A5023552489- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Microbial Community Ecology and Physiology
- Marine and coastal plant biology
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- Seaweed-derived Bioactive Compounds
- Coral and Marine Ecosystems Studies
- Genetic diversity and population structure
- Protist diversity and phylogeny
- Chromosomal and Genetic Variations
- Gene Regulatory Network Analysis
- Machine Learning in Bioinformatics
- Historical, Religious, and Philosophical Studies
- Legume Nitrogen Fixing Symbiosis
- Algal biology and biofuel production
- Biomedical Text Mining and Ontologies
- Glycosylation and Glycoproteins Research
- Evolution and Paleontology Studies
- Single-cell and spatial transcriptomics
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Parasitic Infections and Diagnostics
- Marine Biology and Ecology Research
The University of Queensland
2014-2023
Westmead Institute for Medical Research
2019
QIMR Berghofer Medical Research Institute
2016-2019
Peter MacCallum Cancer Centre
2019
University of Cambridge
2019
Australian Research Council
2006-2016
ARC Centre of Excellence in Advanced Molecular Imaging
2005-2016
Indian Institute of Technology Roorkee
2016
National University of Singapore
2013-2016
The University of Sydney
2013
Epidermal changes caused by a chytridiomycete fungus (Chytridiomycota; Chytridiales) were found in sick and dead adult anurans collected from montane rain forests Queensland (Australia) Panama during mass mortality events associated with significant population declines. We also have this new disease morbidity wild captive additional locations Australia Central America. This is the first report of parasitism vertebrate member phylum Chytridiomycota. Experimental data support conclusion that...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins many RNAs. One-third encoded have no detectable homologs in other sequenced genomes. Moreover, 40% appear to be archaeal-specific, only 12% 2.3% are shared exclusively with bacteria eukarya, respectively. shows high level plasticity 200 diverse insertion sequence elements, putative nonautonomous mobile evidence integrase-mediated events. There also long clusters...
The extent to which lateral genetic transfer has shaped microbial genomes major implications for the emergence of community structures. We have performed a rigorous phylogenetic analysis >220,000 proteins from 144 prokaryotes determine contribution gene sharing current prokaryotic diversity, and identify “highways” between lineages. inferred relationships suggest pattern inheritance that is largely vertical, but with notable exceptions among closely related taxa, distantly organisms live...
The causative agent of toxicity in cultured mussels from a localized area eastern Prince Edward Island has been identified as domoic acid, neuroexcitatory amino acid. toxin was isolated by number different bioassay-directed separation techniques including high-performance liquid chromatography, high-voltage paper electrophoresis, and ion-exchange characterized spectroscopic ultraviolet, infrared, mass spectrometry, nuclear magnetic resonance. isolation purification methods are described...
Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed model plants and crops. Here, we examine the multiple phyla including lycopods, ferns, gymnosperms, angiosperms across chronosequence using 16S rRNA gene amplicon profiling. We confirm is primary determinant root-associated bacterial community composition, but also observe...
Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there large gaps in our knowledge their diversity ecology. The 'Biomes Australian Soil Environments' (BASE) project has generated a database microbial with associated metadata across extensive environmental gradients at continental scale. As the characterisation microbes rapidly expands, BASE provides an evolving platform for interrogating integrating function. currently amplicon sequences contextual data...
Abstract Fungi play important roles as decomposers, plant symbionts and pathogens in soils. The structure of fungal communities the rhizosphere is result complex interactions among selection factors that may favour beneficial or detrimental relationships. Using culture-independent community profiling, we have investigated effects nitrogen fertilizer dosage on soil field-grown sugarcane. results show concentration strongly modifies composition but not taxon richness rhizosphere. Increased has...
Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms trophic foundation world's coral reef ecosystems. Here we present first draft genome goreaui (Clade C, type C1: 1.03 Gbp), one most ubiquitous endosymbionts associated with corals, an improved kawagutii F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures this symbiosis. Comparative analysis four available genomes against other dinoflagellate led identification 2460 nuclear gene families...
Diazotrophic bacteria potentially supply substantial amounts of biologically fixed nitrogen to crops, but their occurrence may be suppressed by high fertilizer application. Here, we explored the impact rates on presence diazotrophs in field-grown sugarcane with industry-standard or reduced Despite large differences soil microbial communities between test sites, a core root microbiome was identified. The root-enriched taxa overlap those Arabidopsis thaliana raising possibility that certain...
Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability several genomes offers an unprecedented opportunity study the evolution We introduce set statistical methods patterns rearrangement circular...
A phylogeny of marine Rhodophyta has been inferred by a number methods from nucleotide sequences nuclear genes encoding small subunit rRNA 39 species in 15 orders. Sequence divergences are relatively large, especially among bangiophytes and even congeners this group. Subclass Bangiophycidae appears polyphyletic, encompassing at least three lineages, with Porphyridiales distributed between two these. Florideophycidae is monophyletic, Hildenbrandiales, Corallinales, Ahnfeltiales, close...
The significance of whole-genome duplications (WGD) for vertebrate evolution remains controversial, in part because the mechanisms by which WGD contributed to functional or speciation are still incompletely characterized. Fish genomes provide an ideal context examine consequences WGD, teleost lineage experienced additional soon after divergence from tetrapods and five available comparative analysis. Here we present integrated approach characterize these post-duplication based on genome-scale...
Abstract Background Proteins of the mammalian PYHIN (IFI200/HIN-200) family are involved in defence against infection through recognition foreign DNA. The member absent melanoma 2 (AIM2) binds cytosolic DNA via its HIN domain and initiates inflammasome formation pyrin domain. AIM2 lies within a cluster related genes, many which uncharacterised mouse. To better understand evolution, orthology function these we have documented range genes present representative species, undertaken phylogenetic...
Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimaginable only a few years ago. Phylogenomics – the study evolutionary relationships based on comparative analysis genome-scale data has so far been developed as industrial-scale molecular phylogenetics, proceeding two classical steps: multiple alignment homologous sequences, followed by...
Inference of gene regulatory network from expression data is a challenging task. Many methods have been developed to this purpose but comprehensive evaluation that covers unsupervised, semi-supervised and supervised methods, provides guidelines for their practical application, lacking.
Altered networks of gene regulation underlie many complex conditions, including cancer. Inferring regulatory from high-throughput microarray expression data is a fundamental but challenging task in computational systems biology and its translation to genomic medicine. Although diverse statistical approaches have been brought bear on the network inference problem, their relative strengths disadvantages remain poorly understood, largely because comparative analyses usually consider only small...
To identify biologically relevant groupings or clusters of nuclear receptors (NR) that are associated with breast neoplasia, potentially diagnostic, discriminant prognostic value, we quantitated mRNA expression levels all 48 members the human NR superfamily by TaqMan low-density array analysis in 116 curated tissue samples, including pre- and postmenopausal normal both ERα+ ERα− tumor tissue. In addition, have determined independent cohorts tamoxifen-treated samples. There were differences...
Despite the ecological significance of relationship between reef-building corals and intracellular photosynthetic dinoflagellates genus Symbiodinium, very little is known about molecular mechanisms involved in its establishment. Indeed, microarray-based analyses point to conclusion that host gene expression largely or completely unresponsive during establishment symbiosis with a competent strain Symbiodinium. In this study, use Illumina RNA-Seq technology allowed detection transient period...
Abstract Background Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts cnidarians (such as corals) and other coral reef organisms. Breakdown of coral-dinoflagellate symbiosis due to environmental stress (i.e. bleaching) can lead death potential collapse ecosystems. However, evolution genomes, its implications for coral, is little understood. Genome sequences remain scarce part their large genome sizes (1–5 Gbp) idiosyncratic features. Results Here, we...