Research graph
References from Distinct phases of immune system programming during ART-suppressed immunodeficiency virus infection. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
External reference
Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy
10.1073/pnas.0800050105 · 2008 · External reference
HIV associated epigenetic trends and chronic diseases: insights into the hidden burden of chronic infection
10.1186/s13148-025-02045-1 · 2026 · External reference
Interferons in HIV-1 infection: mechanisms, antiviral potentials, and therapeutic challenges
10.3389/fimmu.2025.1736658 · 2025 · External reference
Residual immune dysfunction under antiretroviral therapy
10.1016/j.smim.2021.101471 · 2021 · External reference
Type I interferons and TGF-beta cooperate to induce liver fibrosis during HIV-1 infection under antiretroviral therapy
10.1172/jci.insight.152738 · 2022 · External reference
Ageing with HIV-1: immunological challenges for effective vaccination
10.1186/s12979-025-00544-6 · 2025 · External reference
Systemic Inflammation and the Increased Risk of Inflamm-Aging and Age-Associated Diseases in People Living With HIV on Long Term Suppressive Antiretroviral Therapy
10.3389/fimmu.2019.01965 · 2019 · External reference
Immunological approaches to HIV cure
10.1016/j.smim.2020.101412 · 2021 · External reference
CD4(+) T-cell depletion in HIV infection: mechanisms of immunological failure
10.1111/imr.12066 · 2013 · External reference
Microbial translocation is a cause of systemic immune activation in chronic HIV infection
10.1038/nm1511 · 2006 · External reference
Systemic effects of inflammation on health during chronic HIV infection
10.1016/j.immuni.2013.10.001 · 2013 · External reference
Double, double toil and trouble: transforming growth factor beta (TGF-beta) in HIV infection
2025 · External reference
Positive effects of combined antiretroviral therapy on CD4+ T cell homeostasis and function in advanced HIV disease
10.1126/science.277.5322.112 · 1997 · External reference
Dynamics of immune reconstitution and activation markers in HIV+ treatment-naïve patients treated with raltegravir, tenofovir disoproxil fumarate and emtricitabine
10.1371/journal.pone.0083514 · 2013 · External reference
Soluble CD163 made by monocyte/macrophages is a novel marker of HIV activity in early and chronic infection prior to and after anti-retroviral therapy
10.1093/infdis/jir214 · 2011 · External reference
Inflammatory monocytes expressing tissue factor drive SIV and HIV coagulopathy
10.1126/scitranslmed.aam5441 · 2017 · External reference
Nonhuman Primate Models for Studies of AIDS Virus Persistence During Suppressive Combination Antiretroviral Therapy
2018 · External reference
Tissue-specific HIV-1 infection: why it matters
10.2217/fvl.11.48 · 2011 · External reference
Lymphoid organs function as major reservoirs for human immunodeficiency virus
10.1073/pnas.88.21.9838 · 1991 · External reference
Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy
10.1086/527324 · 2008 · External reference
Initial sites of SIV rebound after antiretroviral treatment cessation in rhesus macaques
10.1038/s41564-025-02258-3 · 2026 · External reference
Short Communication: Comparative Evaluation of Coformulated Injectable Combination Antiretroviral Therapy Regimens in Simian Immunodeficiency Virus-Infected Rhesus Macaques
10.1089/aid.2015.0130 · 2016 · External reference
Early antiretroviral therapy in SIV-infected rhesus macaques reveals a multiphasic, saturable dynamic accumulation of the rebound competent viral reservoir
10.1371/journal.ppat.1012135 · 2024 · External reference
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
10.1093/bioinformatics/btp616 · 2010 · External reference
Enhanced interpretation of immune cell phenotype and function through a rhesus macaque single-cell atlas
2025 · External reference
A practical solution to pseudoreplication bias in single-cell studies
10.1038/s41467-021-21038-1 · 2021 · External reference
Confronting false discoveries in single-cell differential expression
10.1038/s41467-021-25960-2 · 2021 · External reference
A balanced measure shows superior performance of pseudobulk methods in single-cell RNA-sequencing analysis
10.1038/s41467-022-35519-4 · 2022 · External reference
Acute HIV-1 Infection
10.1056/nejmra1011874 · 2011 · External reference
The acute HIV infection: implications for intervention, prevention and development of an effective AIDS vaccine
10.1016/j.coviro.2011.05.007 · 2011 · External reference
Immunophenotypic alterations in acute and early HIV infection
10.1016/j.clim.2007.08.011 · 2007 · External reference
Innate immunity in acute HIV-1 infection
10.1097/coh.0b013e3283495996 · 2011 · External reference
Generalized immune activation and innate immune responses in simian immunodeficiency virus infection
10.1097/coh.0b013e3283499cf6 · 2011 · External reference
Primary infection with simian immunodeficiency virus: plasmacytoid dendritic cell homing to lymph nodes, type I interferon, and immune suppression
10.1182/blood-2008-06-162651 · 2008 · External reference
The effect of HAART-induced HIV suppression on circulating markers of inflammation and immune activation
10.1097/qad.0000000000000545 · 2015 · External reference
mixOmics: An R package for 'omics feature selection and multiple data integration
10.1371/journal.pcbi.1005752 · 2017 · External reference
GIMAP Proteins in T-Lymphocytes
10.1155/2010/268589 · 2010 · External reference
Analyses of phenotypic and functional characteristics of CX3CR1-expressing natural killer cells
10.1111/j.1365-2567.2011.03409.x · 2011 · External reference
10.1016/j.csbj.2021.06.043 · 2021 · Admitted local publication
Aging-associated transcriptional programs in T cells signify constituents of TGF-beta signaling for immunosenescence
10.1186/s12915-025-02484-5 · 2025 · External reference
Antiviral Monocytes Increase Prior to Detectable HIV-1 Rebound Viremia
10.1093/infdis/jiaf367 · 2025 · External reference
The Review of Current Knowledge on Neutrophil Gelatinase-Associated Lipocalin (NGAL)
10.3390/ijms241310470 · 2023 · External reference
TWEAK/Fn14 axis is an important player in fibrosis
10.1002/jcp.30089 · 2021 · External reference
ERK MAP kinase links cytokine signals to activation of latent HIV-1 infection by stimulating a cooperative interaction of AP-1 and NF-kappaB
10.1074/jbc.274.39.27981 · 1999 · External reference
Transactivation of naturally occurring HIV-1 long terminal repeats by the JNK signaling pathway. The most frequent naturally occurring length polymorphism sequence introduces a novel binding site for AP-1 factors
10.1074/jbc.m001149200 · 2000 · External reference
AP-1 and NF-κB synergize to transcriptionally activate latent HIV upon T-cell receptor activation
10.1002/1873-3468.14033 · 2021 · External reference
Perturbation-response genes reveal signaling footprints in cancer gene expression
10.1038/s41467-017-02391-6 · 2018 · External reference
Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy
10.1186/s12865-022-00523-2 · 2022 · External reference
Significance and clinical management of persistent low-level viremia and very-low-level viremia in HIV-1-infected patients
10.1128/aac.00076-14 · 2014 · External reference
Immune activation and HIV persistence: implications for curative approaches to HIV infection
10.1111/imr.12065 · 2013 · External reference
Persistent, Albeit Reduced, Chronic Inflammation in Persons Starting Antiretroviral Therapy in Acute HIV Infection
10.1093/cid/ciw683 · 2017 · External reference
Ageing with HIV: Challenges and biomarkers
10.1016/j.ebiom.2022.103896 · 2022 · External reference
Transforming growth factor beta and noncytopathic mechanisms of immunodeficiency in human immunodeficiency virus infection
10.1073/pnas.87.21.8321 · 1990 · External reference
Association of circulating receptor Fc gamma RIII-positive monocytes in AIDS patients with elevated levels of transforming growth factor-beta
10.1172/jci115196 · 1991 · External reference
Lack of decay of HIV-1 in gut-associated lymphoid tissue reservoirs in maximally suppressed individuals
10.1097/01.qai.0000230524.71717.14 · 2006 · External reference
Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaques
10.1371/journal.ppat.1009565 · 2021 · External reference
Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV Infection
2020 · External reference
Mucosal tenofovir 1% gel stimulates cell proliferation and type I/III interferon pathways
10.1128/spectrum.01680-25 · 2026 · External reference
Genetically-barcoded SIV facilitates enumeration of rebound variants and estimation of reactivation rates in nonhuman primates following interruption of suppressive antiretroviral therapy
10.1371/journal.ppat.1006359 · 2017 · External reference
Immune clearance of highly pathogenic SIV infection
10.1038/nature12519 · 2013 · External reference
Rational design and in vivo selection of SHIVs encoding transmitted/founder subtype C HIV-1 envelopes
2019 · External reference
CD40L-adjuvanted DNA/modified vaccinia virus Ankara simian immunodeficiency virus SIV239 vaccine enhances SIV-specific humoral and cellular immunity and improves protection against a heterologous SIVE660 mucosal challenge
10.1128/jvi.00975-14 · 2014 · External reference
Primate resident memory T cells activate humoral and stromal immunity
10.1016/j.immuni.2025.09.009 · 2025 · External reference
Laparoscopic Technique for Serial Collection of Liver and Mesenteric Lymph Nodes in Macaques
10.3791/55617 · 2017 · External reference
Development and homeostasis of T cell memory in rhesus macaque
10.4049/jimmunol.168.1.29 · 2002 · External reference
MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
10.1038/s41592-019-0433-8 · 2019 · External reference
NULISA: a proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing
10.1038/s41467-023-42834-x · 2023 · External reference
GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing
10.1186/s13059-020-02084-2 · 2020 · External reference
Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
10.1038/s41467-019-10756-2 · 2019 · External reference
BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data
10.1093/bioinformatics/btac213 · 2022 · External reference
DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors
10.1016/j.cels.2019.03.003 · 2019 · External reference
Dictionary learning for integrative, multimodal and scalable single-cell analysis
10.1038/s41587-023-01767-y · 2024 · External reference
limma powers differential expression analyses for RNA-sequencing and microarray studies
10.1093/nar/gkv007 · 2015 · External reference
Complex heatmaps reveal patterns and correlations in multidimensional genomic data
10.1093/bioinformatics/btw313 · 2016 · External reference
clusterProfiler: an R package for comparing biological themes among gene clusters
10.1089/omi.2011.0118 · 2012 · External reference
brms: An R package for Bayesian multilevel models using Stan
10.18637/jss.v080.i01 · 2017 · External reference
Stan: A Probabilistic Programming Language
10.18637/jss.v076.i01 · 2017 · External reference
Evaluating significance in linear mixed-effects models in R
10.3758/s13428-016-0809-y · 2017 · External reference
decoupleR: ensemble of computational methods to infer biological activities from omics data
10.1093/bioadv/vbac016 · 2022 · External reference
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
10.1186/s13059-014-0550-8 · 2014 · External reference
