Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

Genome-wide discovery of human splicing branchpoints

(2015) Tim R. Mercer et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

(2014) Tim R Mercer et al.   Nature Protocols

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

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

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

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

The Reality of Pervasive Transcription

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

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

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

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

The Human Gene Mutation Database: 2008 update

(2009) Peter D Stenson et al.   Genome Medicine