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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

artículo científico publicado en 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

artículo científico publicado en 2020

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

artículo científico publicado en 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

artículo científico publicado en 2013

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

artículo científico publicado en 2007

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

artículo científico publicado en 2009

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

artículo científico publicado en 2020

An integrated hierarchical Bayesian model for multivariate eQTL mapping.

artículo científico publicado en 2012

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

artículo científico publicado en 2011

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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

Analyzing Peptide Microarray Data with the R pepStat Package

artículo científico publicado en 2016

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.

artículo científico publicado en 2016

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

artículo científico publicado en 2008

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

artículo científico publicado en 2012

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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 2017

Combining Mixture Components for Clustering ⬇️

artículo científico publicado el 1 de junio de 2010

Comparability and reproducibility of biomedical data

artículo científico publicado en 2013

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

artículo científico publicado en 2021

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

artículo científico publicado en 2015

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

artículo científico publicado en 2014

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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.

artículo científico publicado en 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.

artículo científico publicado en 2013

CytoML for cross-platform cytometry data sharing.

artículo científico publicado en 2018

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.

artículo científico publicado en 2017

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

artículo científico publicado en 2012

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

artículo científico publicado en 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

artículo científico publicado en 2018

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

artículo científico publicado en 2019

Evaluation of the host transcriptional response to human cytomegalovirus infection

artículo científico publicado en 2004

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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

Flexible empirical Bayes models for differential gene expression

artículo científico publicado en 2006

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

artículo científico publicado en 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.

artículo científico publicado en 2018

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

artículo científico publicado en 2013

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

artículo científico publicado en 2017

High-throughput flow cytometry data normalization for clinical trials.

artículo científico publicado en 2013

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

artículo científico publicado en 2017

Highly multiplexed quantitation of gene expression on single cells

artículo científico publicado en 2013

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

artículo científico publicado en 2018

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

artículo científico publicado en 2015

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

artículo científico publicado en 2020

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

artículo científico publicado en 2013

Integrated analysis of multimodal single-cell data

artículo científico publicado en 2021

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).

artículo científico publicado en 2015

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

artículo científico publicado en 2003

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

artículo científico publicado en 2015

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

artículo científico publicado en 2008

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.

artículo científico publicado en 2006

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

artículo científico publicado en 2014

Mucosal effects of tenofovir 1% gel

artículo científico publicado en 2015

Mucosal effects of tenofovir 1% gel

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

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2022

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

artículo científico publicado en 2010

Orchestrating Single-Cell Analysis with Bioconductor

Orchestrating high-throughput genomic analysis with Bioconductor

artículo científico publicado en 2015

Orchestrating single-cell analysis with Bioconductor

artículo científico publicado en 2019

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

artículo científico publicado en 2020

PICS: probabilistic inference for ChIP-seq

artículo científico publicado en 2011

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

artículo científico publicado en 2013

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

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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

artículo científico publicado en 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

artículo científico publicado en 2012

Probabilistic segmentation and intensity estimation for microarray images.

artículo científico publicado en 2005

Promises and Pitfalls of High-Throughput Biological Assays

artículo científico publicado en 2016

Publisher Correction: Orchestrating single-cell analysis with Bioconductor

artículo científico publicado en 2020

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

artículo científico publicado en 2012

Quality Control and Robust Estimation for cDNA Microarrays With Replicates

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

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 2021

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

artículo científico publicado en 2016

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

artículo científico publicado en 2015

Statistical analysis of microarray data: a Bayesian approach ⬇️

artículo científico publicado el 1 de octubre de 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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2018

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

artículo científico publicado en 2019

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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2022

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

artículo científico publicado en 2012

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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 2009

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

artículo científico publicado en 2014

ggCyto: next generation open-source visualization software for cytometry

artículo científico publicado en 2018

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

artículo científico publicado en 2013

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

artículo científico publicado en 2010

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