Adaptation and conservation insights from the koala genome

Characterisation of MHC class I genes in the koala

(2017) Yuanyuan Cheng et al.   IMMUNOGENETICS

Human occupation of northern Australia by 65,000 years ago

(2017) Chris Clarkson et al.   NATURE

Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline

(2017) Matthew Hobbs et al.   Scientific Reports

Population genetics of the koala (Phascolarctos cinereus) in north-eastern New South Wales and south-eastern Queensland

(2016) S. Dennison et al.   AUSTRALIAN JOURNAL OF ZOOLOGY

Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome

(2016) Janine E. Deakin et al.   BMC GENOMICS

Use of expert knowledge to elicit population trends for the koala (Phascolarctos cinereus)

(2016) Christine Adams-Hosking et al.   DIVERSITY AND DISTRIBUTIONS

Characterization of the antimicrobial peptide family defensins in the Tasmanian devil (Sarcophilus harrisii), koala (Phascolarctos cinereus), and tammar wallaby (Macropus eugenii)

(2016) Elizabeth A. Jones et al.   IMMUNOGENETICS

Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia)

(2016) Niccolò Alfano et al.   JOURNAL OF VIROLOGY

Genetic drift, selection and the evolution of the mutation rate

(2016) Michael Lynch et al.   NATURE REVIEWS GENETICS

Climate change not to blame for late Quaternary megafauna extinctions in Australia

(2016) Frédérik Saltré et al.   Nature Communications

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data

(2016) Hugo Varet et al.   PLoS One

Phylogeography of the Koala, (Phascolarctos cinereus), and Harmonising Data to Inform Conservation

(2016) Linda E. Neaves et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Conserving koalas: A review of the contrasting regional trends, outlooks and policy challenges

(2015) Clive McAlpine et al.   BIOLOGICAL CONSERVATION

Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice

(2015) Arikuni Uchimura et al.   GENOME RESEARCH

The process, biotic impact, and global implications of the human colonization of Sahul about 47,000 years ago

(2015) J.F. O'Connell et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Trachoma and Ocular Chlamydial Infection in the Era of Genomics

(2015) Tamsyn Derrick et al.   MEDIATORS OF INFLAMMATION

Exon capture phylogenomics: efficacy across scales of divergence

(2015) Jason G. Bragg et al.   Molecular Ecology Resources

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

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Ongoing unraveling of a continental fauna: Decline and extinction of Australian mammals since European settlement

(2015) John C. Z. Woinarski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathogenesis of Progressive Scarring Trachoma in Ethiopia and Tanzania and Its Implications for Disease Control: Two Cohort Studies

(2015) Matthew J. Burton et al.   PLoS Neglected Tropical Diseases

The koala immunological toolkit: sequence identification and comparison of key markers of the koala (Phascolarctos cinereus) immune response

(2014) Katrina Morris et al.   AUSTRALIAN JOURNAL OF ZOOLOGY

A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity

(2014) Matthew Hobbs et al.   BMC GENOMICS

Bearing up well? Understanding the past, present and future of Australia's koalas

(2014) Karen H. Black et al.   GONDWANA RESEARCH

Frequent Expansions of the Bitter Taste Receptor Gene Repertoire during Evolution of Mammals in the Euarchontoglires Clade

(2014) Takashi Hayakawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

In vitro hepatic microsomal metabolism of meloxicam in koalas (Phascolarctos cinereus), brushtail possums (Trichosurus vulpecula), ringtail possums (Pseudocheirus peregrinus), rats (Rattus norvegicus) and dogs (Canis lupus familiaris)

(2013) B. Kimble et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Diet Shapes the Evolution of the Vertebrate Bitter Taste Receptor Gene Repertoire

(2013) Diyan Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Climate sensitivity, sea level and atmospheric carbon dioxide

(2013) J. Hansen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

An exogenous retrovirus isolated from koalas with malignant neoplasias in a US zoo

(2013) W. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent advances in understanding the biology, epidemiology and control of chlamydial infections in koalas

(2013) Adam Polkinghorne et al.   VETERINARY MICROBIOLOGY

Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus)

(2012) Kyriakos Tsangaras et al.   BMC GENETICS

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

(2012) Elizabeth P. Murchison et al.   CELL

Centromere Remodeling in Hoolock leuconedys (Hylobatidae) by a New Transposable Element Unique to the Gibbons

(2012) Lucia Carbone et al.   Genome Biology and Evolution

Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation

(2012) Jennifer Grant et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Using integrated population modelling to quantify the implications of multiple threatening processes for a rapidly declining population

(2011) Jonathan R. Rhodes et al.   BIOLOGICAL CONSERVATION

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Immunome database for marsupials and monotremes

(2011) Emily SW Wong et al.   BMC IMMUNOLOGY

Predicting the Probability of Outbreeding Depression

(2011) RICHARD FRANKHAM et al.   CONSERVATION BIOLOGY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Looking for the archaeological signature in Australian Megafaunal extinctions

(2011) Judith Field et al.   QUATERNARY INTERNATIONAL

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

(2011) Marilyn B Renfree et al.   GENOME BIOLOGY

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Phylogenetic and Functional Analysis of the Vertebrate Cytochrome P450 2 Family

(2010) Nina Kirischian et al.   JOURNAL OF MOLECULAR EVOLUTION

coancestry: a program for simulating, estimating and analysing relatedness and inbreeding coefficients

(2010) JINLIANG WANG   Molecular Ecology Resources

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Molecular Receptive Ranges of Human TAS2R Bitter Taste Receptors

(2009) Wolfgang Meyerhof et al.   CHEMICAL SENSES

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Inbreeding and testicular abnormalities in a bottlenecked population of koalas (Phascolarctos cinereus)

(2009) Romane Cristescu et al.   WILDLIFE RESEARCH

A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres

(2008) Dawn M. Carone et al.   CHROMOSOMA

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

Frequency and distribution of cyanogenic glycosides in Eucalyptus L’Hérit

(2008) Roslyn M. Gleadow et al.   PHYTOCHEMISTRY