Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

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

(2014) Claudia Angelini et al.   BMC BIOINFORMATICS

TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads

(2014) Naoki Nariai et al.   BMC GENOMICS

Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates

(2014) Sahar Al Seesi et al.   BMC GENOMICS

Building Robust Transcriptomes with Master Splicing Factors

(2014) Mohini Jangi et al.   CELL

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

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

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells

(2014) Andreas R. Gruber et al.   Nature Communications

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference

(2013) Naoki Nariai et al.   BIOINFORMATICS

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Flexible analysis of RNA-seq data using mixed effects models

(2013) Ernest Turro et al.   BIOINFORMATICS

Benchmarking short sequence mapping tools

(2013) Ayat Hatem et al.   BMC BIOINFORMATICS

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

(2013) Hong Han et al.   NATURE

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

(2013) Stefan Wilkening et al.   NUCLEIC ACIDS RESEARCH

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

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads

(2012) Wei Li et al.   BIOINFORMATICS

Identifying differentially expressed transcripts from RNA-seq data with biological variation

(2012) Peter Glaus et al.   BIOINFORMATICS

Extensive alternative polyadenylation during zebrafish development

(2012) I. Ulitsky et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Snail Represses the Splicing Regulator Epithelial Splicing Regulatory Protein 1 to Promote Epithelial-Mesenchymal Transition

(2012) Lauren M. Reinke et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis

(2012) Sophie Schbath et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution

(2012) Robert K. Bradley et al.   PLOS BIOLOGY

Estimation of alternative splicing isoform frequencies from RNA-Seq data

(2011) Marius Nicolae et al.   Algorithms for Molecular Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

(2011) P. J. Shepard et al.   RNA

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

(2011) Ernest Turro et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Turning on a Fuel Switch of Cancer: hnRNP Proteins Regulate Alternative Splicing of Pyruvate Kinase mRNA

(2010) M. Chen et al.   CANCER RESEARCH

An ESRP-regulated splicing programme is abrogated during the epithelial–mesenchymal transition

(2010) Claude C Warzecha et al.   EMBO JOURNAL

Deciphering the splicing code

(2010) Yoseph Barash 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

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

(2010) M. Khorshid et al.   NUCLEIC ACIDS RESEARCH

3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples

(2010) Andrew H. Beck et al.   PLoS One

Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme

(2010) Kristian Ovaska et al.   Genome Medicine

Differential expression analysis for sequence count data

(2010) Simon Anders 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

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

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

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS