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

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

(2016) Alfonso Benítez-Páez et al.   GigaScience

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Computational approaches for isoform detection and estimation: good and bad news

(2014) Claudia Angelini et al.   BMC BIOINFORMATICS

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

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

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

(2014) Joshua Quick et al.   GigaScience

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

(2013) Marco Ferrarini et al.   BMC GENOMICS

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

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

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?

(2009) Arnold Stein et al.   NUCLEIC ACIDS RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE