Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia

(2012) Larry Mansouri et al.   AMERICAN JOURNAL OF HEMATOLOGY

Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children

(2012) M Sällman Almén et al.   INTERNATIONAL JOURNAL OF OBESITY

Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice

(2012) Lisa S. Andersson et al.   NATURE

Life Technologies promises $1,000 genome

(2012) Laura DeFrancesco   NATURE BIOTECHNOLOGY

Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors

(2012) K. Edlund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos

(2012) Per-Henrik Holmqvist et al.   PLoS Genetics

The future of DNA sequence archiving

(2012) Guy Cochrane et al.   GigaScience

GigaDB: announcing the GigaScience database

(2012) Tam P Sneddon et al.   GigaScience

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute

(2011) Gen-Tao Chiang et al.   BMC BIOINFORMATICS

Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits

(2011) Ghazal Zaboli et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Ultra-Deep Sequencing of Mouse Mitochondrial DNA: Mutational Patterns and Their Origins

(2011) Adam Ameur et al.   PLoS Genetics

Challenges of sequencing human genomes

(2010) D. C. Koboldt et al.   BRIEFINGS IN BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Computational solutions to large-scale data management and analysis

(2010) Eric E. Schadt et al.   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

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

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Establishing a Successful Bioinformatics Core Facility Team

(2009) Fran Lewitter et al.   PLoS Computational Biology

Managing and Analyzing Next-Generation Sequence Data

(2009) Brent G. Richter et al.   PLoS Computational Biology

Searching for SNPs with cloud computing

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE