The evolution of two transmissible cancers in Tasmanian devils

Genetic instability from a single S phase after whole-genome duplication

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Restoring faith in conservation action: maintaining wild genetic diversity through the Tasmanian devil insurance program

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Significantly improving the quality of genome assemblies through curation

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Quantifying 25 years of disease‐caused declines in Tasmanian devil populations: host density drives spatial pathogen spread

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Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Extensive phylogenies of human development inferred from somatic mutations

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Comparative Cytogenetic Mapping and Telomere Analysis Provide Evolutionary Predictions for Devil Facial Tumour 2

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Spontaneous Tumor Regression in Tasmanian Devils Associated with RASL11A Activation

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A transmissible cancer shifts from emergence to endemism in Tasmanian devils

(2020) Austin H. Patton et al.   SCIENCE

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

(2020) Young Mi Kwon et al.   PLOS BIOLOGY

The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease

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Individual and temporal variation in pathogen load predicts long-term impacts of an emerging infectious disease

(2019) Konstans Wells et al.   ECOLOGY

Resolving genetic heterogeneity in cancer

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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

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Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Tracing the rise of malignant cell lines: distribution, epidemiology and evolutionary interactions of two transmissible cancers in Tasmanian devils

(2019) Samantha James et al.   Evolutionary Applications

Somatic evolution and global expansion of an ancient transmissible cancer lineage

(2019) Adrian Baez-Ortega et al.   SCIENCE

Targeting transmissible cancers in animals

(2019) Amanda Patchett et al.   SCIENCE

Two of a kind: transmissible Schwann cell cancers in the endangered Tasmanian devil (Sarcophilus harrisii)

(2019) Amanda L. Patchett et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Contemporary demographic reconstruction methods are robust to genome assembly quality: A case study in Tasmanian Devils

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Pan-cancer whole-genome analyses of metastatic solid tumours

(2019) Peter Priestley et al.   NATURE

Genetic predisposition to mosaic Y chromosome loss in blood

(2019) Deborah J. Thompson et al.   NATURE

The landscape of somatic mutation in normal colorectal epithelial cells

(2019) Henry Lee-Six et al.   NATURE

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

(2019) Hannes P. Eggertsson et al.   Nature Communications

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils

(2018) Maximilian R. Stammnitz et al.   CANCER CELL

SvABA: genome-wide detection of structural variants and indels by local assembly

(2018) Jeremiah A. Wala et al.   GENOME RESEARCH

Density trends and demographic signals uncover the long-term impact of transmissible cancer in Tasmanian devils

(2018) Billie T. Lazenby et al.   JOURNAL OF APPLIED ECOLOGY

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Adaptation and conservation insights from the koala genome

(2018) Rebecca N. Johnson et al.   NATURE GENETICS

The newly-arisen Devil facial tumour disease 2 (DFT2) reveals a mechanism for the emergence of a contagious cancer

(2018) Alison Caldwell et al.   eLife

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COSMIC: the Catalogue Of Somatic Mutations In Cancer

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Tasman-PCR: a genetic diagnostic assay for Tasmanian devil facial tumour diseases

(2018) Young Mi Kwon et al.   Royal Society Open Science

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

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Accurate assembly of transcripts through phase-preserving graph decomposition

(2017) Mingfu Shao et al.   NATURE BIOTECHNOLOGY

Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer

(2017) Jarno Drost et al.   SCIENCE

Identification of candidate genes for devil facial tumour disease tumourigenesis

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Tissue-specific mutation accumulation in human adult stem cells during life

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Phased diploid genome assembly with single-molecule real-time sequencing

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The identification of immune genes in the milk transcriptome of the Tasmanian devil (Sarcophilus harrisii)

(2016) Rehana V. Hewavisenti et al.   PeerJ

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

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Toll-like receptor signaling is functional in immune cells of the endangered Tasmanian devil

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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

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A second transmissible cancer in Tasmanian devils

(2015) Ruth J. Pye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

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Infernal 1.1: 100-fold faster RNA homology searches

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TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

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Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Reversible epigenetic down-regulation of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer

(2013) H. V. Siddle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RetroSeq: transposable element discovery from next-generation sequencing data

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Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

(2012) Elizabeth P. Murchison et al.   CELL

Genomic Restructuring in the Tasmanian Devil Facial Tumour: Chromosome Painting and Gene Mapping Provide Clues to Evolution of a Transmissible Tumour

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genBlastG: using BLAST searches to build homologous gene models

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(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

(2011) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

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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 Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer

(2010) E. P. Murchison et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Transmission dynamics of Tasmanian devil facial tumor disease may lead to disease-induced extinction

(2009) Hamish McCallum et al.   ECOLOGY

Distribution and abundance of roadkill on Tasmanian highways: human management options

(2008) Alistair J. Hobday et al.   WILDLIFE RESEARCH