Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines

A Novel Ras Inhibitor (MDC-1016) Reduces Human Pancreatic Tumor Growth in Mice

(2015) Gerardo G Mackenzie et al.   NEOPLASIA

Policy: NIH plans to enhance reproducibility

(2014) Francis S. Collins et al.   NATURE

BioBlend: automating pipeline analyses within Galaxy and CloudMan

(2013) C. Sloggett et al.   BIOINFORMATICS

Web-based visual analysis for high-throughput genomics

(2013) Jeremy Goecks et al.   BMC GENOMICS

Treatment of BRAF-Mutant Melanoma: The Role of Vemurafenib and Other Therapies

(2013) S Jang et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Biomarkers of drugs targeting HER-family signalling in cancer

(2013) Filippo Montemurro et al.   JOURNAL OF PATHOLOGY

Which drug, and when, for patients with BRAF-mutant melanoma?

(2013) Sekwon Jang et al.   LANCET ONCOLOGY

Small molecule inhibition of the KRAS–PDEδ interaction impairs oncogenic KRAS signalling

(2013) Gunther Zimmermann et al.   NATURE

Drug for an 'undruggable' protein

(2013) Nicole M. Baker et al.   NATURE

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas

(2013) Larsson Omberg et al.   NATURE GENETICS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

DGIdb: mining the druggable genome

(2013) Malachi Griffith et al.   NATURE METHODS

A new approach for blocking KRAS

(2013) Man Tsuey Tse   NATURE REVIEWS DRUG DISCOVERY

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

(2013) Emma M. Quinn et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comprehensive Genomic Studies

(2012) Sandra A. McDonald et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

Identification of novel germline polymorphisms governing capecitabine sensitivity

(2012) Peter H. O'Donnell et al.   CANCER

KRas Induces a Src/PEAK1/ErbB2 Kinase Amplification Loop That Drives Metastatic Growth and Therapy Resistance in Pancreatic Cancer

(2012) J. A. Kelber et al.   CANCER RESEARCH

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

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

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

NGS analyses by visualization with Trackster

(2012) Jeremy Goecks et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genome-Wide Characterization of Pancreatic Adenocarcinoma Patients Using Next Generation Sequencing

(2012) Winnie S. Liang et al.   PLoS One

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

Making whole genome multiple alignments usable for biologists

(2011) Daniel Blankenberg et al.   BIOINFORMATICS

Oncogene addiction as a foundational rationale for targeted anti-cancer therapy: promises and perils

(2011) Davide Torti et al.   EMBO Molecular Medicine

Impact of KRAS Mutations on Clinical Outcomes in Pancreatic Cancer Patients Treated with First-line Gemcitabine-Based Chemotherapy

(2011) S. T. Kim et al.   MOLECULAR CANCER THERAPEUTICS

Harnessing cloud computing with Galaxy Cloud

(2011) Enis Afgan et al.   NATURE BIOTECHNOLOGY

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

(2011) Paul B. Chapman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Exploring the Genomes of Cancer Cells: Progress and Promise

(2011) M. R. Stratton   SCIENCE

Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

(2011) S. Roychowdhury et al.   Science Translational Medicine

Integrating diverse databases into an unified analysis framework: a Galaxy approach

(2011) D. Blankenberg et al.   Database-The Journal of Biological Databases and Curation

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

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

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

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes 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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Principles of Cancer Therapy: Oncogene and Non-oncogene Addiction

(2009) Ji Luo et al.   CELL

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Oncogene Addiction

(2008) I. B. Weinstein et al.   CANCER RESEARCH