Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes

Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays

(2011) Johannes Eichner et al.   BMC BIOINFORMATICS

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

(2011) M. Hafner et al.   RNA

A spatial and temporal map of C. elegans gene expression

(2010) W. C. Spencer et al.   GENOME RESEARCH

Strand-specific deep sequencing of the transcriptome

(2010) A. P. Vivancos et al.   GENOME RESEARCH

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome

(2010) A. T. Lamm et al.   GENOME RESEARCH

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

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

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Transcriptome Analysis of Pseudomonas syringae Identifies New Genes, Noncoding RNAs, and Antisense Activity

(2010) M. J. Filiatrault et al.   JOURNAL OF BACTERIOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Deep SAGE analysis of the Caenorhabditis elegans transcriptome

(2010) Peter Ruzanov et al.   NUCLEIC ACIDS RESEARCH

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

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

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

(2010) Joseph K. Pickrell et al.   PLoS Genetics

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

(2010) Moran Yassour et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

(2009) Daniel A Hahn et al.   BMC GENOMICS

mGene: Accurate SVM-based gene finding with an application to nematode genomes

(2009) G. Schweikert et al.   GENOME RESEARCH

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Regulatory roles of natural antisense transcripts

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

WormBase: a comprehensive resource for nematode research

(2009) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

(2009) Timothy T. Perkins et al.   PLoS Genetics

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

(2008) Ryan Lister et al.   CELL

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

(2008) Andrzej T. Wierzbicki et al.   CELL

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

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

(2008) Qun Pan et al.   NATURE GENETICS

Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation

(2008) Francois Vigneault et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Divergent Transcription from Active Promoters

(2008) Amy C. Seila 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