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List of works by Raphael Gottardo

3M-052, a synthetic TLR-7/8 agonist, induces durable HIV-1 envelope-specific plasma cells and humoral immunity in nonhuman primates

scientific article published on 01 June 2020

A Functional Toll-Interacting Protein Variant Is Associated with Bacillus Calmette-Guérin-Specific Immune Responses and Tuberculosis

scientific article published on 2 May 2017

A Potent Anti-Malarial Human Monoclonal Antibody Targets Circumsporozoite Protein Minor Repeats and Neutralizes Sporozoites in the Liver

scientific article published on 15 September 2020

A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level

scientific article published on 01 April 2020

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

scientific article published on 08 October 2015

A composite immune signature parallels disease progression across T1D subjects

scientific article published on 05 December 2019

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

scientific article published on 13 June 2013

A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments

scientific article published on 20 September 2007

A pipeline for automated analysis of flow cytometry data: preliminary results on lymphoma sub-type diagnosis.

scientific article

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA

scientific article published in Nature Communications

Aggregating transcript-level analyses for single-cell differential gene expression

scientific article published on 01 June 2020

An integrated hierarchical Bayesian model for multivariate eQTL mapping.

scientific article

An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.

scientific article

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

scientific article

Analysis of V2 antibody responses induced in vaccinees in the ALVAC/AIDSVAX HIV-1 vaccine efficacy trial

scientific article

Analyzing Peptide Microarray Data with the R pepStat Package

scientific article

Antibody Fc effector functions and IgG3 associate with decreased HIV-1 risk

scientific article published on 01 November 2019

Automated analysis of flow cytometry data comes of age.

scientific article published in January 2016

Automated gating of flow cytometry data via robust model-based clustering

scientific article

B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma

scientific article

BCG revaccination boosts adaptive polyfunctional Th1/Th17 and innate effectors in IGRA+ and IGRA- Indian adults

scientific article published on 19 December 2019

Bayesian hierarchical modeling for subject-level response classification in peptide microarray immunoassays

scientific article published on 8 April 2016

Bayesian robust inference for differential gene expression in microarrays with multiple samples

scientific article published in March 2006

CD32 and PD-1 Lymph Node CD4 T Cells Support Persistent HIV-1 Transcription in Treated Aviremic Individuals

article

CD32+and PD-1+Lymph Node CD4 T Cells Support Persistent HIV-1 Transcription in Treated Aviremic Individuals

article

COMPASS identifies T-cell subsets correlated with clinical outcomes

scientific article

Characterization of two in vivo challenge models to measure functional activity of monoclonal antibodies to Plasmodium falciparum circumsporozoite protein

scientific article published on 17 March 2020

Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy

scientific article published on 10 January 2020

Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells

scientific article

Combining Mixture Components for Clustering ⬇️

scientific article published on June 1, 2010

Comparability and reproducibility of biomedical data ⬇️

scientific article (publication date: July 2013)

Comparative analysis of TCR and CAR signaling informs CAR designs with superior antigen sensitivity and in vivo function

scientific article published on 24 August 2021

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial

scientific article

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

scientific article

Controlled Human Malaria Infection Leads to Long-Lasting Changes in Innate and Innate-like Lymphocyte Populations.

scientific article published on 2 June 2017

Correction for Hraber et al., "Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments".

scientific article

Correction for Kibler et al., "Replication-Competent NYVAC-KC Yields Improved Immunogenicity to HIV-1 Antigens in Rhesus Macaques Compared to Nonreplicating NYVAC"

scientific article published on 15 October 2019

Correction: Musosal effects for tenofovir 1% gel.

scientific article published on 24 March 2015

Critical assessment of automated flow cytometry data analysis techniques

Critical assessment of automated flow cytometry data analysis techniques

Critical assessment of automated flow cytometry data analysis techniques.

scientific article

CytoML for cross-platform cytometry data sharing.

scientific article

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.

scientific article published on 20 September 2017

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.

scientific article

DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis

article by Greg Finak et al published 10 July 2018 in Gates Open Research

Development of a clinically relevant ovarian cancer model incorporating surgical cytoreduction to evaluate treatment of micro-metastatic disease

scientific article published on 20 November 2020

Distinct activation thresholds of human conventional and innate-like memory T cells

scientific article published on June 2016

Effect of Adding Motolimod to Standard Combination Chemotherapy and Cetuximab Treatment of Patients With Squamous Cell Carcinoma of the Head and Neck: The Active8 Randomized Clinical Trial

scientific article published on 01 November 2018

Engineered Adoptive T-cell Therapy Prolongs Survival in a Preclinical Model of Advanced-Stage Ovarian Cancer

scientific article published on 23 July 2019

Evaluation of the host transcriptional response to human cytomegalovirus infection

scientific article published on 17 June 2004

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

scientific article

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

scientific article

Flexible empirical Bayes models for differential gene expression

scientific article published on 30 November 2006

Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution

scientific article published on January 2012

GRAPHICAL MODELS FOR ZERO-INFLATED SINGLE CELL GENE EXPRESSION

scientific article published on 17 June 2019

Generation and characterization of a bivalent protein boost for future clinical trials: HIV-1 subtypes CR01_AE and B gp120 antigens with a potent adjuvant

scientific article published on 26 April 2018

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

scientific article

HIV/AIDS Vaccine Candidates Based on Replication-Competent Recombinant Poxvirus NYVAC-C-KC Expressing Trimeric gp140 and Gag-Derived Virus-Like Particles or Lacking the Viral Molecule B19 That Inhibits Type I Interferon Activate Relevant HIV-1-Speci

scientific article published on 8 February 2017

High-throughput flow cytometry data normalization for clinical trials.

scientific article

Higher T-Cell Responses Induced by DNA/rAd5 HIV-1 Preventive Vaccine Are Associated With Lower HIV-1 Infection Risk in an Efficacy Trial

scientific article published on 12 February 2017

Highly multiplexed quantitation of gene expression on single cells

scientific article published on 13 March 2013

Human MAIT cells exit peripheral tissues and recirculate via lymph in steady state conditions.

scientific article published on 5 April 2018

Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data.

scientific article

Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade

scientific article published on 01 December 2020

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

scientific article published on 18 December 2013

Integrated analysis of multimodal single-cell data

scientific article

Integrated systems approach defines the antiviral pathways conferring protection by the RV144 HIV vaccine

article

Late-Stage Cancer Patients Remain Highly Responsive to Immune Activation by the Selective TLR8 Agonist Motolimod (VTX-2337).

scientific article published on 7 July 2015

Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria

scientific article

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

scientific article

MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis

scientific article

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

scientific article published on 24 July 2013

Model-based analysis of tiling-arrays for ChIP-chip.

scientific article

Modeling and analysis of ChIP-chip experiments

scientific article published on January 2009

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

scientific article (publication date: July 2014)

Mucosal effects of tenofovir 1% gel

scientific article (publication date: 3 February 2015)

Mucosal effects of tenofovir 1% gel

Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19

scientific article published on 28 October 2020

Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories

scientific article published on 31 July 2020

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

scientific article

Optimal priming of poxvirus vector (NYVAC)-based HIV vaccine regimens for T cell responses requires three DNA injections. Results of the randomized multicentre EV03/ANRS VAC20 Phase I/II Trial

scientific article published on 26 June 2020

Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models

scientific article published on 01 November 2020

Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention

scientific article published on 06 April 2022

Optimizing transformations for automated, high throughput analysis of flow cytometry data

scientific article

Orchestrating Single-Cell Analysis with Bioconductor

Orchestrating high-throughput genomic analysis with Bioconductor

scientific article

Orchestrating single-cell analysis with Bioconductor

scientific article published on 02 December 2019

PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy

scientific article published on 01 November 2020

PICS: probabilistic inference for ChIP-seq

scientific article

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

scientific article

Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments

scientific article

Phosphoproteomic analysis of chimeric antigen receptor signaling reveals kinetic and quantitative differences that affect cell function

scientific article published on 21 August 2018

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

scientific article

Potential To Streamline Heterologous DNA Prime and NYVAC/Protein Boost HIV Vaccine Regimens in Rhesus Macaques by Employing Improved Antigens

scientific article published on 10 February 2016

Priming with a potent HIV-1 DNA vaccine frames the quality of immune responses prior to a poxvirus and protein boost

article

Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data

scientific article

Probabilistic segmentation and intensity estimation for microarray images

scientific article published on 27 July 2005

Promises and Pitfalls of High-Throughput Biological Assays

scientific article

Publisher Correction: Orchestrating single-cell analysis with Bioconductor

scientific article published on 01 February 2020

QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data.

scientific article

Quality Control and Robust Estimation for cDNA Microarrays With Replicates

Recent bioinformatics advances in the analysis of high throughput flow cytometry data.

scientific article

Recombinant HIV-1 vaccine candidates based on replication-defective flavivirus vector

scientific article published on 27 December 2019

Replication-competent NYVAC-KC yields improved immunogenicity to HIV-1 antigens in rhesus macaques, compared to non-replicating NYVAC

article

Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first-in-human phase 1 clinical trial

scientific article published on 25 July 2017

Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120.

scientific article published on 17 November 2017

Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes.

scientific article published on 31 May 2017

Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression

scientific article published on 12 April 2021

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

scientific article

State-of-the-Art in the Computational Analysis of Cytometry Data.

scientific article published in July 2015

Statistical analysis of microarray data: a Bayesian approach ⬇️

scientific article published on October 1, 2003

Superiority in Rhesus Macaques of Targeting HIV-1 Env gp140 to CD40 versus LOX-1 in Combination with Replication-Competent NYVAC-KC for Induction of Env-Specific Antibody and T Cell Responses

scientific article published on 15 February 2017

T Cell Responses against Mycobacterial Lipids and Proteins Are Poorly Correlated in South African Adolescents

scientific article

T Cell-Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis

scientific article published on 24 September 2018

T cell receptor gene therapy targeting WT1 prevents acute myeloid leukemia relapse post-transplant

scientific article published on 24 June 2019

Targeting HIV-1 Env gp140 to LOX-1 Elicits Immune Responses in Rhesus Macaques

scientific article

Targeting an alternate Wilms’ tumor antigen 1 peptide bypasses immunoproteasome dependency

scientific article published in 2022

Th2-Biased Transcriptional Profile Predicts HIV Envelope-Specific Polyfunctional CD4<sup>+</sup> T Cells That Correlated with Reduced Risk of Infection in RV144 Trial

scientific article published in 2022

The Thai Phase III HIV Type 1 Vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120.

scientific article

The contribution of cell cycle to heterogeneity in single-cell RNA-seq data

scientific article

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

scientific article

Therapeutic vaccination expands and improves the function of the HIV-specific memory T-cell repertoire

scientific article published on 12 March 2013

Transcriptional correlates of malaria in RTS,S/AS01-vaccinated African children: a matched case-control study

scientific article published on 21 January 2022

Tumor suppression of novel anti-PD-1 antibodies mediated through CD28 costimulatory pathway

scientific article published on 23 May 2019

Vaccine-induced Human Antibodies Specific for the Third Variable Region of HIV-1 gp120 Impose Immune Pressure on Infecting Viruses

scientific article

Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period.

scientific article published on 19 June 2018

cytometree: A binary tree algorithm for automatic gating in cytometry analysis

scientific article published on 02 October 2018

flowCL: ontology-based cell population labelling in flow cytometry

scientific article

flowClust: a Bioconductor package for automated gating of flow cytometry data

scientific article

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

scientific article

ggCyto: next generation open-source visualization software for cytometry

scientific article published on 01 November 2018

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

scientific article

rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments

scientific article published on 19 January 2010

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