Center-Authored Papers

Filters: Author is Gottardo, Raphael  [Clear All Filters]
2010
Finak G, Perez J-M, Weng A, Gottardo R.  2010.  Optimizing transformations for automated, high throughput analysis of flow cytometry data.. BMC bioinformatics. 11:546. Abstract
2012
Scott-Boyer MP, Imholte GC, Tayeb A, Labbe A, Deschepper CF, Gottardo R.  2012.  An Integrated Hierarchical Bayesian Model for Multivariate eQTL Mapping.. Statistical applications in genetics and molecular biology. 11(4) Abstract
Zhang X, Robertson G, Woo S, Hoffman BG, Gottardo R.  2012.  Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data.. PloS one. 7(2):e32095. Abstract
Huang Y, Gottardo R.  2012.  Comparability and reproducibility of biomedical data.. Briefings in bioinformatics. Abstract
Lo K, Gottardo R.  2012.  Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution.. Statistics and computing. 22(1):33-52. Abstract
Bashashati A, Johnson NA, Khodabakhshi AH, Whiteside MD, Zare H, Scott DW, Lo K, Gottardo R, Brinkman FSL, Connors JM et al..  2012.  B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma.. American journal of clinical pathology. 137(5):805-14. Abstract
Karasavvas N, Billings E, Rao M, Williams C, Zolla-Pazner S, Bailer RT, Koup RA, Madnote S, Arworn D, Shen X et al..  2012.  The Thai Phase III HIV Type 1 Vaccine Trial (RV144) Regimen Induces Antibodies That Target Conserved Regions Within the V2 Loop of gp120.. AIDS research and human retroviruses. 28(11):1444-57. Abstract
Finak G, Jiang W, Pardo J, Asare A, Gottardo R.  2012.  QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data.. BMC bioinformatics. 13(1):252. Abstract
Caron F, Doucet A, Gottardo R.  2012.  On-line changepoint detection and parameter estimation with application to genomic data. Statistics and Computing. 22(2):579-595.
2013
Zolla-Pazner S, Decamp AC, Cardozo T, Karasavvas N, Gottardo R, Williams C, Morris DE, Tomaras G, Rao M, Billings E et al..  2013.  Analysis of V2 antibody responses induced in vaccinees in the ALVAC/AIDSVAX HIV-1 vaccine efficacy trial.. PloS one. 8(1):e53629. Abstract
Gottardo R, Bailer RT, Korber BT, Gnanakaran S, Phillips J, Shen X, Tomaras GD, Turk E, Imholte G, Eckler L et al..  2013.  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.. PloS one. 8(9):e75665. Abstract
Casazza JP, Bowman KA, Adzaku S, Smith EC, Enama ME, Bailer RT, Price DA, Gostick E, Gordon IJ, Ambrozak DR et al..  2013.  Therapeutic Vaccination Expands and Improves the Function of the HIV-Specific Memory T-Cell Repertoire.. The Journal of infectious diseases. Abstract
Woo S, Zhang X, Sauteraud R, Robert F, Gottardo R.  2013.  PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.. Bioinformatics (Oxford, England). 29(16):2049-50. Abstract
Finak G, Jiang W, Krouse K, Wei C, Sanz I, Phippard D, Asare A, De Rosa SC, Self S, Gottardo R.  2013.  High-throughput flow cytometry data normalization for clinical trials.. Cytometry. Part A : the journal of the International Society for Analytical Cytology. Abstract
Finak G, McDavid A, Chattopadhyay P, Dominguez M, De Rosa S, Roederer M, Gottardo R.  2013.  Mixture models for single-cell assays with applications to vaccine studies.. Biostatistics (Oxford, England). Abstract
Imholte GC, Sauteraud R, Korber B, Bailer RT, Turk ET, Shen X, Tomaras GD, Mascola JR, Koup RA, Montefiori DC et al..  2013.  A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling.. Journal of immunological methods. Abstract
Aghaeepour N, Finak G, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH.  2013.  Critical assessment of automated flow cytometry data analysis techniques.. Nature methods. 10(3):228-38. Abstract
Dominguez MH, Chattopadhyay PK, Ma S, Lamoreaux L, McDavid A, Finak G, Gottardo R, Koup RA, Roederer M.  2013.  Highly multiplexed quantitation of gene expression on single cells.. Journal of immunological methods. 391(1-2):133-45. Abstract
Imholte GC, Scott-Boyer M-P, Labbe A, Deschepper CF, Gottardo R.  2013.  iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.. Bioinformatics (Oxford, England). Abstract
2014
Vojtech L, Woo S, Hughes S, Levy C, Ballweber L, Sauteraud RP, Strobl J, Westerberg K, Gottardo R, Tewari M et al..  2014.  Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions.. Nucleic acids research. 42(11):7290-304. Abstract
Lemos MP, Lama JR, Karuna ST, Fong Y, Montano SM, Ganoza C, Gottardo R, Sanchez J, McElrath MJ.  2014.  The inner foreskin of healthy males at risk of HIV infection harbors epithelial CD4+ CCR5+ cells and has features of an inflamed epidermal barrier.. PloS one. 9(9):e108954. Abstract
McDavid A, Dennis L, Danaher P, Finak G, Krouse M, Wang A, Webster P, Beechem J, Gottardo R.  2014.  Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells.. PLoS computational biology. 10(7):e1003696. Abstract
DeCamp A, Hraber P, Bailer RT, Seaman MS, Ochsenbauer C, Kappes J, Gottardo R, Edlefsen P, Self S, Tang H et al..  2014.  Global Panel of HIV-1 Env Reference Strains for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies.. Journal of virology. 88(5):2489-507. Abstract
Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, Kijak GH et al..  2014.  Analysis of HLAA*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial.. Journal of virology. Abstract
Zolla-Pazner S, Edlefsen PT, Rolland M, Kong X-P, DeCamp A, Gottardo R, Williams C, Tovanabutra S, Sharpe-Cohen S, Mullins JI et al..  2014.  Vaccine-induced Human Antibodies Specific for the Third Variable Region of HIV-1 gp120 Impose Immune Pressure on Infecting Viruses.. EBioMedicine. 1(1):37-45. Abstract