Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development

CD44 splice isoform switching determines breast cancer stem cell state

(2019) Honghong Zhang et al.   GENES & DEVELOPMENT

Increased intron retention is a post-transcriptional signature associated with progressive aging and Alzheimer’s disease

(2019) Swarnaseetha Adusumalli et al.   AGING CELL

Recompleting the Caenorhabditis elegans genome

(2019) Jun Yoshimura et al.   GENOME RESEARCH

A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing

(2019) Francesca Angiolini et al.   eLife

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations

(2018) Zuguang Gu et al.   BMC GENOMICS

Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism

(2018) Ying Yang et al.   CELL RESEARCH

A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing

(2018) Bo Wang et al.   GENOME RESEARCH

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

(2018) Manuel Tardaguila et al.   GENOME RESEARCH

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni

(2018) Xiaoliang Ren et al.   NUCLEIC ACIDS RESEARCH

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

Comparative mitochondrial genomics reveals a possible role of a recent duplication of NADH dehydrogenase subunit 5 in gene regulation

(2018) Runsheng Li et al.   DNA RESEARCH

De novo clustering of long reads by gene from transcriptomics data

(2018) Camille Marchet et al.   NUCLEIC ACIDS RESEARCH

Quantitative RNA-seq meta-analysis of alternative exon usage inC. elegans

(2017) Nicolas J. Tourasse et al.   GENOME RESEARCH

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

WormBase 2017: molting into a new stage

(2017) Raymond Y N Lee et al.   NUCLEIC ACIDS RESEARCH

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression

(2016) Runsheng Li et al.   GENOME RESEARCH

The time-resolved transcriptome ofC. elegans

(2016) Max E. Boeck et al.   GENOME RESEARCH

Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes

(2016) Ji-Ann Lee et al.   NEURON

Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites inC. elegans

(2015) James Matthew Ragle et al.   GENOME RESEARCH

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

(2015) Hagen Tilgner et al.   NATURE BIOTECHNOLOGY

Successful test launch for nanopore sequencing

(2015) Nicholas J Loman et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome

(2015) Runsheng Li et al.   Scientific Reports

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

Profiling the RNA editomes of wild-typeC. elegansand ADAR mutants

(2014) Han-Qing Zhao et al.   GENOME RESEARCH

Conservation of mRNA and Protein Expression during Development of C. elegans

(2014) Dominic Grün et al.   Cell Reports

The transcription start site landscape of C. elegans

(2013) T. L. Saito et al.   GENOME RESEARCH

The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures

(2013) R. A.- J. Chen et al.   GENOME RESEARCH

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation

(2013) William S Kruesi et al.   eLife

CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

(2012) Weifeng Gu et al.   CELL

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

RNA-seq analysis of the C. briggsae transcriptome

(2012) B. Uyar et al.   GENOME RESEARCH

Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans

(2012) C. S. Maxwell et al.   GENOME RESEARCH

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines

(2012) Décio L. Eizirik et al.   PLoS Genetics

The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates

(2011) J. M. Mudge et al.   MOLECULAR BIOLOGY AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Caenorhabditis briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility and the Evolution of Recombination

(2011) Joseph A. Ross et al.   PLoS Genetics

Trans -splicing

(2011) Erika L. Lasda et al.   Wiley Interdisciplinary Reviews-RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

(2010) A. K. Ramani et al.   GENOME RESEARCH

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

The Landscape of C. elegans 3'UTRs

(2010) M. Mangone et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Alternative Splicing and the Steady-State Ratios of mRNA Isoforms Generated by It Are under Strong Stabilizing Selection in Caenorhabditis elegans

(2008) S. Barberan-Soler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

RNA cytosine methylation analysis by bisulfite sequencing

(2008) M. Schaefer et al.   NUCLEIC ACIDS RESEARCH