Web Access Research Portal

Researcher: Holland, BR (Associate Professor Barbara Holland)

Fields of Research

Biological Mathematics
Phylogeny and Comparative Analysis
Microbial Genetics
Molecular Evolution
Bioinformatics Software
Biostatistics
Stochastic Analysis and Modelling
Microbial Ecology
Biological Adaptation
Population, Ecological and Evolutionary Genetics
Archaeological Science
Galactic Astronomy
Plant Biology
Host-Parasite Interactions
Statistics
Artificial Life
Astronomical and Space Sciences
Behavioural Ecology
Biogeography and Phylogeography
Epidemiology
Bioinformatics
Environmental Science and Management
Speciation and Extinction
Signal Transduction
Evolutionary Impacts of Climate Change
Plant Systematics and Taxonomy
Genomics
Genetic Immunology
Statistical Theory

Research Objectives

Expanding Knowledge in the Biological Sciences
Expanding Knowledge in the Mathematical Sciences
Barley
Expanding Knowledge in the Physical Sciences
Flora, Fauna and Biodiversity at Regional or Larger Scales
Environmental Health
Native Forests
Urban and Industrial Air Quality
Ecosystem Assessment and Management of Forest and Woodlands Environments
Expanding Knowledge in Psychology and Cognitive Sciences
Sparseland, Permanent Grassland and Arid Zone Flora, Fauna and Biodiversity
Effects of Climate Change and Variability on Antarctic and Sub-Antarctic Environments (excl. Social Impacts)
Expanding Knowledge in History and Archaeology
Expanding Knowledge in the Environmental Sciences
Assessment and Evaluation of Curriculum
Pedagogy
Computer Time Leasing, Sharing and Renting Services

Career Best Publications

Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications; Molecular Biology and Evolution
Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees; Algorithms in Bioinformatics: Third International Workshop, WABI 2003
Identifying Cliques of Convergent Characters: Concerted Evolution in the Cormorants and Shags; Systematic Biology
Imputing Supertrees and Supernetworks from Quartets; Systematic Biology
Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach; Molecular Biology and Evolution
Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock-A Simulation Study; Systematic Biology
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005: Improved Consensus Network Techniques for Genome-Scale Phylogeny; Molecular Biology and Evolution
Rates of Evolution in Ancient DNA from Adélie Penguins; Science
Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks; Systematic Biology
Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny; Molecular Biology and Evolution
Using supernetworks to distinguish hybridization from lineage-sorting; BMC Evolutionary Biology

Research Publications

Δ additive and Δ ultra-additive maps, Gromov's trees, and the Farris transform; Discrete Applied Mathematics: Combinatorial Operations Research and Computer Science
Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand; MicrobiologyOpen
A futile act? Thoughts on the reproductive biology of Candida albicans; Mycologist
A novel exploratory method for visual recombination detection; Genome Biology
A tensorial approach to the inversion of group-based phylogenetic models; BMC Evolutionary Biology
Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications; Molecular Biology and Evolution
Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization; BMC Evolutionary Biology
Analysis of Phylogenetics and Evolution with R
Assessing barley malt associated microbial diversity using next generation sequencing; 2011 Australian Society for Microbiology Annual Meeting
Biogeography of Circum-Antarctic springtails. ; Molecular Phylogenetics and Evolution
Book review - Molecular Evolution: A Statistical Approach
Chemical signals in the echidna: differences between seasons, sexes, individuals and gland types; Journal of Zoology
Cognitive models in the extreme; Australian Mathematical Psychology Conference 2016
Comparison of Three Statistical Classification Techniques for Maser Identification; Publications of the Astronomical Society of Australia
Component masses of young, wide, non-magnetic white dwarf binaries in the Sloan Digital Sky Survey Data Release 7; Monthly Notices of the Royal Astronomical Society
Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Aspenium ferns ; Molecular Phylogenetics and Evolution
Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees; Algorithms in Bioinformatics: Third International Workshop, WABI 2003
Deciphering Past Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes; Molecular Biology and Evolution
Detecting selection on temporal and spatial scales: a genomic time-series assessment of selective responses to devil facial tumor disease; PLoS One
Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants; Journal of Mathematical Biology
Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes; Infection, Genetics and Evolution
Endophyte survival without sex; Fungal Endophytes of Grasses
Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods; The Annals of Applied Statistics
Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli; Journal of Molecular Evolution
Evaluation of Monitoring Schemes for Wastewater-Based Epidemiology to Identify Drug Use Trends Using Cocaine, Methamphetamine, MDMA and Methadone; Environmental Science and Technology
Evolution of Campylobacter Species in New Zealand; Campylobacter Ecology and Evolution
Evolutionary analyses of large data sets: Trees and beyond
Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease; Biology Letters
Faster exact maximum parsimony search with XMP; Bioinformatics
Gaps: an elusive source of phylogenetic information; Systematic Biology
Genome BLAST distance phylogenies inferred from whole plastic and whole mitochondrion genome sequences; BMC Bioinformatics
Genomic scans across three eucalypts suggest that adaptation to aridity is a genome-wide phenomenon; Genome Biology and Evolution
Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway; Annuals of Botany
Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2; Molecular Microbiology
Identifying Cliques of Convergent Characters: Concerted Evolution in the Cormorants and Shags; Systematic Biology
Impact of Genetic Background on Allele Selection in a Highly Mutable Candida albicans Gene, PNG; PLOS One
Imputing Supertrees and Supernetworks from Quartets; WABI 2006: 6th International Workshop on Algorithms in Bioinformatics
Imputing Supertrees and Supernetworks from Quartets; Systematic Biology
Is the general time-reversible model bad for molecular phylogenetics?; Systematic Biology
Last hope for the doomed? Thoughts on the importance of a parasexual cycle for the yeast Candida albicans; Current Genetics
LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites; BMC Evolutionary Biology
Low-parameter phylogenetic inference under the general Markov model; Systematic Biology
Maximum likelihood estimates of pairwise rearrangement distances; Journal of Theoretical Biology
Missing data and influential sites: Choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice; Genome Biology and Evolution
Molecular Epidemiology of Campylobacter jejuni Isolates from Wild-Bird Fecal Material in Children's Playgrounds; Applied and Environmental Microbiology
Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses; Journal of Virology
Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach; RECOMB: Fourth Annual International Conference on Computational Molecular Biology
Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach; Molecular Biology and Evolution
Novel distances for Dollo data; Systematic Biology
Optimal alphabets for an RNA world; Proceedings of the Royal Society of London
Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution; Systematic Biology
Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock-A Simulation Study; Systematic Biology
Patterns of reproductive isolation in Eucalyptus - a phylogenetic perspective; Molecular Biology and Evolution
Phylogenetic Invariants; Brenner's Encyclopedia of Genetics
Phylogenetic Invariants and Markov Invariants; Reference Module in Life Sciences
Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree; Systematic Biology
Phylogenetics: Parsimony, Networks, and Distance Methods; Handbook of Statistical Genetics
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005: Improved Consensus Network Techniques for Genome-Scale Phylogeny; Molecular Biology and Evolution
Quantification of historical livestock importation into New Zealand 1860–1979; New Zealand Veterinary Journal
Radiocarbon dating of Sacred Ibis mummies from ancient Egypt; Journal of Archaeological Science: Reports
Rates of Evolution in Ancient DNA from Adélie Penguins; Science
Reconciling molecules and morphology: Molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria); Molecular Phylogenetics and Evolution
Reconstructing past changes in locus-specific recombination rates; BMC Genetics
Searching factors causing implausible non-monophyly: ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats; Molecular Phylogenetics and Evolution
Selecting representative model micro-organisms; BMC Microbiology
Selective advantages of a parasexual cycle for the yeast Candida albicans; Genetics
Simulating and Summarizing Sources of Gene Tree Incongruence; Genome Biology and Evolution
Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus; Genome Research
Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data; Molecular Phylogenetics and Evolution
Tapping into barley malt associated microbial diversity using next generation sequencing; 15th Australian Barley Technical Symposium
Testing the Effect of Metabolic Rate on DNA Variability at the Intra-Specific Level; PLOS One
The Algebra of the General Markov Model on Phylogenetic Trees and Networks; Bulletin of Mathematical Biology
The Emergence of Predators in Early Life: There was No Garden of Eden; PLOS One
The identification of concerted convergence in insect heads corroborates Palaeoptera; Systematic Biology
The Min/Max Squeeze: Guaranteeing a Minimal Tree for Population Data; Molecular Biology and Evolution
The Problem of Rooting Rapid Radiations; Molecular Biology and Evolution
The rise of statistical phylogenetics; Australian and New Zealand Journal of Statistics
To gamma or not to gamma? Testing the fit of rates-across-sites models; Phylomania 2012
Treeness Triangles: Visualising the Loss of Phylogenetic Signal; Molecular Biology and Evolution
Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks; Systematic Biology
Upper bounds on maximum likelihood for phylogenetic trees; Bioinformatics
Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny; Molecular Biology and Evolution
Using supernetworks to distinguish hybridization from lineage-sorting; BMC Evolutionary Biology
ä Plots: A Tool for Analyzing Phylogenetic Distance Data; Molecular Biology and Evolution

Research Projects

Algebraically informed models of biological sequence evolution; Australian Research Council (ARC)
Ancient Ibis Mummies from Egypt: DNA Evolution - Math Modelling ; International Human Frontier Science Program Organization (IHFSP)
How Will Animals Respond to Climate Change? A Genomic Approach; Australian Research Council (ARC)
Increasing Bioinformatics capability across UTas ; University of Tasmania (UTAS)
Interpreting biological sequence information: untangling hybridisation; Australian Research Council (ARC)
NARGS - Recovering complex evolutionary histories with censored data; University of Tasmania (UTAS)
Phylogenetics: Mathematics, Models and Applications - UK, 2011; University of Tasmania (UTAS)
Reconstructing the evolution of climatic tolerances in conifers; Australian Research Council (ARC)
Redesigning the introductory statistics classroom to the 'inverted' style to improve student experience and material retention; Office for Learning & Teaching (OLT)
The 17th Annual New Zealand Phylogenomics Meeting; University of Tasmania (UTAS)

Research Candidate Supervision

Investigation and Application of Statistical Techniques when Using Wastewater Analysis to Monitor Illicit Drug Use
Mathematical Models for Microsatellite Evolution
Molecular Evolution of the Tasmanian Devil
New Algebraic Structures in Phylogenetics