RNA sequencing: advances, challenges and opportunities

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

Polyadenylation and degradation of incomplete RNA polymerase I transcripts in mammalian cells

(2010) Natalia Shcherbik et al.   EMBO REPORTS

Digital transcriptome profiling from attomole-level RNA samples

(2010) F. Ozsolak et al.   GENOME RESEARCH

Integrative analysis of the melanoma transcriptome

(2010) M. F. Berger et al.   GENOME RESEARCH

The Lkb1 metabolic sensor maintains haematopoietic stem cell survival

(2010) Sushma Gurumurthy et al.   NATURE

New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism

(2010) Philipp Kapranov et al.   NATURE

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma

(2010) Nallasivam Palanisamy et al.   NATURE MEDICINE

Amplification-free digital gene expression profiling from minute cell quantities

(2010) Fatih Ozsolak et al.   NATURE METHODS

FRT-seq: amplification-free, strand-specific transcriptome sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

A paired-end sequencing strategy to map the complex landscape of transcription initiation

(2010) Ting Ni et al.   NATURE METHODS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Replication of individual DNA molecules under electronic control using a protein nanopore

(2010) Felix Olasagasti et al.   Nature Nanotechnology

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

(2010) Hugues Richard et al.   NUCLEIC ACIDS RESEARCH

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Global analysis of trans-splicing in Drosophila

(2010) C. J. McManus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global and unbiased detection of splice junctions from RNA-seq data

(2010) Adam Ameur et al.   GENOME BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Circulating Tumor Cells Are Transcriptionally Similar to the Primary Tumor in a Murine Prostate Model

(2009) K. T. Helzer et al.   CANCER RESEARCH

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

Next generation sequencing of microbial transcriptomes: challenges and opportunities

(2009) Arnoud H.M. van Vliet   FEMS MICROBIOLOGY LETTERS

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Quantification of the yeast transcriptome by single-molecule sequencing

(2009) Doron Lipson et al.   NATURE BIOTECHNOLOGY

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human

(2009) Kun Zhang et al.   NATURE METHODS

Is sequencing enlightenment ending the dark age of the transcriptome?

(2009) Piero Carninci   NATURE METHODS

Virtual terminator nucleotides for next-generation DNA sequencing

(2009) Jayson Bowers et al.   NATURE METHODS

Limitations and possibilities of small RNA digital gene expression profiling

(2009) Sam E V Linsen et al.   NATURE METHODS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA

(2009) Alon Goren et al.   NATURE METHODS

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

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

(2009) Iouri Chepelev et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Enhanced Generation of Induced Pluripotent Stem Cells from a Subpopulation of Human Fibroblasts

(2009) James A. Byrne et al.   PLoS One

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line

(2009) Qi Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chimeric transcript discovery by paired-end transcriptome sequencing

(2009) C. A. Maher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

(2009) J. B. Li et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

(2009) Joshua Z Levin et al.   GENOME BIOLOGY

When good transcripts go bad: artifactual RT-PCR ‘splicing’ and genome analysis

(2008) Scott William Roy et al.   BIOESSAYS

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Chromatin structure analyses identify miRNA promoters

(2008) F. Ozsolak et al.   GENES & DEVELOPMENT

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

(2008) E. Valen et al.   GENOME RESEARCH

Characterizing the mouse ES cell transcriptome with Illumina sequencing

(2008) Ruben Rosenkranz et al.   GENOMICS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Fixing the front end

(2008) Ken Garber   NATURE BIOTECHNOLOGY

Direct multiplexed measurement of gene expression with color-coded probe pairs

(2008) Gary K Geiss et al.   NATURE BIOTECHNOLOGY

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Exploration of Small RNAs

(2008) Hideya Kawaji et al.   PLoS Genetics

A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells

(2008) H. Li et al.   SCIENCE

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

(2008) Jia Qian Wu et al.   GENOME BIOLOGY