VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

Early Prediction of Response to Tyrosine Kinase Inhibitors by Quantification of EGFR Mutations in Plasma of NSCLC Patients

(2015) Antonio Marchetti et al.   Journal of Thoracic Oncology

Acquired EGFR C797S mutation mediates resistance to AZD9291 in non–small cell lung cancer harboring EGFR T790M

(2015) Kenneth S Thress et al.   NATURE MEDICINE

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

(2015) Adam D Ewing et al.   NATURE METHODS

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

A defining decade in DNA sequencing

(2014) John D McPherson   NATURE METHODS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Next-generation sequencing in the clinic

(2013) Jason Y Park et al.   NATURE BIOTECHNOLOGY

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Clinical significance of large rearrangements inBRCA1andBRCA2

(2012) Thaddeus Judkins et al.   CANCER

Identifying and Targeting ROS1 Gene Fusions in Non-Small Cell Lung Cancer

(2012) K. D. Davies et al.   CLINICAL CANCER RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Olaparib Maintenance Therapy in Platinum-Sensitive Relapsed Ovarian Cancer

(2012) Jonathan Ledermann et al.   NEW ENGLAND JOURNAL OF MEDICINE

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Molecular Mechanisms of Resistance to Cetuximab and Panitumumab in Colorectal Cancer

(2010) Alberto Bardelli et al.   JOURNAL OF CLINICAL ONCOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

K-rasMutations and Benefit from Cetuximab in Advanced Colorectal Cancer

(2008) Christos S. Karapetis et al.   NEW ENGLAND JOURNAL OF MEDICINE