Fields of Research

Genetics
Infectious diseases
Veterinary parasitology
Phylogeny and comparative analysis
Biological mathematics
Host-parasite interactions
Systems biology
Microbial ecology
Higher education
Applications in life sciences
Computational complexity and computability
Health informatics and information systems
Conservation and biodiversity
Genome structure and regulation
Modelling and simulation
Forestry management and environment
Pattern recognition
Structural biology (incl. macromolecular modelling)
Networking and communications
Bioinformatic methods development
Speciation and extinction
Proteins and peptides
Animal systematics and taxonomy
Computational ecology and phylogenetics
Disease surveillance
Behavioural ecology
Genomics
Biological network analysis
Australian history
Veterinary epidemiology
Multimorbidity
Cellular nervous system
Terrestrial ecology
Mortality
Environmental assessment and monitoring
Epigenetics (incl. genome methylation and epigenomics)
Human information interaction and retrieval
Virology
Cyberphysical systems and internet of things
Pollution and contamination
Gene expression (incl. microarray and other genome-wide approaches)
Microbial taxonomy
Aboriginal and Torres Strait Islander history

Research Objectives

Expanding knowledge in the biological sciences
Clinical health
Control of pests, diseases and exotic species in terrestrial environments
Terrestrial biodiversity
Teaching and instruction technologies
Expanding knowledge in the environmental sciences
Expanding knowledge in the mathematical sciences
Evaluation, allocation, and impacts of land use
Animal welfare
Coastal or estuarine biodiversity
Application software packages
Network systems and services
Ecosystem adaptation to climate change
Prevention of human diseases and conditions
Native forests
Health surveillance
Applied computing
Disease distribution and transmission (incl. surveillance and response)
Expanding knowledge in history, heritage and archaeology
Evaluation of health outcomes
Climate change mitigation strategies
Demography
Assessment and management of freshwater ecosystems
Expanding knowledge in the biomedical and clinical sciences
Assessment and management of terrestrial ecosystems
Rehabilitation or conservation of terrestrial environments

Career Best Publications

A simple model explains the dynamics of preferential host switching among mammal RNA viruses; Evolution
Adaptive collective foraging in groups with conflicting nutritional needs; Royal Society Open Science
Australian spiny mountain crayfish and their temnocephalan ectosymbionts: an ancient association on the edge of coextinction?; Proceedings of the Royal Society of London: Biological Sciences
Collective foraging in spatially complex nutritional environments; Philosophical Transactions of the Royal Society B-Biological Sciences
Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences; Mycologia
Modelling nutrition across organizational levels: from individuals to superorganisms; Journal of Insect Physiology
Node fingerprinting: an efficient heuristic for aligning biological networks; Journal of Computational Biology
Node handprinting: a scalable and accurate algorithm for aligning multiple biological networks; Journal of Computational Biology
Nutritional ecology beyond the individual: a conceptual framework for integrating nutrition and social interactions; Ecology Letters
RASCAL: A randomized approach for coevolutionary analysis; Journal of Computational Biology
Wing patterning genes and coevolution of Müllerian mimicry in Heliconius butterflies: support from phylogeography, cophylogeny, and divergence times; Evolution

Research Publications

A conceptual model for reflecting on expected learning vs. demonstrated student performance; 15th Australasian Computing Education Conference (ACE2013)
A review of visualisations of protein fold networks and their relationship with sequence and function; Biological reviews of the Cambridge Philosophical Society
A simple model explains the dynamics of preferential host switching among mammal RNA viruses; Evolution
A sub-quadratic time and space complexity solution for the dated tree reconciliation problem for select tree topologies; Workshop on Algorithms in Bioinformatics 2015
A time and space complexity reduction for coevolutionary analysis of trees generated under both a Yule and Uniform model; Computational Biology and Chemistry
Active subnetwork recovery with a mechanism-dependent scoring function; with application to angiogenesis and organogenesis studies; Bioinformatics
Adaptive collective foraging in groups with conflicting nutritional needs; Royal Society Open Science
An improved node mapping algorithm for the cophylogeny reconstruction problem; Coevolution: An Open Access Journal
Australian spiny mountain crayfish and their temnocephalan ectosymbionts: an ancient association on the edge of coextinction?; Proceedings of the Royal Society of London: Biological Sciences
Benchmarking methods of protein structure alignment; Journal of Molecular Evolution
Bioacoustics data analysis - a taxonomy, survey and open challenges; IEEE Access
Biological Network Edit Distance; Journal of Computational Biology
Collective foraging in spatially complex nutritional environments; Philosophical Transactions of the Royal Society B-Biological Sciences
Cospeciation; Encyclopedia of Evolutionary Biology
Cospeciation
Draft Genome Sequence of Subantarctic Rhodococcus sp. Strain 1139; Genome Announcements
Draft genome sequences of three sub-Antarctic Rhodococcus spp., including two novel psychrophilic genomospecies; Genome Announcements
Draft genome sequences of two novel sub-Antarctic Williamsia species; Genome Announcements
Ecology and Control of Vector-Borne Disease Dynamics Across Australia; Presentation to the Tasmanian Department of Health and Human Services
Ecology and control of vector-borne disease dynamics across Australia; Talk presented to University of Melbourne, Department of BioSciences
Ecology and Control of Vector-borne Disease Dynamics Across Australia; Presentation at the Tasmanian branch meeting for the Australian Society of Parasitology
Ecology and Control of Vector-Borne Disease Dynamics Across Australia; Presentation at Hokkaido University, Faculty of Fisheries
Ecology and epidemiology of vector-borne disease dynamics across Australia, Ross River virus; 13th Mosquito Control Association of Australia Conference
Ecology and epidemiology of vector-borne disease dynamics across Australia, Ross River virus; 2019 Wildlife Disease Association Australasia Conference
Emerging phylogenetic structure of the SARS-CoV-2 pandemic; Virus Evolution
Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia; Briefings in Bioinformatics
Evaluation of the RelatiPerformance of the Subflattenings Method for Phylogenetic Inference; Bulletin of Mathematical Biology
Event-Based Cophylogenetic Comparative Analysis; Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology
Evolution of endogenous retroviruses in the Suidae: evidence for different viral subpopulations in African and Eurasian host species; Bmc Evolutionary Biology
Evolving nutritional strategies in the presence of competition: a geometric agent-based model; PLoS Computational Biology
Fluralaner as a novel treatment for sarcoptic mange in the bare-nosed wombat (Vombatus ursinus): safety, pharmacokinetics, efficacy and practicable use; Parasites and Vectors
From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem; Molecular Phylogenetics and Evolution
Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences; Mycologia
How to test bioinformatics software?; Biophysical Reviews
Hunting alters viral transmission and evolution in a large carnivore; Nature Ecology & Evolution
Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem; BMC Bioinformatics
Long-term spatiotemporal dynamics and factors associated with trends in bare-nosed wombats; Journal of Wildlife Management
Macronutrient intakes and the lifespan-fecundity trade-off: a geometric framework agent-based model; Journal of the Royal Society Interface
Mainstreaming microbes across biomes; Bioscience
Methods of analysing patterns of multimorbidity using network analysis: a scoping review; Journal of Public Health
Methods of analyzing patterns of multimorbidity using network analysis: a scoping review protocol; JBI Evidence Synthesis
Mining autograding data in computer science education; 18th Australasian Computer Science Week
Mitochondrial genome sequencing reveals potential origins of the scabies mite Sarcoptes scabiei infesting two iconic Australian marsupials; BMC Evolutionary Biology
Modelling nutrition across organizational levels: from individuals to superorganisms; Journal of Insect Physiology
MrIML: Multi-response interpretable machine learning to model genomic landscapes; Molecular Ecology Resources
Neighbor-joining uses the optimal weight for net divergence; Molecular Phylogenetics and Evolution
Network modelling of gene regulation; Biophysical Reviews
Node fingerprinting: an efficient heuristic for aligning biological networks; Journal of Computational Biology
Node handprinting: a scalable and accurate algorithm for aligning multiple biological networks; Journal of Computational Biology
Nutritional ecology beyond the individual: a conceptual framework for integrating nutrition and social interactions; Ecology Letters
Optimising predictive modelling of Ross River virus using meteorological variables; PLoS Neglected Tropical Diseases
Performance of AIC and BIC in selecting Partition Models and Mixture Models; Systematic biology
Phylogenetic codivergence supports coevolution of mimetic Heliconius butterflies; PLoS One
Phylogeny; Reference Module in Life Sciences (LIFE)
Phylogeny
RASCAL: A randomized approach for coevolutionary analysis; Journal of Computational Biology
Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker; Bioinformatics
The emergence of sarcoptic mange in Australian wildlife: an unresolved debate; Parasites and Vectors
The forecasting of dynamical Ross River virus outbreaks: Victoria, Australia; Epidemics
Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem; Algorithms for Molecular Biology
Unattained geometric configurations of secondary structure elements in protein structural space; Journal of Structural Biology
Verification of phylogenetic inference programs using metamorphic testing; Journal of Bioinformatics and Computational Biology
Wing patterning genes and coevolution of Müllerian mimicry in Heliconius butterflies: support from phylogeography, cophylogeny, and divergence times; Evolution
WiSPA: a new approach for dealing with widespread parasitism; Quantitative Biology

Research Projects

A new integrated approach for ecologically sustainable forest management; Australian Research Council (ARC)
Developing feasible in situ control of mange disease in wombats; Australian Research Council (ARC)
Evolutionary history and impact of adeno-associated viruses in Australia; Australian Research Council (ARC)
Intergenerational Transmission of Inequality; Australian Research Council (ARC)
Managing infectious disease through partial wildlife social networks; Australian Research Council (ARC)
Machine learning algorithms to classify bird calls from acoustic data

Research Candidate Supervision