(Q47548194)

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A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

scientific article published on 29 January 2018

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers (English)

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

reproducibility

1 reference

based on heuristic

inferred from title

single cell transcriptomics

1 reference

A curated database reveals trends in single-cell transcriptomics

https://www.nxn.se/single-cell-studies/data.tsv

7 February 2021

1 reference

based on heuristic

inferred from title

Bruce D. Walker

9

object named as

Bruce D Walker

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

12

object named as

Xu G Yu

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

11

object named as

Alex K Shalek

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

6

object named as

Samuel W Kazer

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

Jose Ordovas-Montanes

7

object named as

Jose Ordovas-Montanes

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

Mathias Lichterfeld

8

object named as

Mathias Lichterfeld

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

Enrique Martín-Gayo

1

object named as

Enrique Martin-Gayo

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

Jacqueline Cronin

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object named as

Jacqueline Cronin

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

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object named as

Kellie E Kolb

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

author name string

Michael B Cole

2

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

Zhengyu Ouyang

4

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

Nir Yosef

10

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

publication date

29 January 2018

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

external data available at URL

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108445

1 reference

A curated database reveals trends in single-cell transcriptomics

https://www.nxn.se/single-cell-studies/data.tsv

7 February 2021

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

19

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

1

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

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1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

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DESeq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

https://scigraph.springernature.com/pub.10.1186/s13059-017-1385-x

0 references

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

1 reference

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22 May 2018

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Lymph nodes from HIV-infected individuals harbor mature dendritic cells and increased numbers of PD-L1+ conventional dendritic cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

The cGAS-STING Defense Pathway and Its Counteraction by Viruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Type I and Type II Interferon Coordinately Regulate Suppressive Dendritic Cell Fate and Function during Viral Persistence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Control of Transcript Variability in Single Mammalian Cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Human genetic basis of interindividual variability in the course of infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Single-cell messenger RNA sequencing reveals rare intestinal cell types

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Potent Cell-Intrinsic Immune Responses in Dendritic Cells Facilitate HIV-1-Specific T Cell Immunity in HIV-1 Elite Controllers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Genetic absence of PD-1 promotes accumulation of terminally differentiated exhausted CD8+ T cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Control of adaptive immunity by the innate immune system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Cytoplasmic sensing of viral nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Human macrophage SCN5A activates an innate immune signaling pathway for antiviral host defense.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Bayesian approach to single-cell differential expression analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

HIV-1 persistence in CD4+ T cells with stem cell-like properties

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Accounting for technical noise in single-cell RNA-seq experiments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Dynamic regulatory network controlling TH17 cell differentiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Fast gapped-read alignment with Bowtie 2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Transcriptional and epigenetic control of T helper cell specification: molecular mechanisms underlying commitment and plasticity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Systematic discovery of TLR signaling components delineates viral-sensing circuits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

HIV-1 adaptation to NK-cell-mediated immune pressure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Immune signaling by RIG-I-like receptors

1 reference

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22 May 2018

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

HIV infection of dendritic cells subverts the IFN induction pathway via IRF-1 and inhibits type 1 IFN production

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

CD4+ T cells from elite controllers resist HIV-1 infection by selective upregulation of p21

1 reference

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22 May 2018

Functional characteristics of the high affinity IgG receptor, FcγRI.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

A cryptic sensor for HIV-1 activates antiviral innate immunity in dendritic cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Leukocyte immunoglobulin-like receptors maintain unique antigen-presenting properties of circulating myeloid dendritic cells in HIV-1-infected elite controllers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Antiviral response dictated by choreographed cascade of transcription factors.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Ribosomal protein mRNAs are translationally-regulated during human dendritic cells activation by LPS.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Effector mechanisms in HIV-1 infected elite controllers: highly active immune responses?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Dynamic proteomics of individual cancer cells in response to a drug.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Peripheral B cell subsets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

HIV controllers exhibit potent CD8 T cell capacity to suppress HIV infection ex vivo and peculiar cytotoxic T lymphocyte activation phenotype

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Regulation of the lifespan in dendritic cell subsets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Selected Toll-like receptor agonist combinations synergistically trigger a T helper type 1-polarizing program in dendritic cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

A novel lysosome-associated membrane glycoprotein, DC-LAMP, induced upon DC maturation, is transiently expressed in MHC class II compartment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

22 May 2018

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

14 August 2018

Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5789701

14 August 2018

AIDS restriction HLA allotypes target distinct intervals of HIV-1 pathogenesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29378643

12 December 2020

based on heuristic

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Evolution of the functional profile of HIV-specific CD8+ T cells in patients with different progression of HIV infection over 4 years

1 reference

https://pubmed.ncbi.nlm.nih.gov/29378643

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/S13059-017-1385-X

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

Dimensions Publication ID

0 references

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

21 February 2018

http://europepmc.org/abstract/PMC/5789701

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