ArticleChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology2011
Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.
Article in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 56 citations in OpenAlex.
- Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes.BMC biology · 2023Article
- Transposable Elements in the Genome of Human ParasiteTropical medicine and infectious disease · 2021Review
- RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads.BMC bioinformatics · 2020Article
- Identification and characterization of large-scale genomic rearrangements during wheat evolution.PloS one · 2020Article
- A novel miniature transposon-like element discovered in the coding sequence of a gene that encodes for 5-formyltetrahydrofolate in wheat.BMC plant biology · 2019Article
- Physical location of tandem repeats in the wheat genome and application for chromosome identification.Planta · 2019Article
- Genome-wide analysis of a recently active retrotransposon, Au SINE, in wheat: content, distribution within subgenomes and chromosomes, and gene associations.Plant cell reports · 2018Article
- Article
- In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.Bioinformatics and biology insights · 2017Article
- Tc1-like Transposase Thm3 of Silver Carp (Hypophthalmichthys molitrix) Can Mediate Gene Transposition in the Genome of Blunt Snout Bream (Megalobrama amblycephala).G3 (Bethesda, Md.) · 2015Article
- Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2015Article
- Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.BMC bioinformatics · 2015Article
- DNA transposons have colonized the genome of the giant virus Pandoravirus salinus.BMC biology · 2015Article
- Tc1-like transposable elements in plant genomes.Mobile DNA · 2014Article
- CRISPR-Cas immunity and mobile DNA: a new superfamily of DNA transposons encoding a Cas1 endonuclease.Mobile DNA · 2014Article
- Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat.The Plant journal : for cell and molecular biology · 2013Article
- MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements.BMC bioinformatics · 2013Article
- Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification.Plant physiology · 2013Article
- Birth of three stowaway-like MITE families via microhomology-mediated miniaturization of a Tc1/Mariner element in the yellow fever mosquito.Genome biology and evolution · 2013Article
- Why assembling plant genome sequences is so challenging.Biology · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out "junk" sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.
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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.