Systematic evaluation of spliced alignment programs for RNA-seq data

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

All your base: a fast and accurate probabilistic approach to base calling

(2012) Tim Massingham et al.   GENOME BIOLOGY

High levels of RNA-editing site conservation amongst 15 laboratory mouse strains

(2012) Petr Daneck et al.   GENOME BIOLOGY

Comparative analysis of information contents relevant to recognition of introns in many species

(2011) Hiroaki Iwata et al.   BMC GENOMICS

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Critical assessment of methods of protein structure prediction (CASP)-round IX

(2011) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2010) T. D. Wu 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

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

PASS: a program to align short sequences

(2009) D. Campagna et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS