ArticleGene2006
Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms.
Article in Gene, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 66 citations in OpenAlex.
- TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.PLoS computational biology · 2026Article
- The identification of retro-DNAs in primate genomes as DNA transposons mobilizing via retrotransposition.F1000Research · 2023Article
- Transposable elements that have recently been mobile in the human genome.BMC genomics · 2021Article
- Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective.International journal of molecular sciences · 2020Article
- Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families.Genome biology and evolution · 2019Article
- Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition.Systematic biology · 2018Article
- Discovery and characterization of Alu repeat sequences via precise local read assembly.Nucleic acids research · 2015Article
- Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression.BMC genetics · 2015Article
- Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.Genome biology and evolution · 2015Article
- Article
- Transposable elements in cancer as a by-product of stress-induced evolvability.Frontiers in genetics · 2014Article
- Study of Modern Human Evolution via Comparative Analysis with the Neanderthal Genome.Genomics & informatics · 2013Review
- Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements.Mobile DNA · 2013Article
- Detecting Alu insertions from high-throughput sequencing data.Nucleic acids research · 2013Article
- Transposable elements are a significant contributor to tandem repeats in the human genome.Comparative and functional genomics · 2012Article
- The human genome: a multifractal analysis.BMC genomics · 2011Article
- Distributions of transposable elements reveal hazardous zones in mammalian introns.PLoS computational biology · 2011Article
- Alu distribution and mutation types of cancer genes.BMC genomics · 2011Article
- RISCI--Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes.BMC bioinformatics · 2010Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human genome. By computationally comparing the public and Celera sequence assemblies of the human genome, we identified a total of 800 polymorphic Alu elements. We used polymerase chain reaction-based assays to screen a randomly selected set of 16 of these 800 Alu insertion polymorphisms using a human diversity panel to demonstrate the efficiency of our approach. Based on sequence analysis of the 800 Alu polymorphisms, we report three new Alu subfamilies, Ya3, Ya4b, and Yb11, with Yb11 being the smallest known Alu subfamily. Analysis of retrotransposition activity revealed Yb11, Ya8, Ya5, Yb9, and Yb8 as the most active Alu subfamilies and the maintenance of a very low level of retrotransposition activity or recent gene conversion events involving S subfamilies. The 800 polymorphic Alu insertions are characterized by the presence of target site duplications (TSDs) and longer than average polyA-tail length. Their pre-integration sites largely follow an extended "NT-AARA" motif. Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes.
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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.