Long-read direct RNA sequencing by 5’-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

(2018) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Characterized cantharidin distribution and related gene expression patterns in tissues of blister beetles, Epicauta chinensis

(2017) Ming Jiang et al.   Insect Science

Comparative genomic analysis of SET domain family reveals the origin, expansion, and putative function of the arthropod-specific SmydA genes as histone modifiers in insects

(2017) Feng Jiang et al.   GigaScience

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing

(2016) Maria Cartolano et al.   PLoS One

Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals

(2015) Federico Abascal et al.   BIOINFORMATICS

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

RNA sequencing: from tag-based profiling to resolving complete transcript structure

(2014) Eleonora de Klerk et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity inDrosophilaovarian cell cultures

(2014) Yuliya A. Sytnikova et al.   GENOME RESEARCH

Genome-wide identification of transcript start and end sites by transcript isoform sequencing

(2014) Vicent Pelechano et al.   Nature Protocols

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

The locust genome provides insight into swarm formation and long-distance flight

(2014) Xianhui Wang et al.   Nature Communications

PCR amplification of repetitive DNA: a limitation to genome editing technologies and many other applications

(2014) Carl Maximilian Hommelsheim et al.   Scientific Reports

Molecular Mechanisms of Phase Change in Locusts

(2013) Xianhui Wang et al.   Annual Review of Entomology

Multiple roles for Piwi in silencing Drosophila transposons

(2013) N. V. Rozhkov et al.   GENES & DEVELOPMENT

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

(2013) A. Le Thomas et al.   GENES & DEVELOPMENT

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley et al.   PLoS Genetics

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression

(2012) Grzegorz Sienski et al.   CELL

A Role for Neuronal piRNAs in the Epigenetic Control of Memory-Related Synaptic Plasticity

(2012) Priyamvada Rajasethupathy et al.   CELL

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

(2012) E. W. Loomis et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Large-Scale Transcriptome Analysis of Retroelements in the Migratory Locust, Locusta migratoria

(2012) Feng Jiang et al.   PLoS One

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Bioinformatic analysis of TE-spliced new exons within human, mouse and zebrafish genomes

(2010) Dae-Soo Kim et al.   GENOMICS

Molecular cloning and temporal–spatial expression of I element in gregarious and solitary locusts

(2010) W. Guo et al.   JOURNAL OF INSECT PHYSIOLOGY

The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates

(2010) Noa Sela et al.   GENOME BIOLOGY

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

(2009) Schraga Schwartz et al.   PLoS Computational Biology

Alternative splicing of Alu exons—two arms are better than one

(2008) Nurit Gal-Mark et al.   NUCLEIC ACIDS RESEARCH