Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis

(2020) Yvonne A. Evrard et al.   CANCER RESEARCH

Unstable genome and transcriptome dynamics during tumor metastasis contribute to therapeutic heterogeneity in colorectal cancers

(2019) Sung-Yup Cho et al.   CLINICAL CANCER RESEARCH

Neoantigen-directed immune escape in lung cancer evolution

(2019) Rachel Rosenthal et al.   NATURE

Integrative pharmacogenomics analysis of patient-derived xenografts

(2019) Arvind Singh Mer et al.   CANCER RESEARCH

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

(2019) Yuanhang Liu et al.   Scientific Reports

PDXliver: a database of liver cancer patient derived xenograft mouse models

(2018) Sheng He et al.   BMC CANCER

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

Oncogenic Signaling Pathways in The Cancer Genome Atlas

(2018) Francisco Sanchez-Vega et al.   CELL

Noise cancellation using total variation for copy number variation detection

(2018) Fatima Zare et al.   BMC BIOINFORMATICS

Human Disease Ontology 2018 update: classification, content and workflow expansion

(2018) Lynn M Schriml et al.   NUCLEIC ACIDS RESEARCH

High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts

(2018) Hyunsoo Kim et al.   Scientific Reports

Multiregion Genomic Analysis of Serially Transplanted Patient-derived Xenograft Tumors

(2018) KUNIAKI SATO et al.   Cancer Genomics & Proteomics

Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer

(2017) Klara M. Giessler et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway

(2017) Vasanthi S. Viswanathan et al.   NATURE

Patient-derived xenografts undergo mouse-specific tumor evolution

(2017) Uri Ben-David et al.   NATURE GENETICS

Tracking the Evolution of Non–Small-Cell Lung Cancer

(2017) Mariam Jamal-Hanjani et al.   NEW ENGLAND JOURNAL OF MEDICINE

Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer

(2017) Claudio Isella et al.   Nature Communications

Pan-cancer analysis of bi-allelic alterations in homologous recombination DNA repair genes

(2017) Nadeem Riaz et al.   Nature Communications

GenVisR: Genomic Visualizations in R

(2016) Zachary L. Skidmore et al.   BIOINFORMATICS

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

(2016) Alejandra Bruna et al.   CELL

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

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

Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq

(2016) Uri Weissbein et al.   Nature Communications

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Uncovering the genomic heterogeneity of multifocal breast cancer

(2015) Christine Desmedt et al.   JOURNAL OF PATHOLOGY

Pharmacogenomic agreement between two cancer cell line data sets

(2015) Nicolas Stransky et al.   NATURE

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

Stromal contribution to the colorectal cancer transcriptome

(2015) Claudio Isella et al.   NATURE GENETICS

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

(2015) Hui Gao et al.   NATURE MEDICINE

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

NAMPT Is the Cellular Target of STF-31-Like Small-Molecule Probes

(2014) Drew J. Adams et al.   ACS Chemical Biology

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

Focal chromosomal copy number aberrations in cancer—Needles in a genome haystack

(2014) Oscar Krijgsman et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Patient-Derived Xenografts from Non-Small Cell Lung Cancer Brain Metastases Are Valuable Translational Platforms for the Development of Personalized Targeted Therapy

(2014) H. W. Lee et al.   CLINICAL CANCER RESEARCH

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

(2014) Ilari Scheinin et al.   GENOME RESEARCH

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

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

(2014) Peter Eirew et al.   NATURE

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

(2014) Marco Gerlinger et al.   NATURE GENETICS

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

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

Patient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research

(2014) M. Hidalgo et al.   Cancer Discovery

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

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Virtual karyotyping of pluripotent stem cells on the basis of their global gene expression profiles

(2013) Uri Ben-David et al.   Nature Protocols

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

(2013) Shunqiang Li et al.   Cell Reports

Xenome--a tool for classifying reads from xenograft samples

(2012) T. Conway et al.   BIOINFORMATICS

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

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

Characterization of a Large Panel of Patient-Derived Tumor Xenografts Representing the Clinical Heterogeneity of Human Colorectal Cancer

(2012) S. Julien et al.   CLINICAL CANCER RESEARCH

Focal aberrations indicateEYA2andhsa-miR-375as oncogene and tumor suppressor in cervical carcinogenesis

(2012) Mariska Bierkens et al.   GENES CHROMOSOMES & CANCER

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

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

(2012) Jordi Barretina et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Patient-derived tumour xenografts as models for oncology drug development

(2012) John J. Tentler et al.   Nature Reviews Clinical Oncology

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

The Impact of Errors in Copy Number Variation Detection Algorithms on Association Results

(2012) Nathan E. Wineinger et al.   PLoS One

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

A Pilot Clinical Study of Treatment Guided by Personalized Tumorgrafts in Patients with Advanced Cancer

(2011) M. Hidalgo et al.   MOLECULAR CANCER THERAPEUTICS

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

Humanized Mouse Model of Ovarian Cancer Recapitulates Patient Solid Tumor Progression, Ascites Formation, and Metastasis

(2011) Richard B. Bankert et al.   PLoS One

Cross-species hybridization of microarrays for studying tumor transcriptome of brain metastasis

(2011) E. S. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Humanized mouse models to study human diseases

(2011) Michael A Brehm et al.   Current Opinion in Endocrinology Diabetes and Obesity

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Signatures of mutation and selection in the cancer genome

(2010) Graham R. Bignell et al.   NATURE

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

(2010) Li Ding et al.   NATURE

Anticancer drug development: the grand challenges

(2010) William N. Hait   NATURE REVIEWS DRUG DISCOVERY

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Mouse xenograft models vs GEM models for human cancer therapeutics

(2008) A. Richmond et al.   Disease Models & Mechanisms

Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers

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