| Author | Pubmed_ID | Title | Journal | Year | Comments |
|---|
| Bale, MJ et al. | 33832973  | Early Emergence and Long-Term Persistence of HIV-Infected T Cell Clones in Children | mBio | 2021 | |
| Brandt, LD et al. | temp0000001 | 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 | Use this link: journals.plos.org/plospathogens/article/asset?unique&id=info:doi/10.1371/journal.ppat.1009141.s012 to access the full dataset. Mapping instruction in Supplemental File 1 |
| Simonetti, FR et al. | 33301425 | Antigen-driven clonal selection shapes the persistence of HIV-1 infected CD4+ T cells in vivo | JCI | 2021 | |
| Yamakawa, T et al. | 33313334 | A methodology for assessing tumor clonality of adult T-cell leukemia/lymphoma | Molecular Therapy - Methods & Clinical Development | 2020 | |
| Yoon, J 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 |
| 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 | |
| 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 | |
| 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 | |
