Publications

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. Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first-in-human phase 1 clinical trial. Lancet, (390), 10101, pp. 1511–1520, 2017.

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. Higher T-Cell Responses Induced by DNA/rAd5 HIV-1 Preventive Vaccine Are Associated With Lower HIV-1 Infection Risk in an Efficacy Trial. J. Infect. Dis., (215), 9, pp. 1376–1385, 2017.

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. DNA Priming Increases Frequency of T-Cell Responses to a Vesicular Stomatitis Virus HIV Vaccine with Specific Enhancement of CD8+ T-Cell Responses by Interleukin-12 Plasmid DNA. Clin. Vaccine Immunol., (24), 11, 2017.

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. Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells. PLoS Pathog., (13), 6, pp. e1006445, 2017.

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. Circulating Mycobacterium tuberculosis DosR latency antigen-specific, polyfunctional, regulatory IL10+ Th17 CD4 T-cells differentiate latent from active tuberculosis. Sci Rep, (7), 1, pp. 11948, 2017.

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. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium. Sci Rep, (6), pp. 20686, 2016.

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. The contribution of cell cycle to heterogeneity in single-cell RNA-seq data. Nat. Biotechnol., (34), 6, pp. 591–593, 2016.

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. Promises and Pitfalls of High-Throughput Biological Assays. Methods Mol. Biol., (1415), pp. 225–243, 2016.

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. Pooled-Peptide Epitope Mapping Strategies Are Efficient and Highly Sensitive: An Evaluation of Methods for Identifying Human T Cell Epitope Specificities in Large-Scale HIV Vaccine Efficacy Trials. PLoS ONE, (11), 2, pp. e0147812, 2016.

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. Distinct activation thresholds of human conventional and innate-like memory T cells. JCI Insight, (1), 8, 2016.

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. Automated analysis of flow cytometry data comes of age. Cytometry A, (89), 1, pp. 13–15, 2016.

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. A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes. Cytometry A, (89), 1, pp. 16–21, 2016.

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. COMPASS identifies T-cell subsets correlated with clinical outcomes. Nat. Biotechnol., (33), 6, pp. 610–616, 2015.

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. flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification. Bioinformatics, (31), 4, pp. 606–607, 2015.

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. Thinking outside the gate: single-cell assessments in multiple dimensions. Immunity, (42), 4, pp. 591–592, 2015.

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. T Cell Responses against Mycobacterial Lipids and Proteins Are Poorly Correlated in South African Adolescents. J. Immunol., (195), 10, pp. 4595–4603, 2015.

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. State-of-the-Art in the Computational Analysis of Cytometry Data. Cytometry A, (87), 7, pp. 591–593, 2015.

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. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol., (16), pp. 278, 2015.

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. Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data. Cytometry A, (87), 7, pp. 675–682, 2015.

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. OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis. PLoS Comput. Biol., (10), 8, pp. e1003806, 2014.

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. Modeling bi-modality improves characterization of cell cycle on gene expression in single cells. PLoS Comput. Biol., (10), 7, pp. e1003696, 2014.

. Mixture models for single-cell assays with applications to vaccine studies. Biostatistics, (15), 1, pp. 87–101, 2014.

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. High-throughput flow cytometry data normalization for clinical trials. Cytometry A, (85), 3, pp. 277–286, 2014.

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. Highly multiplexed quantitation of gene expression on single cells. J. Immunol. Methods, (391), 1-2, pp. 133–145, 2013.

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. Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics, (29), 4, pp. 461–467, 2013.

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. Critical assessment of automated flow cytometry data analysis techniques. Nat. Methods, (10), 3, pp. 228–238, 2013.

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. QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data. BMC Bioinformatics, (13), pp. 252, 2012.

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. Hypoxia promotes ligand-independent EGF receptor signaling via hypoxia-inducible factor-mediated upregulation of caveolin-1. Proc. Natl. Acad. Sci. U.S.A., (109), 13, pp. 4892–4897, 2012.

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. Gene-expression profiling of microdissected breast cancer microvasculature identifies distinct tumor vascular subtypes. Breast Cancer Res., (14), 4, pp. R120, 2012.

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. Optimizing transformations for automated, high throughput analysis of flow cytometry data. BMC Bioinformatics, (11), pp. 546, 2010.

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. In silico ascription of gene expression differences to tumor and stromal cells in a model to study impact on breast cancer outcome. PLoS ONE, (5), 11, pp. e14002, 2010.

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. [The tumor microenvironment: a new tool to predict breast cancer outcome]. Med Sci (Paris), (25), 5, pp. 439–441, 2009.

. Regulation of endocytosis via the oxygen-sensing pathway. Nat. Med., (15), 3, pp. 319–324, 2009.

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. Merging mixture components for cell population identification in flow cytometry. Adv Bioinformatics, pp. 247646, 2009.

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. Stromal gene expression predicts clinical outcome in breast cancer. Nat. Med., (14), 5, pp. 518–527, 2008.

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. Gene expression signatures of morphologically normal breast tissue identify basal-like tumors. Breast Cancer Res., (8), 5, pp. R58, 2006.

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. BIAS: Bioinformatics Integrated Application Software. Bioinformatics, (21), 8, pp. 1745–1746, 2005.

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. An NMR approach to structural proteomics. Proc. Natl. Acad. Sci. U.S.A., (99), 4, pp. 1825–1830, 2002.

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