Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

Speciation network in Laurasiatheria: retrophylogenomic signals

(2017) Liliya Doronina et al.   GENOME RESEARCH

Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia

(2017) Ray Tobler et al.   NATURE

Size, shape, and form: concepts of allometry in geometric morphometrics

(2016) Christian Peter Klingenberg   DEVELOPMENT GENES AND EVOLUTION

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

Cultural innovation and megafauna interaction in the early settlement of arid Australia

(2016) Giles Hamm et al.   NATURE

Causes of molecular convergence and parallelism in protein evolution

(2016) Jay F. Storz   NATURE REVIEWS GENETICS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

(2016) Andrej Kuritzin et al.   PLoS Computational Biology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species

(2015) Klaus-Peter Koepfli et al.   CURRENT BIOLOGY

The definition, recognition, and interpretation of convergent evolution, and two new measures for quantifying and assessing the significance of convergence

(2015) C. Tristan Stayton   EVOLUTION

Disentangling the Relationship of the Australian Marsupial Orders Using Retrotransposon and Evolutionary Network Analyses

(2015) Susanne Gallus et al.   Genome Biology and Evolution

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

Abrogation of both short and long forms of latent transforming growth factor-β binding protein-1 causes defective cardiovascular development and is perinatally lethal

(2015) Masahito Horiguchi et al.   MATRIX BIOLOGY

Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

(2015) Zhengting Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

(2015) Mark Lipson et al.   PLoS Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen

(2014) H. A. Adissu et al.   Disease Models & Mechanisms

A METHOD FOR ASSESSING PHYLOGENETIC LEAST SQUARES MODELS FOR SHAPE AND OTHER HIGH-DIMENSIONAL MULTIVARIATE DATA

(2014) Dean C. Adams   EVOLUTION

A method for analysis of phenotypic change for phenotypes described by high-dimensional data

(2014) M L Collyer et al.   HEREDITY

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

(2014) Mikkel Schubert et al.   Nature Protocols

A Generalized K Statistic for Estimating Phylogenetic Signal from Shape and Other High-Dimensional Multivariate Data

(2014) Dean C. Adams   SYSTEMATIC BIOLOGY

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Statistical support for the hypothesis of developmental constraint in marsupial skull evolution

(2013) C Verity Bennett et al.   BMC BIOLOGY

Ancestry of the Australian Termitivorous Numbat

(2013) Anja Zemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide signatures of convergent evolution in echolocating mammals

(2013) Joe Parker et al.   NATURE

SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion

(2013) Travis Ingram et al.   Methods in Ecology and Evolution

geomorph: anrpackage for the collection and analysis of geometric morphometric shape data

(2013) Dean C. Adams et al.   Methods in Ecology and Evolution

ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments

(2012) Zhang Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

(2012) Elizabeth P. Murchison et al.   CELL

The Evolution of Marsupial and Monotreme Chromosomes

(2012) J.E. Deakin et al.   CYTOGENETIC AND GENOME RESEARCH

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Mandible shape in marsupial and placental carnivorous mammals: a morphological comparative study using geometric morphometrics

(2011) FRANCISCO J. PREVOSTI et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia

(2010) Johannes Krause et al.   CURRENT BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MorphoJ: an integrated software package for geometric morphometrics

(2010) CHRISTIAN PETER KLINGENBERG   Molecular Ecology Resources

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Biting through constraints: cranial morphology, disparity and convergence across living and fossil carnivorous mammals

(2010) A. Goswami et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Brpf1, a subunit of the MOZ histone acetyl transferase complex, maintains expression of anterior and posterior Hox genes for proper patterning of craniofacial and caudal skeletons

(2009) Kenta Hibiya et al.   DEVELOPMENTAL BIOLOGY

The Neandertal genome and ancient DNA authenticity

(2009) Richard E Green et al.   EMBO JOURNAL

The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

(2009) W. Miller et al.   GENOME RESEARCH

Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals

(2008) Janine E. Deakin et al.   CHROMOSOME RESEARCH

Resurrection of DNA Function In Vivo from an Extinct Genome

(2008) Andrew J. Pask et al.   PLoS One