Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors

Genomic alterations in breast cancer: level of evidence for actionability according to ESMO Scale for Clinical Actionability of molecular Targets (ESCAT)

(2019) R Condorelli et al.   ANNALS OF ONCOLOGY

Database of evidence for precision oncology portal

(2018) Sam Q Sun et al.   BIOINFORMATICS

Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

(2018) Filip Mundt et al.   CANCER RESEARCH

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

The Genomic Landscape of Mucinous Breast Cancer

(2018) Fresia Pareja et al.   JNCI-Journal of the National Cancer Institute

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

(2017) Kuan-lin Huang et al.   Nature Communications

A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer

(2017) Paul Savage et al.   Cell Reports

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds

(2016) Alejandra Bruna et al.   CELL

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis

(2016) Uri Ben-David et al.   Nature Communications

Treatment and Prognosis of Rare Breast Cancers

(2015) Alicia M. Terando et al.   ANNALS OF SURGICAL ONCOLOGY

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Genomic landscape of adenoid cystic carcinoma of the breast

(2015) Luciano G Martelotto et al.   JOURNAL OF PATHOLOGY

High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response

(2015) Hui Gao et al.   NATURE MEDICINE

Clinical management of breast cancer heterogeneity

(2015) Dimitrios Zardavas et al.   Nature Reviews Clinical Oncology

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Patient-Derived Tumor Xenografts Are Susceptible to Formation of Human Lymphocytic Tumors

(2015) Gennadiy Bondarenko et al.   NEOPLASIA

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

(2014) Peter Eirew et al.   NATURE

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

A Renewable Tissue Resource of Phenotypically Stable, Biologically and Ethnically Diverse, Patient-Derived Human Breast Cancer Xenograft Models

(2013) X. Zhang et al.   CANCER RESEARCH

Clinical Approval Success Rates for Investigational Cancer Drugs

(2013) J A DiMasi et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Modelling vemurafenib resistance in melanoma reveals a strategy to forestall drug resistance

(2013) Meghna Das Thakur et al.   NATURE

Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts

(2013) Shunqiang Li et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

(2012) Sohrab P. Shah et al.   NATURE

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

(2011) Brian D. Lehmann et al.   JOURNAL OF CLINICAL INVESTIGATION

Everolimus plus octreotide long-acting repeatable for the treatment of advanced neuroendocrine tumours associated with carcinoid syndrome (RADIANT-2): a randomised, placebo-controlled, phase 3 study

(2011) Marianne E Pavel et al.   LANCET

Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes

(2011) Yoko S DeRose et al.   NATURE MEDICINE

FGFR1 Amplification Drives Endocrine Therapy Resistance and Is a Therapeutic Target in Breast Cancer

(2010) N. Turner et al.   CANCER RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Metastatic Behavior of Breast Cancer Subtypes

(2010) Hagen Kennecke et al.   JOURNAL OF CLINICAL ONCOLOGY

Triple-Negative Breast Cancer

(2010) William D. Foulkes et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A Primary Xenograft Model of Small-Cell Lung Cancer Reveals Irreversible Changes in Gene Expression Imposed by Culture In vitro

(2009) V. C. Daniel et al.   CANCER RESEARCH

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE