The Human Transcriptome: An Unfinished Story

Detection of Redundant Fusion Transcripts as Biomarkers or Disease-Specific Therapeutic Targets in Breast Cancer

(2012) Y. W. Asmann et al.   CANCER RESEARCH

Knowledge-Based Reconstruction of mRNA Transcripts with Short Sequencing Reads for Transcriptome Research

(2012) Junhee Seok et al.   PLoS One

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) J. K. Pickrell et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) W. Lin et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) C. L. Kleinman et al.   SCIENCE

RNA Editing adds flavor to complexity

(2011) C. P. Godfried Sie et al.   BIOCHEMISTRY-MOSCOW

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

(2011) Philipp Kapranov et al.   BMC BIOLOGY

The noncoding universe

(2011) Kester Jarvis et al.   BMC BIOLOGY

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

The central role of RNA in human development and cognition

(2011) John S. Mattick   FEBS LETTERS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

(2011) Wei Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Inference of Isoforms from Short Sequence Reads

(2011) Jianxing Feng et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

lncRNAs: Finding the Forest Among the Trees?

(2011) Marcel E Dinger   MOLECULAR THERAPY

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Very Few RNA and DNA Sequence Differences in the Human Transcriptome

(2011) Daniel R. Schrider et al.   PLoS One

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

Response to “The Reality of Pervasive Transcription”

(2011) Harm van Bakel et al.   PLOS BIOLOGY

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

The architecture of RNA polymerase fidelity

(2010) Craig D Kaplan   BMC BIOLOGY

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

(2010) Ashish Agarwal et al.   BMC GENOMICS

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

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Between a chicken and a grape: estimating the number of human genes

(2010) Mihaela Pertea et al.   GENOME BIOLOGY

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Non-coding RNAs: regulators of disease

(2009) Ryan J Taft et al.   JOURNAL OF PATHOLOGY

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Evidence for large diversity in the human transcriptome created by Alu RNA editing

(2009) Michal Barak et al.   NUCLEIC ACIDS RESEARCH

Genomic Clues to DNA Treasure Sometimes Lead Nowhere

(2009) D. Monroe   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Long intronic noncoding RNA transcription: Expression noise or expression choice?

(2008) Rodrigo Louro et al.   GENOMICS

Noncoding RNA in development

(2008) Paulo P. Amaral et al.   MAMMALIAN GENOME

Genomics: Protein fossils live on as RNA

(2008) Rajkumar Sasidharan et al.   NATURE

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

(2008) John C Castle et al.   NATURE GENETICS

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

(2008) Qun Pan et al.   NATURE GENETICS

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

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE