ArticleMethods (San Diego, Calif.)2009
Methods for integration site distribution analyses in animal cell genomes.
Article in Methods (San Diego, Calif.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 46 citations in OpenAlex.
- Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells.Science translational medicine · 2012Trial
- Efficient generation of germline chimeras in a non-rodent species using rabbit induced pluripotent stem cells.Nature communications · 2025Article
- Article
- A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations.PLoS computational biology · 2019Article
- Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.BMC bioinformatics · 2017Article
- GCN2 phosphorylates HIV-1 integrase and decreases HIV-1 replication by limiting viral integration.Scientific reports · 2017Article
- Integration site selection by retroviruses and transposable elements in eukaryotes.Nature reviews. Genetics · 2017Review
- INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.Molecular therapy. Methods & clinical development · 2017Article
- Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus.Scientific reports · 2017Article
- Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites.Journal of visualized experiments : JoVE · 2016Article
- Article
- Bioinformatics and HIV latency.Current HIV/AIDS reports · 2015Review
- Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions.Molecular therapy. Methods & clinical development · 2015Article
- Host Factors in Retroviral Integration and the Selection of Integration Target Sites.Microbiology spectrum · 2014Review
- BET-independent MLV-based Vectors Target Away From Promoters and Regulatory Elements.Molecular therapy. Nucleic acids · 2014Article
- Allosteric inhibition of human immunodeficiency virus integrase: late block during viral replication and abnormal multimerization involving specific protein domains.The Journal of biological chemistry · 2014Article
- Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo.Genome biology · 2014Article
- Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: implications for the mechanism of target DNA binding.Nucleic acids research · 2014Article
- A large-scale zebrafish gene knockout resource for the genome-wide study of gene function.Genome research · 2013Article
- Quantitation of HIV DNA integration: effects of differential integration site distributions on Alu-PCR assays.Journal of virological methods · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
The question of where retroviral DNA becomes integrated in chromosomes is important for understanding (i) the mechanisms of viral growth, (ii) devising new anti-retroviral therapy, (iii) understanding how genomes evolve, and (iv) developing safer methods for gene therapy. With the completion of genome sequences for many organisms, it has become possible to study integration targeting by cloning and sequencing large numbers of host-virus DNA junctions, then mapping the host DNA segments back onto the genomic sequence. This allows statistical analysis of the distribution of integration sites relative to the myriad types of genomic features that are also being mapped onto the sequence scaffold. Here we present methods for recovering and analyzing integration site sequences.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.