A5081504592- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
- Gestational Diabetes Research and Management
- Endometriosis Research and Treatment
- Vitamin D Research Studies
- Data Visualization and Analytics
- Birth, Development, and Health
- Maternal Mental Health During Pregnancy and Postpartum
- Tryptophan and brain disorders
- Molecular Biology Techniques and Applications
- Reproductive System and Pregnancy
- Fire effects on ecosystems
- Identification and Quantification in Food
- Microbial Metabolic Engineering and Bioproduction
- Probiotics and Fermented Foods
- Cardiac electrophysiology and arrhythmias
- Sensory Analysis and Statistical Methods
- RNA and protein synthesis mechanisms
- Genetic diversity and population structure
- Legionella and Acanthamoeba research
- Electrodeposition and Electroless Coatings
- Hydrocarbon exploration and reservoir analysis
Sutherland Hospital
2022-2024
UNSW Sydney
2022-2024
Queensland University of Technology
2016-2024
Commonwealth Scientific and Industrial Research Organisation
2020-2024
Data61
2020-2024
ACT Government
2021
Mahsa University
2020
The University of Queensland
2016-2019
Queensland Cyber Infrastructure Foundation
2017
Culture independent techniques, such as shotgun metagenomics and 16S rRNA amplicon sequencing have dramatically changed the way we can examine microbial communities. Recently, changes in community structure dynamics been associated with a growing list of human diseases. The identification comparison bacteria driving those requires development sound statistical tools, especially if biomarkers are to be used clinical setting. We present mixMC, novel multivariate data analysis framework for...
ABSTRACT Objective To identify a microbial signature for endometriosis use as diagnostic non‐invasive biomarker. Design Prospective cohort pilot study. Setting Nepean Hospital and UNSW Microbiome Research Centre, Australia. Population Sixty‐four age‐ sex‐matched subjects ( n = 19 healthy control (HC); 24 non‐endometriosis (N‐ENDO) 21 confirmed (ENDO)). All study participants, besides controls, underwent laparoscopic surgical assessment endometriosis, histology was performed on excised...
Abstract Thanks to sequencing technology, modern molecular bioscience datasets are often compositions of counts, e.g. counts amplicons, mRNAs, etc. While there is growing appreciation that compositional data need special analysis and interpretation, less well understood the discrete nature these count (or, as we call them, lattice compositions) impact this has on statistical analysis, particularly log-ratio (LRA) pairwise association. LRA methods scale-invariant, not; consequently,...
Abstract Culture independent techniques, such as shotgun metagenomics and 16S rRNA amplicon sequencing have dramatically changed the way we can examine microbial communities. Recently, changes in community structure dynamics been associated with a growing list of human diseases. The identification comparison bacteria driving those requires development sound statistical tools, especially if biomarkers are to be used clinical setting. We present mixMC , novel multivariate data analysis...
Abstract Natural history collections are repositories of biodiversity and potentially used by molecular ecologists for comparative taxonomic, phylogenetic, biogeographic forensic purposes. Specimens in fish preserved using a combination methods with many fixed formalin then ethanol long‐term storage. Formalin fixation damages DNA, thereby limiting genetic analyses. In this study, the authors compared DNA barcoding identification success frozen formalin‐fixed tissues obtained from specimens...
<ns4:p>Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences. While software for detailing the composition of microbial communities using 16S rRNA marker genes relatively mature, researchers are interested identifying changes exhibited within under differing conditions. In order to gain maximum value from metagenomic sequence data we must improve existing analysis environment by providing accessible scalable computational workflows able generate...
Objective To identify a diagnostic microbial signature for endometriosis. Design Prospective cohort study Setting Nepean Hospital and UNSW Microbiome Research Centre, St George Hospital, Australia Population 64 age- sex-matched subjects ( n=1 9 HC; n= 24 N-ENDO 21 ENDO). All participants, besides healthy controls, underwent laparoscopic surgical assessment endometriosis, histology was performed on excised lesions. Methods Oral, stool, vaginal samples were self-collected at single time point...
Dietary intake during pregnancy may influence the antenatal microbiome, which is proposed to impact maternal and infant health beyond. The aim of this sub-study was examine associations between dietary microbiota diversity using whole metagenomic sequencing in low-risk versus high-risk pregnancies, as well complicated uncomplicated pregnancies. Pregnancy data were analysed from women participating MUMS cohort study Sydney, Australia (women followed trimester 1 1-year postpartum), who had at...
Introduction Vaginal estrogen is a treatment for genitourinary symptoms of menopause (GSM), which comprises vaginal atrophy and urinary dysfunction, including incontinence. Previous studies show that therapy promotes lactobacilli abundance associated with reduced GSM symptoms, reduction stress However, detailed longitudinal characterize how the microbiome changes in response to are scarce. We aimed compare microbiota postmenopausal women, before 12 weeks after cream. Methods A total 44...
<ns4:p>Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences yet analysis workflows remain immature relative to other field such as DNASeq RNASeq pipelines. While software for detailing the composition of microbial communities using 16S rRNA marker genes constantly improving, researchers are interested identifying changes exhibited within under differing conditions. In order gain maximum value from metagenomic sequence data we must improve existing...
The microbiome has been implicated in the development of metabolic conditions which occur at high rates people with schizophrenia and related psychoses. This exploratory proof-of-concept study aimed to: (i) characterize gut microbiota antipsychotic naïve or quasi-naïve first-episode psychosis, established receiving clozapine therapy; (ii) test for changes following a lifestyle intervention included diet exercise education physical activity. Participants were recruited from Eastern Suburbs...
The microbiome has emerged as a key determinant of human health and reproduction, with recent evidence suggesting dysbiotic is implicated in adverse perinatal outcomes. existing research been limited by the sample collection timing, cohort design, lack data on preconception microbiome. This prospective, longitudinal study will recruit 2000 Australian women, order to fully explore role development Participants are enrolled for maximum 7 years, from 1 year preconception, through 5 years...
The advent of Next Generation Sequencing (NGS) technologies has seen explosive growth in genomic datasets, and dense coverage related organisms, supporting study subtle, strain-specific variations as a determinant function. Such data collections present fresh complex challenges for bioinformatics, those comparing models relationships across hundreds even thousands sequences. Transcriptional Regulatory Network (TRN) structures document the influence regulatory proteins called Transcription...
ABSTRACT The success of amplicon sequencing studies environmental DNA (eDNA) depends on the choice primer pairs used to select taxa‐specific regions for amplification then characterize sample composition. This paper presents practical methods visualize extent which different can differentiate taxonomic groups, enabling researchers assess primers might be best suited a study or environment interest. These also review annotations in genomic reference sequence databases. We apply concept...
We sought to explore how knowledge of videogames could inform the design complex digital interfaces for bioinformatics visualization tools. Aquaria is an open-source web resource visual exploration protein structures. present results a series workshops conducted with participants who have expertise in videogame and development. report on emerging themes relating might improvements other Future work described.
Background: Hospitals waters are preferable sites for pathogenic bacteria to exist due the presence of areas that predisposes stagnation as well temperatures optimal microbial growth. Hospitalized patients can be exposed these waterborne pathogens while bathing, improper handwashing or even during contact with medical equipment rinsed such which puts them and healthcare workers at high risk acquiring healthcare-associated infections. Moreover, monitoring in facilities is generally limited by...
Over the last decade, development of a range Next Generation Sequencing (NGS) technologies has led to an enormous increase in size data sets available molecular biology. The scale these presents new challenges for researchers, and visualisation is widely regarded as essential tool exploration detailed analysis candidate relationships. Inevitably, there are cognitive technical limits on information which may usefully be displayed particular device, some tension between analytical utility...