Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

(2022) Simon A. Hardwick et al.   NATURE BIOTECHNOLOGY

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

(2021) Anoushka Joglekar et al.   Nature Communications

Author Correction: Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

(2021) Kristoffer Sahlin et al.   Nature Communications

Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

(2021) Yu H. Sun et al.   Nature Communications

Accurate spliced alignment of long RNA sequencing reads

(2021) Kristoffer Sahlin et al.   BIOINFORMATICS

Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations

(2020) David S. M. Lee et al.   Nature Communications

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

(2020) Alison D. Tang et al.   Nature Communications

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information

(2020) Zhoutao Chen et al.   GENOME RESEARCH

Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome

(2020) Jiawen Cui et al.   Plant Methods

Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data

(2020) Saber Hafezqorani et al.   GigaScience

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

(2019) Daniel P. Depledge et al.   Nature Communications

Single-molecule long-read sequencing reveals the chromatin basis of gene expression

(2019) Yunhao Wang et al.   GENOME RESEARCH

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

(2019) Mandeep Singh et al.   Nature Communications

PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3′ end sequencing

(2019) Christina J Herrmann et al.   NUCLEIC ACIDS RESEARCH

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA

(2018) Roger Volden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

(2017) Hagen Tilgner et al.   GENOME RESEARCH

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

(2017) Ashley Byrne et al.   Nature Communications

A new view of transcriptome complexity and regulation through the lens of local splicing variations

(2016) Jorge Vaquero-Garcia et al.   eLife

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

(2016) Spyros Oikonomopoulos et al.   Scientific Reports

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

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

(2015) Hagen Tilgner et al.   NATURE BIOTECHNOLOGY

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing

(2015) Jason L. Weirather et al.   NUCLEIC ACIDS RESEARCH

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

(2013) Mengyao Zhao et al.   PLoS One

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing

(2013) Hagen Tilgner et al.   G3-Genes Genomes Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes

(2009) P. P.-S. Wang et al.   RNA

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE