Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

(2014) Z.-X. Chen et al.   GENOME RESEARCH

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice

(2013) Sofia M. C. Robb et al.   G3-Genes Genomes Genetics

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

(2012) T. T. Hu et al.   GENOME RESEARCH

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster

(2012) Raquel S. Linheiro et al.   PLoS One

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single HaploidDrosophila melanogasterEmbryo

(2011) Charles H. Langley et al.   GENETICS

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

A vertebrate case study of the quality of assemblies derived from next-generation sequences

(2011) Liang Ye et al.   GENOME BIOLOGY

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data

(2010) Anna-Sophie Fiston-Lavier et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The adaptive role of transposable elements in the Drosophila genome

(2009) Josefa González et al.   GENE

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

A Recent Adaptive Transposable Element Insertion Near Highly Conserved Developmental Loci in Drosophila melanogaster

(2009) J. Gonzalez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster

(2008) Josefa González et al.   PLOS BIOLOGY