefiori DC, Gottardo R.

J Immunol Methods. 2013 Sep 30;395(1-2):1-13. doi: 10.1016/j.jim.2013.06.001. Epub 2013 Jun 13.

PMID:
23770318
[PubMed - indexed for MEDLINE]
Free PMC Article

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