Projects

typo

The typogenetics game from Gödel, Escher, Bach: an Eternal Golden Braid

Gonum

Gonum is a collection of scientific software packages written for the Go programming language.

arrgh

arrgh is a Go interface to the OpenCPU R server system.

bíogo

bíogo is a collection of packages for bioinformatics written in the Go programming language.

ev3go

ev3go is a Go interface to LEGO® Mindstorms-compatible robotics platform built on the ev3dev.org Linux distribution.

utter

utter implements a deep pretty printer for Go data structures.

zalgo

Invoke the hive mind.

Selected Publications

Elephantids are the world’s most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ∼120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant’s ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for ∼500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.
PNAS 115:E2566-E2574

bíogo is a framework designed to ease development and maintenance of computationally intensive bioinformatics applications.
The Journal of Open Source Software

The complexity of the coral Acropora genome is paradoxical, given that this organism contains apparently few tissue types and the simplest extant nervous system consisting of a morphologically homogeneous nerve net.
Current Biology 13:2190-2195

Recent Publications

More Publications

  • Horizontal transfer of BovB and L1 retrotransposons in eukaryotes

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  • Transposable elements and gene expression during the evolution of amniotes

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  • Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse

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  • Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

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  • A comprehensive genomic history of extinct and living elephants

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Teaching

I am teaching the bioinformatics course of the Master of Biotechnology at Adelaide:

  • BIOTECH7005: Bioinformatics and Systems Modelling

Other interests

Dan has other interests outside science and software development. He will share these things face to face.