The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine

The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data

(2014) Xiaojia Tang et al.   NUCLEIC ACIDS RESEARCH

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors

(2014) Matthew D. Wilkerson et al.   NUCLEIC ACIDS RESEARCH

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

(2013) Nicolas C Nalpas et al.   BMC GENOMICS

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The Retinoblastoma Gene Undergoes Rearrangements inBRCA1-Deficient Basal-like Breast Cancer

(2012) Göran Jönsson 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

Can Genomics Bend the Cost Curve?

(2012) Katrina Armstrong   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead 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

Prediction of outcome after diagnosis of metachronous contralateral breast cancer

(2011) Sara Alkner et al.   BMC CANCER

Probe mapping across multiple microarray platforms

(2011) J. D. Allen et al.   BRIEFINGS IN BIOINFORMATICS

Large Scale Library Generation for High Throughput Sequencing

(2011) Erik Borgström et al.   PLoS One

NORDCAN – a Nordic tool for cancer information, planning, quality control and research

(2010) Gerda Engholm et al.   ACTA ONCOLOGICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Identification of Subtypes in Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer Reveals a Gene Signature Prognostic of Outcome

(2010) Johan Staaf et al.   JOURNAL OF CLINICAL ONCOLOGY

Cancer survival in Australia, Canada, Denmark, Norway, Sweden, and the UK, 1995–2007 (the International Cancer Benchmarking Partnership): an analysis of population-based cancer registry data

(2010) MP Coleman et al.   LANCET

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

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

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

BASE - 2nd generation software for microarray data management and analysis

(2009) Johan Vallon-Christersson et al.   BMC BIOINFORMATICS

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

Refining systemic therapy for early breast cancer: difficulties with subtraction

(2009) David Dodwell et al.   LANCET ONCOLOGY

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

An Immune Response Enriched 72-Gene Prognostic Profile for Early-Stage Non-Small-Cell Lung Cancer

(2008) P. Roepman et al.   CLINICAL CANCER RESEARCH

The expression of 16 genes related to the cell of origin and immune response predicts survival in elderly patients with diffuse large B-cell lymphoma treated with CHOP and rituximab

(2008) J-P Jais et al.   LEUKEMIA