Published in Nucleic Acids Res on December 21, 2010
Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One (2014) 1.74
Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet (2013) 1.70
Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet (2012) 1.59
Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS One (2012) 1.40
Population genomics of transposable elements in Drosophila melanogaster. Mol Biol Evol (2010) 1.12
Transposable element detection from whole genome sequence data. Mob DNA (2015) 0.99
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data. Nucleic Acids Res (2014) 0.97
Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. Chromosome Res (2011) 0.96
Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Res (2015) 0.92
TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data. Biology (Basel) (2012) 0.90
Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nat Commun (2014) 0.87
TE-Tracker: systematic identification of transposition events through whole-genome resequencing. BMC Bioinformatics (2014) 0.83
A transposable element insertion confers xenobiotic resistance in Drosophila. PLoS Genet (2014) 0.83
Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae. Genetics (2016) 0.82
A proposal for the reference-based annotation of de novo transposable element insertions. Mob Genet Elements (2012) 0.81
Transposable elements: from DNA parasites to architects of metazoan evolution. Genes (Basel) (2012) 0.78
Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes. BMC Genomics (2016) 0.77
Identification of piggyBac-mediated insertions in Plasmodium berghei by next generation sequencing. Malar J (2013) 0.77
Lack of population differentiation patterns of previously identified putatively adaptive transposable element insertions at microgeographic scales. Biol Direct (2015) 0.77
McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole Genome Shotgun Sequencing Data. G3 (Bethesda) (2017) 0.76
A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads. DNA Res (2016) 0.75
REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads. PLoS One (2016) 0.75
Genomics of Parallel Experimental Evolution in Drosophila. Mol Biol Evol (2017) 0.75
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol (2000) 128.08
The genome sequence of Drosophila melanogaster. Science (2000) 74.32
Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res (2005) 23.41
SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol (2009) 11.24
A unified classification system for eukaryotic transposable elements. Nat Rev Genet (2007) 11.03
Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered (2009) 7.18
Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet (2007) 7.14
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol (2002) 5.80
Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature (1998) 5.47
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol (2008) 5.19
The 1001 genomes project for Arabidopsis thaliana. Genome Biol (2009) 4.10
Transposons in place of telomeric repeats at a Drosophila telomere. Cell (1993) 3.54
Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution (2001) 3.30
Genetics: junk DNA as an evolutionary force. Nature (2006) 3.10
Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc Natl Acad Sci U S A (2006) 2.81
Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature (2009) 2.24
Dramatic amplification of a rice transposable element during recent domestication. Proc Natl Acad Sci U S A (2006) 2.07
The repetitive landscape of the chicken genome. Genome Res (2004) 1.72
Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2007) 1.63
High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol (2008) 1.52
The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. III. Element abundances in heterochromatin. Genet Res (1994) 1.51
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Genomics (2008) 1.45
Transposable element annotation of the rice genome. Bioinformatics (2004) 1.41
Virtual PCR. Bioinformatics (2001) 1.39
Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genet (2010) 1.24
SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics (2010) 1.18
Transposable elements in reptilian and avian (sauropsida) genomes. Cytogenet Genome Res (2010) 1.18
Population genomics of transposable elements in Drosophila melanogaster. Mol Biol Evol (2010) 1.12
The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata. BMC Evol Biol (2010) 1.08
Evolution of a polymorphic regulatory element in interferon-gamma through transposition and mutation. Mol Biol Evol (2002) 0.95
Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites. J Mol Evol (2007) 0.93
A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster. Mol Biol Evol (2009) 0.92
High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol (2008) 4.74
Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet (2009) 4.02
Selection on codon bias. Annu Rev Genet (2008) 3.83
Pervasive natural selection in the Drosophila genome? PLoS Genet (2009) 3.27
Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet (2010) 2.95
Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science (2005) 2.56
Evidence that adaptation in Drosophila is not limited by mutation at single sites. PLoS Genet (2010) 2.41
The large genome constraint hypothesis: evolution, ecology and phenotype. Ann Bot (2005) 2.33
Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol (2004) 1.96
Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics (2007) 1.89
Drosophila melanogaster recombination rate calculator. Gene (2010) 1.78
Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol Biol Evol (2003) 1.72
General rules for optimal codon choice. PLoS Genet (2009) 1.71
Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet (2008) 1.66
Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics (2004) 1.61
Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol Evol (2013) 1.60
Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genet (2012) 1.54
The impact of transposable elements in environmental adaptation. Mol Ecol (2013) 1.53
High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol (2008) 1.52
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. J Mol Evol (2005) 1.45
Reduced selection leads to accelerated gene loss in Shigella. Genome Biol (2007) 1.41
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol (2010) 1.40
Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet (2005) 1.39
Frequent adaptation and the McDonald-Kreitman test. Proc Natl Acad Sci U S A (2013) 1.37
Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet (2013) 1.34
Rates of DNA duplication and mitochondrial DNA insertion in the human genome. J Mol Evol (2003) 1.34
Heterozygote advantage as a natural consequence of adaptation in diploids. Proc Natl Acad Sci U S A (2011) 1.33
Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment. PLoS One (2013) 1.30
Protein evolution in the context of Drosophila development. J Mol Evol (2005) 1.29
X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis. Genetics (2005) 1.26
Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genet (2010) 1.24
Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster. PLoS One (2012) 1.16
Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster. BMC Evol Biol (2007) 1.15
The adaptive role of transposable elements in the Drosophila genome. Gene (2009) 1.14
Broker genes in human disease. Genome Biol Evol (2010) 1.13
[Use of a coronary risk score (the TIMI Risk Score) in a non-selected patient population assessed for chest pain at an emergency department]. Rev Esp Cardiol (2005) 1.13
Population genomics of transposable elements in Drosophila melanogaster. Mol Biol Evol (2010) 1.12
Origins and rates of aneuploidy in human blastomeres. Fertil Steril (2011) 1.10
Codon bias and noncoding GC content correlate negatively with recombination rate on the Drosophila X chromosome. J Mol Evol (2005) 1.09
[Time intervals in primary angioplasty from onset of symptoms until restoration of blood flow]. Rev Esp Cardiol (2002) 1.07
[Program of coronary angioplasty in acute myocardial infarction in the region of Murcia (Spain). APRIMUR Registry]. Rev Esp Cardiol (2002) 1.07
Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol (2009) 1.07
Nonadaptive explanations for signatures of partial selective sweeps in Drosophila. Mol Biol Evol (2008) 1.04
Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter. Genetics (2004) 1.03
How intron splicing affects the deletion and insertion profile in Drosophila melanogaster. Genetics (2002) 1.03
Low occurrence of gene transposition events during the evolution of the genus Drosophila. Evolution (2003) 1.03
SEGE: A database on 'intron less/single exonic' genes from eukaryotes. Bioinformatics (2002) 1.02
Evolutionary biology for the 21st century. PLoS Biol (2013) 1.01
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol (2005) 1.00
Rapid sequence turnover at an intergenic locus in Drosophila. Mol Biol Evol (2004) 1.00
Intravitreal delivery of AAV-NDI1 provides functional benefit in a murine model of Leber hereditary optic neuropathy. Eur J Hum Genet (2012) 0.98
Population genomics of transposable elements in Drosophila. Annu Rev Genet (2014) 0.97
LDx: estimation of linkage disequilibrium from high-throughput pooled resequencing data. PLoS One (2012) 0.95
Matrix metalloproteinases and tissue remodeling in hypertrophic cardiomyopathy. Am Heart J (2008) 0.95
Molecular characterization and chromosomal distribution of Galileo, Kepler and Newton, three foldback transposable elements of the Drosophila buzzatii species complex. Genetics (2005) 0.94
A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution. J Mol Evol (2005) 0.93
Faster than neutral evolution of constrained sequences: the complex interplay of mutational biases and weak selection. Genome Biol Evol (2011) 0.93
Serum levels of high-sensitivity troponin T: a novel marker for cardiac remodeling in hypertrophic cardiomyopathy. J Card Fail (2010) 0.93
Evolution of genome content: population dynamics of transposable elements in flies and humans. Methods Mol Biol (2012) 0.93
A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster. Mol Biol Evol (2009) 0.92
The transposable element Bari-Jheh mediates oxidative stress response in Drosophila. Mol Ecol (2014) 0.90
Abundance and chromosomal distribution of six Drosophila buzzatii transposons: BuT1, BuT2, BuT3, BuT4, BuT5, and BuT6. Chromosoma (2006) 0.87
Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences. BMC Biol (2006) 0.87
Inferring the strength of selection in Drosophila under complex demographic models. Mol Biol Evol (2008) 0.85
Segmental duplication, microinversion, and gene loss associated with a complex inversion breakpoint region in Drosophila. Mol Biol Evol (2012) 0.83
Variables associated with contrast-enhanced cardiovascular magnetic resonance in hypertrophic cardiomyopathy: clinical implications. J Card Fail (2008) 0.83
Molecular evolution of the testis TAFs of Drosophila. Mol Biol Evol (2009) 0.83
Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population. Mol Ecol (2013) 0.82
On the limitations of using ribosomal genes as references for the study of codon usage: a rebuttal. PLoS One (2012) 0.81
Cloning and sequencing of the breakpoint regions of inversion 5g fixed in Drosophila buzzatii. Chromosoma (2009) 0.80
Real-time three-dimensional transoesophageal echocardiography in the assessment of aortic valve stenosis. Eur J Echocardiogr (2009) 0.77
Systolic aortic regurgitation. Eur J Echocardiogr (2008) 0.75
Correction: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1. Elife (2017) 0.75