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Author | Pubmed_ID | Title | Journal | Year | Comments |
---|---|---|---|---|---|
Katusiime, MG et al. | temp0000004 ![]() ![]() | Divergent Populations of HIV-Infected Naïve and Memory CD4+ T-cell Clones in Children on ART | JCI | 2025 |   |
Joy, J et al. | temp0000001 ![]() ![]() | Antigen specificities and proviral integration sites differ in HIV-infected cells by timing of antiretroviral-treatment initiation | JCI | 2024 | Sites mapped hg38 by authors, LiftOver to hg19 by RID; hg38 chr1:143215526,chr14:104797,chr22:27857,chr10:38932016,chr11:51273823,chr20:28116956,chr9:44273175,chr20:29914512,chr16:36360872 not found in hg19 |
Oldroyd, A et al. | temp0000003 ![]() ![]() | Persistent viremia associated with vpr- and tat-deleted HIV and absent HIV-specific T cell responses | to be determined | 2024 | Sites mapped to hg38 by authors, LiftOver to hg19 by RID |
Munshi, M et al. | temp0000002 ![]() ![]() | Cleavage and Polyadenylation Specificity Factor 6 Regulates the Kinetics of HIV-1 Nuclear Import | Cell report | 2023 |   |
White, J et al. | 36602866 ![]() ![]() | Clonally expanded HIV-1 proviruses with 5’-Leader defects can give rise to nonsuppressible residual viremia | JCI | 2023 | hg38 site chr1:522814417 not found in hg19, not entered in RID. |
Einkauf, KB et al. | 35026153 ![]() ![]() | Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses | Cell | 2022 | integration sites liftovered from hg38 to hg19. 27 sites were not found in hg19 |
Gao, S et al. | 36044447 ![]() ![]() | HIV infected CD4+ T cell clones are more stable than uninfected clones during long-term antiretroviral therapy | Plos Pathog. | 2022 | clone size counted based on sampling dates |
Goubran, M et al. | 35632628 ![]() ![]() | Isolation of a Human Betaretrovirus from Patients with Primary Biliary Cholangitis | Viruses | 2022 |   |
Katsuya, H et al. | 33844021 ![]() ![]() | Clonality of HIV-1- and HTLV-1-Infected Cells in Naturally Coinfected Individuals | JID | 2022 | has both HIV1 and HTLV1 |
Sun, C et al. | 35347274 ![]() ![]() | Droplet-microfluidics-assisted sequencing of HIV proviruses and their integration sites in cells from people on antiretroviral therapy | Nat Biomed Eng | 2022 | Sites LiftOver from hg38 to hg19 |
Bale, MJ et al. | 33832973 ![]() ![]() | Early Emergence and Long-Term Persistence of HIV-Infected T Cell Clones in Children | PLOS_pathog | 2021 |   |
Brandt, LD et al. | 34202310 ![]() ![]() | Tracking HIV-1 Infected Cell Clones Using Integration Site-Specific qPCR | Virus | 2021 |   |
Coffin, JM et al. | 33826675 ![]() ![]() | Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy | PLOS_pathog | 2021 | Only a partial of integration sites have been entered in this dataset. The rest are in the datasets of other papers |
Huang, AS et al. | 34636876 ![]() ![]() | Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistence | JEM | 2021 | converted to hg19. Sample43 chr14:106728842 not in hg19 |
Patro, SC et al. | 34960744 ![]() ![]() | New Approaches to Multi-Parametric HIV-1 Genetics Using Multiple Displacement Amplification: Determining the What, How, and Where of the HIV-1 Reservoir | Virus | 2021 |   |
Halvas, EK et al. | 33016926 ![]() ![]() | HIV-1 viremia not suppressible by antiretroviral therapy can originate from large T cell clones producing infectious virus | JCI | 2020 |   |
Yamakawa, T et al. | 33313334 ![]() ![]() | A Methodology for Assessing Tumor Clonality of Adult T Cell Leukemia/Lymphoma | Mol Ther Methods Clin Dev | 2020 |   |
Yoon, JK et al. | 33318172 ![]() ![]() | HIV proviral DNA integration can drive T cell growth ex vivo | PNAS | 2020 |   |
Coffin, JM et al. | 31217357 ![]() ![]() | Clones of infected cells arise early in HIV-infected individuals | JCI Insight | 2019 |   |
Einkauf, Kevin et al. | 30688658 ![]() ![]() | Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy | JCI | 2019 | sites mapped to hg38 by authors, liftover to hg19 by RID. Patient2, site 21 not found in hg19 |
Ferris, AL et al. | 31291371 ![]() ![]() | Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans | PLoS Pathog | 2019 |   |
McManus, W et al. | 31361603 ![]() ![]() | HIV-1 in Lymph Nodes is Maintained by Cellular Proliferation During ART | JCI | 2019 |   |
Ode, H et al. | 30857886 ![]() ![]() | dentifying integration sites of the HIV-1 genome with intact and aberrant ends through deep sequencing | J Virol Methods | 2019 | Patients P1 to P8 are the same as Maldarelli F. et. al., 2014, Science, 345:179-83; Table S2 |
Sharaf, R et al. | 30024859 ![]() ![]() | HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers | JCI | 2019 |   |
Artesi, M et al. | 28811663 ![]() ![]() | Monitoring Molecular Response in Adult T-cell Leukemia/Lymphoma by High-Throughput Sequencing Clonality Analysis | Leukemia | 2017 |   |
Cook, LB et al. | 24735963 ![]() ![]() | The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemia | Blood | 2017 |   |
Furuta, R et al. | 29186194 ![]() ![]() | Human T-cell leukemia virus type 1 infects multiple lineage hematopoietic cells in vivo | PLoS Pathog | 2017 | integration sites were mapped to hg38 by the authors. To make it consistent with RID, the sites have been converted to hg19. 137 sites were not found in hg19 |
Malhotra, S et al. | 29099869 ![]() ![]() | Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomas | PLoS Pathog. | 2017 |   |
Romano, O et al. | 27095295 ![]() ![]() | Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment | Sci Rep | 2016 |   |
Sunshine, S et al. | 26912621 ![]() ![]() | HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay | JV | 2016 |   |
Singh, PK et al. | 26545813 ![]() ![]() | LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes | Genes Dev | 2015 |   |
Singh, PK et al. | SRP065157 ![]() ![]() | direct submission to Genbank SRP065157 by Parmit Kumar Singh, Andrea Ferris, Stephen H. Hughes and Henry L. Levin | NA | 2015 |   |
Wang, W et al. | 25521721 ![]() ![]() | Frequent proviral integration of the human betaretrovirus in biliary epithelium of patients with autoimmune and idiopathic liver disease | Aliment Pharmacol Ther. | 2015 |   |
De Ravin, SS et al. | 24501411 ![]() ![]() | Enhancers are major targets for murine leukemia virus vector integration | J Virol | 2014 |   |
LaFave, MC et al. | 24464997 ![]() ![]() | MLV integration site selection is driven by strong enhancers and active promoters | Nucleic Acids Res | 2014 |   |
Maldarelli, Frank et al. | 24968937 ![]() ![]() | Specific HIV integration sites are linked to clonal expansion and persistence of infected cells | Science | 2014 |   |
Wagner, TA et al. | 25011556 ![]() ![]() | HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection | Science | 2014 | The samples of each patient were collected at several time points |
Sherrill-Mix, S et al. | 23953889 ![]() ![]() | HIV latency and integration site placement in five cell-based models | Retrovirology | 2013 |   |
Han, Y et al. | 15163705 ![]() ![]() | Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes | J Virol | 2010 |   |
Ikeda, T et al. | 17262715 ![]() ![]() | Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T cell populations during effective highly active antiretroviral therapy | JID | 2007 |   |
Mack, KD et al. | 12843741 ![]() ![]() | HIV insertions within and proximal to host cell genes are a common finding in tissues containing high levels of HIV DNA and macrophage-associated p24 antigen expression | J Acquir Immune Defic Syndr | 2003 |   |