Centuries of genome instability and evolution in soft-shell clam, Mya arenaria, bivalve transmissible neoplasia

Epigenetic and genetic population structure is coupled in a marine invertebrate

(2023) Katherine Silliman et al.   Genome Biology and Evolution

The evolution of two transmissible cancers in Tasmanian devils

(2023) Maximilian R. Stammnitz et al.   SCIENCE

Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe

(2022) Daniel Garcia-Souto et al.   eLife

Horizontal transmission of disseminated neoplasia in the widespread clam Macoma balthica from the Southern Baltic Sea

(2022) Alicja Michnowska et al.   MOLECULAR ECOLOGY

Somatic mutation rates scale with lifespan across mammals

(2022) Alex Cagan et al.   NATURE

Pan-Cancer Analyses Identify the CTC1-STN1-TEN1 Complex as a Protective Factor and Predictive Biomarker for Immune Checkpoint Blockade in Cancer

(2022) Lishuai Wang et al.   Frontiers in Genetics

Survival and Detection of Bivalve Transmissible Neoplasia from the Soft-Shell Clam Mya arenaria (MarBTN) in Seawater

(2022) Rachael M. Giersch et al.   Pathogens

Population genetics of clonally transmissible cancers

(2022) Máire Ní Leathlobhair et al.   Nature Ecology & Evolution

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

(2021) Zev N. Kronenberg et al.   Nature Communications

Increased somatic mutation burdens in normal human cells due to defective DNA polymerases

(2021) Philip S. Robinson et al.   NATURE GENETICS

Traits of a mussel transmissible cancer are reminiscent of a parasitic life style

(2021) E. A. V. Burioli et al.   Scientific Reports

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Comprehensive molecular characterization of mitochondrial genomes in human cancers

(2020) Yuan Yuan et al.   NATURE GENETICS

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of the softshell clam Mya arenaria and the evolution of apoptosis

(2020) David Plachetzki et al.   Genome Biology and Evolution

Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer

(2020) Andrea Strakova et al.   Nature Communications

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

(2020) Young Mi Kwon et al.   PLOS BIOLOGY

Somatic evolution and global expansion of an ancient transmissible cancer lineage

(2019) Adrian Baez-Ortega et al.   SCIENCE

A single clonal lineage of transmissible cancer identified in two marine mussel species in South America and Europe

(2019) Marisa A Yonemitsu et al.   eLife

The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils

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

The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations

(2018) Francesca Menghi et al.   CANCER CELL

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Helmsman: fast and efficient mutation signature analysis for massive sequencing datasets

(2018) Jedidiah Carlson et al.   BMC GENOMICS

Bayesian inference of negative and positive selection in human cancers

(2017) Donate Weghorn et al.   NATURE GENETICS

Widespread transmission of independent cancer lineages within multiple bivalve species

(2016) Michael J. Metzger et al.   NATURE

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

(2016) Chen-Shan Chin et al.   NATURE METHODS

Rapid evolutionary response to a transmissible cancer in Tasmanian devils

(2016) Brendan Epstein et al.   Nature Communications

Restricting retrotransposons: a review

(2016) John L. Goodier   Mobile DNA

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads

(2016) Chong Chu et al.   PLoS One

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Horizontal Transmission of Clonal Cancer Cells Causes Leukemia in Soft-Shell Clams

(2015) Michael J. Metzger et al.   CELL

Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor

(2015) Brennan Decker et al.   GENOME RESEARCH

Neoplastic diseases of marine bivalves

(2015) María J. Carballal et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Clock-like mutational processes in human somatic cells

(2015) Ludmil B Alexandrov et al.   NATURE GENETICS

How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis

(2015) Young-Sam Lee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis

(2015) Young-Sam Lee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A context dependent role for DNA methylation in bivalves

(2014) M. R. Gavery et al.   Briefings in Functional Genomics

Estimating telomere length from whole genome sequence data

(2014) Zhihao Ding et al.   NUCLEIC ACIDS RESEARCH

Activation of transcription and retrotransposition of a novel retroelement,Steamer, in neoplastic hemocytes of the molluskMya arenaria

(2014) Gloria Arriagada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage

(2014) E. P. Murchison et al.   SCIENCE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Elizabeth P. Murchison et al.   CELL

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Haemocytic leukemia in Prince Edward Island (PEI) soft shell clam (Mya arenaria): Spatial distribution in agriculturally impacted estuaries

(2012) Annette Muttray et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Mitochondrial Capture by a Transmissible Cancer

(2011) C. A. Rebbeck et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ORIGINS AND EVOLUTION OF A TRANSMISSIBLE CANCER

(2009) Clare A. Rebbeck et al.   EVOLUTION

DNA Polymerase POLN Participates in Cross-Link Repair and Homologous Recombination

(2009) G.-L. Moldovan et al.   MOLECULAR AND CELLULAR BIOLOGY

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Tandem duplication/triplication correlated with poly-cytosine stretch variation in human mitochondrial DNA D-loop region

(2008) W.-Y. Hung et al.   MUTAGENESIS