TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

High-throughput analysis of the satellitome illuminates satellite DNA evolution

(2016) Francisco J. Ruiz-Ruano et al.   Scientific Reports

Satellite DNA in Plants: More than Just Rubbish

(2015) Manuel A. Garrido-Ramos   CYTOGENETIC AND GENOME RESEARCH

Next-generation sequencing detects repetitive elements expansion in giant genomes of annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae)

(2015) G. García et al.   GENETICA

Holocentromeres inRhynchosporaare associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

(2015) André Marques et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

(2015) Jiří Macas et al.   PLoS One

Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping

(2014) Zexi Cai et al.   BMC GENOMICS

Centromere identity from the DNA point of view

(2014) Miroslav Plohl et al.   CHROMOSOMA

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance

(2012) K. G. Lim et al.   BRIEFINGS IN BIOINFORMATICS

Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats

(2012) H. J. T. Pagan et al.   Genome Biology and Evolution

Repeat or not repeat?—Statistical validation of tandem repeat prediction in genomic sequences

(2012) Elke Schaper et al.   NUCLEIC ACIDS RESEARCH

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

(2012) Matko Glunčić et al.   NUCLEIC ACIDS RESEARCH

Repeatless and Repeat-Based Centromeres in Potato: Implications for Centromere Evolution

(2012) Z. Gong et al.   PLANT CELL

The holocentric speciesLuzula elegansshows interplay between centromere and large-scale genome organization

(2012) Stefan Heckmann et al.   PLANT JOURNAL

Independent, Rapid and Targeted Loss of Highly Repetitive DNA in Natural and Synthetic Allopolyploids of Nicotiana tabacum

(2012) Simon Renny-Byfield et al.   PLoS One

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

(2012) Pavel Neumann et al.   PLoS Genetics

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

(2011) Jiří Macas et al.   PLoS One

Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome

(2011) Giovana A. Torres et al.   G3-Genes Genomes Genetics

Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data

(2010) J. Macas et al.   BIOINFORMATICS

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Hypervariable 3′ UTR region of plant LTR-retrotransposons as a source of novel satellite repeats

(2009) Jiří Macas et al.   GENE

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

(2008) G.-F. Richard et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Satellite DNAs between selfishness and functionality: Structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin

(2007) Miroslav Plohl et al.   GENE