Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems (Q33649755)

28 July 2017

Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems (English)

1 reference

28 July 2017

Jamie I MacPherson

1

1 reference

28 July 2017

Jonathan E Dickerson

series ordinal

2

1 reference

28 July 2017

John W Pinney

series ordinal

3

1 reference

28 July 2017

David L Robertson

series ordinal

4

1 reference

28 July 2017

29 July 2010

1 reference

PLOS Computational Biology

28 July 2017

1 reference

28 July 2017

6

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28 July 2017

7

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28 July 2017

e1000863

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Creative Commons Attribution 4.0 International

28 July 2017

start time

29 July 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

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

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21 June 2018

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The requirement for cellular transportin 3 (TNPO3 or TRN-SR2) during infection maps to human immunodeficiency virus type 1 capsid and not integrase

21 June 2018

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Immunopathogenesis of asymptomatic chronic HIV Infection: the calm before the storm

21 June 2018

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Host cell factors in HIV replication: meta-analysis of genome-wide studies

21 June 2018

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21 June 2018

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HIV-host interactions: a map of viral perturbation of the host system.

21 June 2018

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Induction of a Striking Systemic Cytokine Cascade prior to Peak Viremia in Acute Human Immunodeficiency Virus Type 1 Infection, in Contrast to More Modest and Delayed Responses in Acute Hepatitis B and C Virus Infections

21 June 2018

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Linear combinations of docking affinities explain quantitative differences in RTK signaling

21 June 2018

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Induction of HIV transcription by Nef involves Lck activation and protein kinase C theta raft recruitment leading to activation of ERK1/2 but not NF kappa B.

21 June 2018

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Cataloguing the HIV type 1 human protein interaction network

21 June 2018

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21 June 2018

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Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication

21 June 2018

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HIV-1 Vif, APOBEC, and intrinsic immunity

21 June 2018

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The interferon response inhibits HIV particle production by induction of TRIM22

21 June 2018

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The landscape of human proteins interacting with viruses and other pathogens

21 June 2018

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Identification of host proteins required for HIV infection through a functional genomic screen

21 June 2018

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The emerging role of innate immunity in protection against HIV-1 infection.

21 June 2018

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KEGG for linking genomes to life and the environment

21 June 2018

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A two-pronged mechanism for HIV-1 Nef-mediated endocytosis of immune costimulatory molecules CD80 and CD86.

21 June 2018

1 reference

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Human immunodeficiency virus type 1 protease cleaves procaspase 8 in vivo

21 June 2018

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Mechanisms of CD4 T-cell depletion triggered by HIV-1 viral proteins

21 June 2018

1 reference

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Discovering regulated networks during HIV-1 latency and reactivation

21 June 2018

1 reference

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An essential role for LEDGF/p75 in HIV integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Expression of Nef downregulates CXCR4, the major coreceptor of human immunodeficiency virus, from the surfaces of target cells and thereby enhances resistance to superinfection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

HIV protease cleaves poly(A)-binding protein.

21 June 2018

1 reference

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The origins and evolution of functional modules: lessons from protein complexes

21 June 2018

1 reference

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A systematic comparison and evaluation of biclustering methods for gene expression data

21 June 2018

1 reference

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BioGRID: a general repository for interaction datasets

21 June 2018

1 reference

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From genomics to chemical genomics: new developments in KEGG

21 June 2018

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Late budding domains and host proteins in enveloped virus release

21 June 2018

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Tat gets the "green" light on transcription initiation

21 June 2018

1 reference

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Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity

21 June 2018

1 reference

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Synthetic Vpr protein activates activator protein-1, c-Jun N-terminal kinase, and NF-kappaB and stimulates HIV-1 transcription in promonocytic cells and primary macrophages

21 June 2018

1 reference

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Identification of the LEDGF/p75 HIV-1 integrase-interaction domain and NLS reveals NLS-independent chromatin tethering

21 June 2018

1 reference

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Nef-induced alteration of the early/recycling endosomal compartment correlates with enhancement of HIV-1 infectivity

21 June 2018

1 reference

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HIV-1 tat protein modulates the generation of cytotoxic T cell epitopes by modifying proteasome composition and enzymatic activity

21 June 2018

1 reference

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Induction and regulation of IFNs during viral infections

21 June 2018

1 reference

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Partner molecules of accessory protein Vpr of the human immunodeficiency virus type 1

21 June 2018

1 reference

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Resistance to apoptosis: mechanism for the development of HIV reservoirs.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

The CCR5 and CXCR4 coreceptors--central to understanding the transmission and pathogenesis of human immunodeficiency virus type 1 infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Reciprocal regulation of the nuclear factor of activated T cells and HIV-1.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Human protein reference database as a discovery resource for proteomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

The HIV nef and the Kaposi-sarcoma-associated virus K3/K5 proteins: "parasites"of the endocytosis pathway

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Regulation of T cell activation by HIV-1 accessory proteins: Vpr acts via distinct mechanisms to cooperate with Nef in NFAT-directed gene expression and to promote transactivation by CREB

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Cleavage of eIF4G by HIV-1 protease: effects on translation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Recruitment of the Crm1 nuclear export factor is sufficient to induce cytoplasmic expression of incompletely spliced human immunodeficiency virus mRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Slipping through the door: HIV entry into the nucleus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Effects of HIV-1 Nef on cellular gene expression profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Karyopherins and nuclear import

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Ten years of protein kinase B signalling: a hard Akt to follow

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

HIV-1 protease cleaves eukaryotic initiation factor 4G and inhibits cap-dependent translation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

BIND--The Biomolecular Interaction Network Database

21 June 2018

1 reference

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Receptor tyrosine kinases: specific outcomes from general signals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Heat-shock protein 70 can replace viral protein R of HIV-1 during nuclear import of the viral preintegration complex

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Gene ontology: tool for the unification of biology

21 June 2018

1 reference

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KEGG: kyoto encyclopedia of genes and genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Multifaceted activities of the HIV-1 transactivator of transcription, Tat.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Activation of Vav by Nef induces cytoskeletal rearrangements and downstream effector functions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Simian immunodeficiency virus and human immunodeficiency virus type 1 nef proteins show distinct patterns and mechanisms of Src kinase activation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Reciprocal modulatory interaction between human immunodeficiency virus type 1 Tat and transcription factor NFAT1.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

21 June 2018

THE HIV-1 REV PROTEIN

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Nucleoporins nup98 and nup214 participate in nuclear export of human immunodeficiency virus type 1 Rev

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Predicting function: from genes to genomes and back

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Transcription elongation factor P-TEFb mediates Tat activation of HIV-1 transcription at multiple stages

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

The extended protein kinase C superfamily

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

The importin-beta family member Crm1p bridges the interaction between Rev and the nuclear pore complex during nuclear export

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

A role for nucleoporin FG repeat domains in export of human immunodeficiency virus type 1 Rev protein and RNA from the nucleus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

HIV infection in vitro enhances the activity of src-family protein tyrosine kinases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

HIV type 1 glycoprotein 120 amplifies tumor necrosis factor-induced NF-kappa B activation in Jurkat cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Cyclosporin A sensitivity of the HIV-1 long terminal repeat identifies distinct p56lck-dependent pathways activated by CD4 triggering

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

HIV envelope-directed signaling aberrancies and cell death of CD4+ T cells in the absence of TCR co-stimulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Endocytosis of major histocompatibility complex class I molecules is induced by the HIV–1 Nef protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Human immunodeficiency virus-1 recombinant gp120 induces changes in protein kinase C isozymes--a preliminary report

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Envelope glycoproteins of HIV-1 interfere with T-cell-dependent B cell differentiation: role of CD4-MHC class II interaction in the effector phase of T cell help

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Downregulation of cell-surface CD4 expression by simian immunodeficiency virus Nef prevents viral super infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Interaction of HIV gp120 and anti-CD4 antibodies with the CD4 molecule on human CD4+ T cells inhibits the binding activity of NF-AT, NF-kappa B and AP-1, three nuclear factors regulating interleukin-2 gene enhancer activity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

HIV-1 glycoprotein gp120 disrupts CD4-p56lck/CD3-T cell receptor interactions and inhibits CD3 signaling.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

HIV gp120 inhibits T cell activation by interfering with expression of costimulatory molecules CD40 ligand and CD80 (B71)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

The T-cell antigen receptor utilizes Lck, Raf-1, and MEK-1 for activating mitogen-activated protein kinase. Evidence for the existence of a second protein kinase C-dependent pathway in an Lck-negative Jurkat cell mutant

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Identification of common molecular subsequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

The neighbor-joining method: a new method for reconstructing phylogenetic trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Structure and function of cytochrome c oxidase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Stimulation of MAP-2 kinase activity in T lymphocytes by anti-CD3 or anti-Ti monoclonal antibody is partially dependent on protein kinase C.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Human immunodeficiency virus-1 glycoproteins gp120 and gp160 specifically inhibit the CD3/T cell-antigen receptor phosphoinositide transduction pathway

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Protein kinase C plays a role in the induction of tyrosine phosphorylation of lymphoid microtubule-associated protein-2 kinase. Evidence for a CD3-associated cascade that includes pp56lck and that is defective in HPB-ALL

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Human chromosome 12 is required for optimal interactions between Tat and TAR of human immunodeficiency virus type 1 in rodent cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Effects of HIV-1 nef on cellular gene expression profiles

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000863

All duplicates are not equal: the difference between small-scale and genome duplication

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000863

How incorrect annotations evolve--the case of short ORFs

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000863

The Nef protein of human immunodeficiency virus establishes superinfection immunity by a dual strategy to downregulate cell-surface CCR5 and CD4.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000863

Nef is physically recruited into the immunological synapse and potentiates T cell activation early after TCR engagement

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000863

Human immunodeficiency virus type 1 Tat increases cooperation between AP-1 and NFAT transcription factors in T cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000863

Intracellular HIV-1 Tat protein represses constitutive LMP2 transcription increasing proteasome activity by interfering with the binding of IRF-1 to STAT1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000863

Transportin-SR2 imports HIV into the nucleus

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000863

HIV-1 gp120 induces NFAT nuclear translocation in resting CD4+ T-cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000863

HIV-1 Nef triggers Vav-mediated signaling pathway leading to functional and morphological differentiation of dendritic cells

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2912648

Modeling the percolation of annotation errors in a database of protein sequences

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20686668

12 December 2020

inferred from PubMed ID database lookup

CD-3-mediated activation of MAP-2 kinase can be modified by ligation of the CD4 receptor. Evidence for tyrosine phosphorylation during activation of this kinase

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20686668

12 December 2020

inferred from PubMed ID database lookup

Genome-scale RNAi screen for host factors required for HIV replication

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20686668

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000863

1 reference

journals/ploscb/MacPhersonDPR10

28 July 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

28 July 2017

1 reference