Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts

Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models

(2017) Garima Khandelwal et al.   MOLECULAR CANCER RESEARCH

Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

(2017) Maurizio Callari et al.   Genome Medicine

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

(2016) Alejandra Bruna et al.   CELL

Patient-derived tumour xenografts for breast cancer drug discovery

(2016) John W Cassidy et al.   ENDOCRINE-RELATED CANCER

Maintaining Tumor Heterogeneity in Patient-Derived Tumor Xenografts

(2015) J. W. Cassidy et al.   CANCER RESEARCH

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

(2015) Hui Gao et al.   NATURE MEDICINE

Context-Specific Effects of TGF-β/SMAD3 in Cancer Are Modulated by the Epigenome

(2015) Ana Tufegdzic Vidakovic et al.   Cell Reports

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

(2014) S. Anders et al.   BIOINFORMATICS

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

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

(2014) M. Hidalgo et al.   Cancer Discovery

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Xenome--a tool for classifying reads from xenograft samples

(2012) T. Conway et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Patient-derived tumour xenografts as models for oncology drug development

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

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

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

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

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