SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq

(2011) Wen Huang et al.   BMC GENOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing

(2011) Dale N. Richardson et al.   PLoS One

Supersplat--spliced RNA-seq alignment

(2010) D. W. Bryant et al.   BIOINFORMATICS

Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

(2010) Adam Labadorf et al.   BMC GENOMICS

Alternative splicing: global insights

(2010) Martina Hallegger et al.   FEBS Journal

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

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

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery 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

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

(2010) Hugues Richard et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq

(2010) Liguo Wang et al.   PLoS One

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

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach

(2009) Paola Bonizzoni et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

(2009) M. Yassour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Sircah: a tool for the detection and visualization of alternative transcripts

(2008) E. D. Harrington et al.   BIOINFORMATICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

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

(2008) Qun Pan et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Support Vector Machines and Kernels for Computational Biology

(2008) Asa Ben-Hur et al.   PLoS Computational Biology