RID source papers

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Bale, MJ et al.33832973 Show samples for pubmed id 33832973Early Emergence and Long-Term Persistence of HIV-Infected T Cell Clones in ChildrenmBio2021 
Brandt, LD et al.temp0000001 Show samples for pubmed id temp0000001Tracking HIV-1 Infected Cell Clones Using Integration Site-Specific qPCRVirus2021 
Coffin, JM et al.33826675 Show samples for pubmed id 33826675Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapyPLOS_pathog2021Use 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 Show samples for pubmed id 33301425Antigen-driven clonal selection shapes the persistence of HIV-1 infected CD4+ T cells in vivoJCI2021 
Yamakawa, T et al.33313334 Show samples for pubmed id 33313334A methodology for assessing tumor clonality of adult T-cell leukemia/lymphomaMolecular Therapy - Methods & Clinical Development2020 
Yoon, J et al.33318172 Show samples for pubmed id 33318172HIV proviral DNA integration can drive T cell growth ex vivoPNAS2020 
Coffin, JM et al.31217357 Show samples for pubmed id 31217357Clones of infected cells arise early in HIV-infected individualsJCI Insight2019 
Einkauf, Kevin et al.30688658 Show samples for pubmed id 30688658Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapyJCI2019sites mapped to hg38 by authors, liftover to hg19 by RID. Patient2, site 21 not found in hg19
Ferris, AL et al.31291371 Show samples for pubmed id 31291371Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humansPLoS Pathog.2019 
McManus, W et al.31361603 Show samples for pubmed id 31361603HIV-1 in Lymph Nodes is Maintained by Cellular Proliferation During ARTJCI2019 
Ode, H et al.30857886 Show samples for pubmed id 30857886dentifying integration sites of the HIV-1 genome with intact and aberrant ends through deep sequencingJ Virol Methods2019Patients P1 to P8 are the same as Maldarelli F. et. al., 2014, Science, 345:179-83
Sharaf, R et al.30024859 Show samples for pubmed id 30024859HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollersJCI2019 
Artesi, M et al.28811663 Show samples for pubmed id 28811663Monitoring Molecular Response in Adult T-cell Leukemia/Lymphoma by High-Throughput Sequencing Clonality AnalysisLeukemia2017 
Cook, LB et al.24735963 Show samples for pubmed id 24735963The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemiaBlood2017 
Furuta, R et al.29186194 Show samples for pubmed id 29186194Human T-cell leukemia virus type 1 infects multiple lineage hematopoietic cells in vivoPLoS Pathog.2017integration 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 Show samples for pubmed id 29099869Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomasPLoS Pathog.2017 
Romano, O et al.27095295 Show samples for pubmed id 27095295Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitmentSci Rep2016 
Sunshine, S et al.26912621 Show samples for pubmed id 26912621HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing AssayJV2016 
Singh, PK et al.26545813 Show samples for pubmed id 26545813LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genesGenes Dev2015 
Singh, PK et al.SRP065157 Show samples for pubmed id SRP065157direct submission to Genbank SRP065157 by Parmit Kumar Singh, Andrea Ferris, Stephen H. Hughes and Henry L. LevinNA2015 
De Ravin, SS et al.24501411 Show samples for pubmed id 24501411Enhancers are major targets for murine leukemia virus vector integrationJ Virol2014 
LaFave, MC et al.24464997 Show samples for pubmed id 24464997MLV integration site selection is driven by strong enhancers and active promotersNucleic Acids Res2014 
Maldarelli, Frank et al.24968937 Show samples for pubmed id 24968937Specific HIV integration sites are linked to clonal expansion and persistence of infected cellsScience2014 
Wagner, TA et al.25011556 Show samples for pubmed id 25011556HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infectionScience2014 
Sherrill-Mix, S et al.23953889 Show samples for pubmed id 23953889HIV latency and integration site placement in five cell-based modelsRetrovirology2013 
Han, Y et al.15163705 Show samples for pubmed id 15163705Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genesJ Virol2010 
Ikeda, T et al.17262715 Show samples for pubmed id 17262715 Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T cell populations during effective highly active antiretroviral therapyJID2007 
Mack, KD et al.12843741 Show samples for pubmed id 12843741HIV 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 expressionJ Acquir Immune Defic Syndr2003 
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