XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

[1]  Anang A. Shelat,et al.  Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors , 2017, Nature.

[2]  Rameen Beroukhim,et al.  Patient-derived xenografts undergo murine-specific tumor evolution , 2017, Nature Genetics.

[3]  Marek Dynowski,et al.  Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models , 2017, Molecular Cancer Research.

[4]  Hans Clevers,et al.  Interrogating open issues in cancer precision medicine with patient-derived xenografts , 2017, Nature Reviews Cancer.

[5]  P. Kristel,et al.  Mechanisms of Therapy Resistance in Patient-Derived Xenograft Models of BRCA1-Deficient Breast Cancer. , 2016, Journal of the National Cancer Institute.

[6]  John W. Cassidy,et al.  A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds , 2016, Cell.

[7]  D. Adams,et al.  BRAFV600E Kinase Domain Duplication Identified in Therapy-Refractory Melanoma Patient-Derived Xenografts , 2016, Cell reports.

[8]  R. Irizarry,et al.  Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation , 2015, Nature Biotechnology.

[9]  Joshua M. Korn,et al.  High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response , 2015, Nature Medicine.

[10]  R. Scharpf,et al.  The Genomic Landscape of Response to EGFR Blockade in Colorectal Cancer , 2015, Nature.

[11]  Thomas M. Keane,et al.  The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes , 2015, Mammalian Genome.

[12]  D. Adams,et al.  Intra- and inter-tumor heterogeneity in a vemurafenib-resistant melanoma patient and derived xenografts , 2015, EMBO molecular medicine.

[13]  Rory Stark,et al.  Progesterone receptor modulates estrogen receptor-α action in breast cancer , 2015, Nature.

[14]  G. Inghirami,et al.  Stromal contribution to the colorectal cancer transcriptome , 2015, Nature Genetics.

[15]  Raphael Gottardo,et al.  Orchestrating high-throughput genomic analysis with Bioconductor , 2015, Nature Methods.

[16]  P. Vrignaud,et al.  Setting up a wide panel of patient-derived tumor xenografts of non–small cell lung cancer by improving the preanalytical steps , 2014, Cancer medicine.

[17]  Mingming Jia,et al.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..

[18]  Kai-Yuen Tso,et al.  Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts? , 2014, BMC Genomics.

[19]  Marcela Dávila López,et al.  Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions , 2014, Oncotarget.

[20]  Manuel Hidalgo,et al.  Patient-derived xenograft models: an emerging platform for translational cancer research. , 2014, Cancer discovery.

[21]  David M. Thomas,et al.  Next-Generation Sequence Analysis of Cancer Xenograft Models , 2013, PloS one.

[22]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[23]  Jeremy Wazny,et al.  Xenome—a tool for classifying reads from xenograft samples , 2012, Bioinform..

[24]  Davide Corà,et al.  A molecularly annotated platform of patient-derived xenografts ("xenopatients") identifies HER2 as an effective therapeutic target in cetuximab-resistant colorectal cancer. , 2011, Cancer discovery.

[25]  Mark T. W. Ebbert,et al.  Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes , 2011, Nature Medicine.

[26]  Thomas M. Keane,et al.  Mouse genomic variation and its effect on phenotypes and gene regulation , 2011, Nature.

[27]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[28]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[29]  Cole Trapnell,et al.  Role of Rodent Secondary Motor Cortex in Value-based Action Selection Nih Public Access Author Manuscript , 2006 .

[30]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[31]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[32]  R. Hruban,et al.  An In vivo Platform for Translational Drug Development in Pancreatic Cancer , 2006, Clinical Cancer Research.

[33]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.