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RID source papers
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| Author | Pubmed_ID | Title | Journal | Year | Comments |
|---|---|---|---|---|---|
| Boritz, Perez et al. | temp0000003 | PD-1 Blockade Promotes In Vivo Expansion of HIV-infected CD4 T Cell Clones under Antiretroviral Therapy | tbd | 2026 | |
| Kearney, Katusiime et al. | 40048262 | Divergent Populations of HIV-Infected Naïve and Memory CD4+ T-cell Clones in Children on ART | J Clin Invest | 2025 | |
| Frenkel, Joy et al. | 38833307 | Antigen specificities and proviral integration sites differ in HIV-infected cells by timing of antiretroviral-treatment initiation | J Clin Invest | 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. | temp0000002 | Persistent viremia associated with vpr- and tat-deleted HIV and absent HIV-specific T cell responses | tbd | 2024 | Sites mapped to hg38 by authors, LiftOver to hg19 by RID |
| Munshi, M et al. | temp0000001 | Cleavage and Polyadenylation Specificity Factor 6 Regulates the Kinetics of HIV-1 Nuclear Import | Cell report | 2023 | |
| Simonetti, White et al. | 36602866 | Clonally expanded HIV-1 proviruses with 5’-Leader defects can give rise to nonsuppressible residual viremia | J Clin Invest | 2023 | hg38 site chr1:522814417 not found in hg19, not entered in RID. |
| Abate, Sun 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 |
| Hughes, Gao 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 |
| Lichterfeld, Einkauf 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 |
| Mason, Goubran et al. | 35632628 | Isolation of a Human Betaretrovirus from Patients with Primary Biliary Cholangitis | Viruses | 2022 | |
| Mellors, Joseph et al. | 35674431 | Deep Sequencing Analysis of Individual HIV-1 Proviruses Reveals Frequent Asymmetric Long Terminal Repeats | J Virol | 2022 | |
| Satou, Katsuya et al. | 33844021 | Clonality of HIV-1- and HTLV-1-Infected Cells in Naturally Coinfected Individuals | J Infect Dis | 2022 | has both HIV1 and HTLV1 |
| Cohn, Huang et al. | 34636876 | Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistence | J Exp Med | 2021 | converted to hg19. Sample43 chr14:106728842 not in hg19 |
| Hughes, Coffin 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 |
| Kearney, Bale et al. | 33832973 | Early Emergence and Long-Term Persistence of HIV-Infected T Cell Clones in Children | mBio | 2021 | |
| Kearney, Patro 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 | Viruses | 2021 | |
| Mellors, Brandt et al. | 34202310 | Tracking HIV-1 Infected Cell Clones Using Integration Site-Specific qPCR | Viruses | 2021 | |
| Silliciano, Simonetti et al. | 33301425 | Antigen-driven clonal selection shapes the persistence of HIV-1-infected CD4+ T cells in vivo | J Clin Invest | 2021 | |
| Coffin, Yoon et al. | 33318172 | HIV proviral DNA integration can drive T cell growth ex vivo | Proc Natl Acad Sci U S A | 2020 | |
| Mellors, Halvas et al. | 33016926 | HIV-1 viremia not suppressible by antiretroviral therapy can originate from large T cell clones producing infectious virus | J Clin Invest | 2020 | |
| Yanagihara, Yamakawa et al. | 33313334 | A Methodology for Assessing Tumor Clonality of Adult T Cell Leukemia/Lymphoma | Mol Ther Methods Clin Dev | 2020 | |
| Hughes, Coffin et al. | 31217357 | Clones of infected cells arise early in HIV-infected individuals | JCI Insight | 2019 | |
| Hughes, Ferris 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 | |
| Iwatani, Ode 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 |
| Kearnet, McManus et al. | 31361603 | HIV-1 in Lymph Nodes is Maintained by Cellular Proliferation During ART | J Clin Invest | 2019 | |
| Li, Sharaf et al. | 30024859 | HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers | J Clin Invest | 2019 | |
| Lichterfeld, Einkauf et al. | 30688658 | Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy | J Clin Invest | 2019 | sites mapped to hg38 by authors, liftover to hg19 by RID. Patient2, site 21 not found in hg19 |
| Beemon, Malhotra et al. | 29099869 | Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomas | PLoS Pathog | 2017 | |
| den Broeke, Artesi et al. | 28811663 | Monitoring Molecular Response in Adult T-cell Leukemia/Lymphoma by High-Throughput Sequencing Clonality Analysis | Leukemia | 2017 | |
| Matsuoka, Furuta 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 |
| Li, Sunshine et al. | 26912621 | HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay | J Virol | 2016 | |
| Maldarelli, Simonetti et al. | 26858442 | Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo | Proc Natl Acad Sci U S A | 2016 | |
| Miccio, Romano et al. | 27095295 | Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment | Sci Rep | 2016 | |
| Levin, Singh et al. | 26545813 | LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes | Genes Dev | 2015 | |
| Mason, Wang 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 | |
| Singh, PK et al. | SRP065157 | direct submission to Genbank SRP065157 by Parmit Kumar Singh, Andrea Ferris, Stephen H. Hughes and Henry L. Levin | none | 2015 | |
| Bangham, Cook et al. | 24735963 | The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemia | Blood | 2014 | |
| Burgess, La Fave et al. | 24464997 | MLV integration site selection is driven by strong enhancers and active promoters | Nucleic Acids Res | 2014 | |
| Frenkel, Wagner 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 |
| Hughes, Maldarelli et al. | 24968937 | Specific HIV integration sites are linked to clonal expansion and persistence of infected cells | Science | 2014 | |
| Wu, De Ravin et al. | 24501411 | Enhancers are major targets for murine leukemia virus vector integration | J Virol | 2014 | |
| Bushman, Sherill-Mix et al. | 23953889 | HIV latency and integration site placement in five cell-based models | Retrovirology | 2013 | |
| Siliciano, Han 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 | |
| Matsushita, Ikeda et al. | 17262715 | Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T cell populations during effective highly active antiretroviral therapy | J Infect Dis | 2007 | |
| McGrath, Mack 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 |