The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils

[1]  Menna E. Jones,et al.  Density trends and demographic signals uncover the long-term impact of transmissible cancer in Tasmanian devils. , 2018, The Journal of applied ecology.

[2]  Y. Kwon,et al.  Tasman-PCR: a genetic diagnostic assay for Tasmanian devil facial tumour diseases , 2018, bioRxiv.

[3]  Francesca Giordano,et al.  scanPAV: a pipeline for extracting presence–absence variations in genome pairs , 2018, Bioinform..

[4]  A. Stemmer-Rachamimov,et al.  Programming of Schwann Cells by Lats1/2-TAZ/YAP Signaling Drives Malignant Peripheral Nerve Sheath Tumorigenesis. , 2018, Cancer cell.

[5]  J. Deakin,et al.  Identification of candidate genes for devil facial tumour disease tumourigenesis , 2017, Scientific Reports.

[6]  Adrian Baez-Ortega,et al.  Computational approaches for discovery of mutational signatures in cancer , 2017, bioRxiv.

[7]  S. Pyecroft,et al.  ERBB3: A potential serum biomarker for early detection and therapeutic target for devil facial tumour 1 (DFT1) , 2017, PloS one.

[8]  E. Wang,et al.  WWC3 regulates the Wnt and Hippo pathways via Dishevelled proteins and large tumour suppressor 1, to suppress lung cancer invasion and metastasis , 2017, The Journal of pathology.

[9]  Jincheng Wang,et al.  A reciprocal regulatory loop between TAZ/YAP and G-protein Gαs regulates Schwann cell proliferation and myelination , 2017, Nature Communications.

[10]  Menna E. Jones,et al.  Variants in the host genome may inhibit tumour growth in devil facial tumours: evidence from genome-wide association , 2017, Scientific Reports.

[11]  M. Hurles,et al.  Somatic mutations reveal asymmetric cellular dynamics in the early human embryo , 2017, Nature.

[12]  A. B. Lyons,et al.  Regression of devil facial tumour disease following immunotherapy in immunised Tasmanian devils , 2017, Scientific Reports.

[13]  Joachim Weischenfeldt,et al.  SvABA: genome-wide detection of structural variants and indels by local assembly , 2018, Genome research.

[14]  D. Parkinson,et al.  Merlin controls the repair capacity of Schwann cells after injury by regulating Hippo/YAP activity , 2017, The Journal of cell biology.

[15]  T. Lange,et al.  Telomeres in cancer: tumour suppression and genome instability , 2017, Nature Reviews Molecular Cell Biology.

[16]  Jiqiang Guo,et al.  Stan: A Probabilistic Programming Language. , 2017, Journal of statistical software.

[17]  Hans Clevers,et al.  Tissue-specific mutation accumulation in human adult stem cells during life , 2016, Nature.

[18]  A. B. Lyons,et al.  Demonstration of immune responses against devil facial tumour disease in wild Tasmanian devils , 2016, Biology Letters.

[19]  Elizabeth P. Murchison,et al.  Rapid evolutionary response to a transmissible cancer in Tasmanian devils , 2016, Nature Communications.

[20]  W. Hong,et al.  Targeting the Hippo Signaling Pathway for Tissue Regeneration and Cancer Therapy , 2016, Genes.

[21]  Stefano Piccolo,et al.  YAP/TAZ at the Roots of Cancer. , 2016, Cancer cell.

[22]  S. Baldwin,et al.  Widespread transmission of independent cancer lineages within multiple bivalve species , 2016, Nature.

[23]  Eleni Fotopoulou,et al.  Mitochondrial genetic diversity, selection and recombination in a canine transmissible cancer , 2016, eLife.

[24]  Francesco Iorio,et al.  Multilevel models improve precision and speed of IC50 estimates. , 2016, Pharmacogenomics.

[25]  David C. Jones,et al.  Landscape of somatic mutations in 560 breast cancer whole genome sequences , 2016, Nature.

[26]  Menna E. Jones,et al.  Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease , 2016, PloS one.

[27]  C. Roberts,et al.  Targeting EZH2 in cancer , 2016, Nature Medicine.

[28]  Arthur Wuster,et al.  Timing, rates and spectra of human germline mutation , 2015, Nature Genetics.

[29]  A. B. Lyons,et al.  A second transmissible cancer in Tasmanian devils , 2015, Proceedings of the National Academy of Sciences.

[30]  M. Stratton,et al.  Clock-like mutational processes in human somatic cells , 2015, Nature Genetics.

[31]  Bin Zhao,et al.  Hippo Pathway in Organ Size Control, Tissue Homeostasis, and Cancer , 2015, Cell.

[32]  Serena Nik-Zainal,et al.  A mutational signature in gastric cancer suggests therapeutic strategies , 2015, Nature Communications.

[33]  S. Goff,et al.  Horizontal Transmission of Clonal Cancer Cells Causes Leukemia in Soft-Shell Clams , 2015, Cell.

[34]  Jessica Zucman-Rossi,et al.  Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets , 2015, Nature Genetics.

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

[36]  Kun-Liang Guan,et al.  The emerging roles of YAP and TAZ in cancer , 2015, Nature Reviews Cancer.

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

[38]  Menna E. Jones,et al.  Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease , 2014, Biology Letters.

[39]  Roland Eils,et al.  circlize implements and enhances circular visualization in R , 2014, Bioinform..

[40]  G. McVean,et al.  Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications , 2014, Nature Genetics.

[41]  G. Weinstock,et al.  TIGRA: A targeted iterative graph routing assembler for breakpoint assembly , 2014, Genome research.

[42]  Peter J. Campbell,et al.  Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage , 2014, Science.

[43]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[44]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[45]  L. Dahlin,et al.  Repair of the Peripheral Nerve—Remyelination that Works , 2013, Brain sciences.

[46]  D. Phalen,et al.  Vincristine Chemotherapy Trials and Pharmacokinetics in Tasmanian Devils with Tasmanian Devil Facial Tumor Disease , 2013, PloS one.

[47]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[48]  Menna E. Jones,et al.  Reversible epigenetic down-regulation of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer , 2013, Proceedings of the National Academy of Sciences.

[49]  Sridhar Ramaswamy,et al.  Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells , 2012, Nucleic Acids Res..

[50]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[51]  Menna E. Jones,et al.  Biting injuries and transmission of Tasmanian devil facial tumour disease. , 2013, The Journal of animal ecology.

[52]  Margaret A. Strong,et al.  Extreme Telomere Length Dimorphism in the Tasmanian Devil and Related Marsupials Suggests Parental Control of Telomere Length , 2012, PloS one.

[53]  A. Børresen-Dale,et al.  Mutational Processes Molding the Genomes of 21 Breast Cancers , 2012, Cell.

[54]  Arul M Chinnaiyan,et al.  PARP-1 inhibition as a targeted strategy to treat Ewing's sarcoma. , 2012, Cancer research.

[55]  Heng Li,et al.  Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly , 2012, Bioinform..

[56]  S. Ramaswamy,et al.  Systematic identification of genomic markers of drug sensitivity in cancer cells , 2012, Nature.

[57]  Carolyn Tregidgo,et al.  Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer , 2012, Cell.

[58]  C. Amemiya,et al.  Genomic Restructuring in the Tasmanian Devil Facial Tumour: Chromosome Painting and Gene Mapping Provide Clues to Evolution of a Transmissible Tumour , 2012, PLoS genetics.

[59]  S. Hochreiter,et al.  cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate , 2012, Nucleic acids research.

[60]  K. Belov,et al.  Allorecognition in the Tasmanian Devil (Sarcophilus harrisii), an Endangered Marsupial Species with Limited Genetic Diversity , 2011, PloS one.

[61]  Tom H. Pringle,et al.  Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil) , 2011, Proceedings of the National Academy of Sciences.

[62]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[63]  A. Papenfuss,et al.  Tumor-Specific Diagnostic Marker for Transmissible Facial Tumors of Tasmanian Devils , 2011, Veterinary pathology.

[64]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[65]  Janet Rossant,et al.  The Crumbs complex couples cell density sensing to Hippo-dependent control of the TGF-β-SMAD pathway. , 2010, Developmental cell.

[66]  Daniel Rios,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[67]  F. Baas,et al.  Mouse Schwann cells activate MHC class I and II restricted T-cell responses, but require external peptide processing for MHC class II presentation , 2010, Neurobiology of Disease.

[68]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[69]  Manolis Kellis,et al.  The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer , 2009, Science.

[70]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[71]  A. Burt,et al.  Origins and Evolution of a Transmissible Cancer , 2009, Evolution; international journal of organic evolution.

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

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

[74]  M. Meyerson,et al.  BIBW2992, an irreversible EGFR/HER2 inhibitor highly effective in preclinical lung cancer models , 2008, Oncogene.

[75]  William Pao,et al.  MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance to gefitinib or erlotinib , 2007, Proceedings of the National Academy of Sciences.

[76]  Katherine Belov,et al.  Transmission of a fatal clonal tumor by biting occurs due to depleted MHC diversity in a threatened carnivorous marsupial , 2007, Proceedings of the National Academy of Sciences.

[77]  A. Hyatt,et al.  Towards a Case Definition for Devil Facial Tumour Disease: What Is It? , 2007, EcoHealth.

[78]  Bronwen L. Aken,et al.  Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences , 2007, Nature.

[79]  T. Jin,et al.  Apolipoprotein E deficiency enhances the antigen‐presenting capacity of Schwann cells , 2007, Glia.

[80]  A. O'hara,et al.  The Immunohistochemical Characterization of Devil Facial Tumor Disease (DFTD) in the Tasmanian Devil (Sarcophilus harrisii) , 2006, Veterinary pathology.

[81]  R. Sharpe,et al.  The Pathology of Devil Facial Tumor Disease (DFTD) in Tasmanian Devils (Sarcophilus harrisii) , 2006, Veterinary pathology.

[82]  Robin A. Weiss,et al.  Clonal Origin and Evolution of a Transmissible Cancer , 2006, Cell.

[83]  Clare E. Hawkins,et al.  Emerging disease and population decline of an island endemic, the Tasmanian devil Sarcophilus harrisii , 2006 .

[84]  A. Pearse,et al.  Allograft theory: Transmission of devil facial-tumour disease , 2006, Nature.

[85]  H. Lane,et al.  ERBB Receptors and Cancer: The Complexity of Targeted Inhibitors , 2005, Nature Reviews Cancer.

[86]  Menna E. Jones,et al.  Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore , 2004, Molecular ecology.

[87]  J. Mullikin,et al.  The phusion assembler. , 2003, Genome research.

[88]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[89]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[90]  R. O’Neill,et al.  De novo insertion of an intron into the mammalian sex determining gene, SRY. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[91]  R. O’Neill,et al.  Low levels of sequence divergence in rock wallabies (Petrogale) suggest a lack of positive directional selection in SRY. , 1997, Molecular biology and evolution.

[92]  E. Guiler.  Temporal and spatial distribution of the Tasmanian Devil, Sarcophilus harrisi (Dasyuridae: Marsupialia) , 1982 .

[93]  L. Griner.  Neoplasms in Tasmanian devils (Sarcophilus harrisii). , 1979, Journal of the National Cancer Institute.

[94]  E. Guiler.  Obsevations on the Tasmanian Devil, Sarcophilus harrisii (Marsupialia : Dasyuridae) I. Numbers, home, range, movements and food in two populations , 1970 .

[95]  E. Guiler.  Observations on the Tasmanian Devil, Sarcophilus harrisii (Marsupialia : Dasyuridae) II. Reproduction, breeding and growth of pouch young , 1970 .