Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

SEQanswers: an open access community for collaboratively decoding genomes

(2012) Jing-Woei Li et al.   BIOINFORMATICS

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Raise standards for preclinical cancer research

(2012) C. Glenn Begley et al.   NATURE

The 1000 Genomes Project: data management and community access

(2012) Laura Clarke 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

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

(2012) A. Auton et al.   SCIENCE

Galaxy CloudMan: delivering cloud compute clusters

(2011) Enis Afgan et al.   BMC BIOINFORMATICS

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Harnessing cloud computing with Galaxy Cloud

(2011) Enis Afgan et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Coding your way out of a problem

(2011) Jeffrey M. Perkel   NATURE METHODS

GeneProf: analysis of high-throughput sequencing experiments

(2011) Florian Halbritter et al.   NATURE METHODS

Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1

(2011) N. Agrawal et al.   SCIENCE

The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

(2011) N. Stransky et al.   SCIENCE

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

(2011) Laurence D. Parnell et al.   PLoS Computational Biology

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study

(2011) Hiroki Goto et al.   GENOME BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Accessible Reproducible Research

(2010) J. P. Mesirov   SCIENCE

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Mobyle: a new full web bioinformatics framework

(2009) B. Neron et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Repeatability of published microarray gene expression analyses

(2009) John P A Ioannidis et al.   NATURE GENETICS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS