Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases

Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers

(2016) Christopher A. Miller et al.   Nature Communications

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

(2015) Giovanni Ciriello et al.   CELL

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers

(2015) Melissa Q McCreery et al.   NATURE MEDICINE

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

The Genetic Evolution of Melanoma from Precursor Lesions

(2015) A. Hunter Shain et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets

(2015) P. K. Brastianos et al.   Cancer Discovery

Loss of INPP4B causes a DNA repair defect through loss of BRCA1, ATM and ATR and can be targeted with PARP inhibitor treatment

(2015) Laura R. H. Ip et al.   Oncotarget

Spatial and Temporal Heterogeneity in High-Grade Serous Ovarian Cancer: A Phylogenetic Analysis

(2015) Roland F. Schwarz et al.   PLOS MEDICINE

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

Concordance of Genomic Alterations between Primary and Recurrent Breast Cancer

(2014) F. Meric-Bernstam et al.   MOLECULAR CANCER THERAPEUTICS

Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor

(2014) Dejan Juric et al.   NATURE

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

(2014) Simon A. Forbes 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

Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing

(2014) J. Zhang et al.   SCIENCE

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

(2014) Christopher A. Miller et al.   PLoS Computational Biology

Genomic evolution from primary breast carcinoma to distant metastasis: Few copy number changes of breast cancer related genes

(2013) Cathy B. Moelans et al.   CANCER LETTERS

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

(2013) K. Chen et al.   GENOME RESEARCH

Metastatic progression of breast cancer: insights from 50 years of autopsies

(2013) Margaret C Cummings et al.   JOURNAL OF PATHOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Impact of Breast Cancer Subtypes and Treatment on Survival: An Analysis Spanning Two Decades

(2012) R. Haque et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

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

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

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival

(2011) Victor J. Weigman et al.   BREAST CANCER RESEARCH AND TREATMENT

Genomic analysis identifies unique signatures predictive of brain, lung, and liver relapse

(2011) J. Chuck Harrell et al.   BREAST CANCER RESEARCH AND TREATMENT

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Evidence that Inositol Polyphosphate 4-Phosphatase Type II Is a Tumor Suppressor that Inhibits PI3K Signaling

(2009) Christina Gewinner et al.   CANCER CELL

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

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

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

Subtypes of Breast Cancer Show Preferential Site of Relapse

(2008) M. Smid et al.   CANCER RESEARCH

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

(2008) P. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA