Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)

A Splice-Site Mutation in a Retina-Specific Exon of BBS8 Causes Nonsyndromic Retinitis Pigmentosa

(2010) S. Amer Riazuddin et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

(2010) Jeffrey Martin et al.   BMC GENOMICS

Next generation sequencing in functional genomics

(2010) T. Werner   BRIEFINGS IN BIOINFORMATICS

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

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

(2010) Sarah B Ng et al.   NATURE GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

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

HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data

(2010) Michelle T. Dimon et al.   PLoS One

MLL2 Is Required in Oocytes for Bulk Histone 3 Lysine 4 Trimethylation and Transcriptional Silencing

(2010) Claudia V. Andreu-Vieyra et al.   PLOS BIOLOGY

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

BCL9 Promotes Tumor Progression by Conferring Enhanced Proliferative, Metastatic, and Angiogenic Properties to Cancer Cells

(2009) M. Mani et al.   CANCER RESEARCH

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

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

(2009) Ben Langmead et al.   GENOME BIOLOGY