A5045801615- HIV, Drug Use, Sexual Risk
- Hepatitis C virus research
- Criminal Justice and Corrections Analysis
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- COVID-19 epidemiological studies
- Genomics and Phylogenetic Studies
- Hepatitis B Virus Studies
- Bacteriophages and microbial interactions
- Viral Infections and Outbreaks Research
- HIV/AIDS Research and Interventions
- Protein Structure and Dynamics
- Peptidase Inhibition and Analysis
- Homelessness and Social Issues
- Enzyme Structure and Function
- RNA Research and Splicing
- Sex work and related issues
- Advanced Statistical Process Monitoring
- Endoplasmic Reticulum Stress and Disease
- Liver Disease Diagnosis and Treatment
- HIV Research and Treatment
- Biochemical and Structural Characterization
- Interprofessional Education and Collaboration
- Infection Control and Ventilation
- Forecasting Techniques and Applications
University of South Australia
2021-2024
Novo Nordisk Foundation
2023
Aarhus University
2023
UNSW Sydney
2014-2019
Australian Government
2018
Government of Western Australia Department of Health
2018
Yuan Ze University
2011-2015
Imperial College London
2015
National Cheng Kung University
2012
Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability activity of a protein; thus altering protein function. Due to high throughput mass spectrometry (MS)-based methods in identifying site-specific modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) updated integrate experimental PTMs obtained from public resources as well manually curated MS/MS peptides associated with research...
Bioinformatics research often requires conservative analyses of a group sequences associated with specific biological function (e.g. transcription factor binding sites, micro RNA target sites or protein post-translational modification sites). Due to the difficulty in exploring conserved motifs on large-scale sequence data involved various signals, new method, MDDLogo, is developed. MDDLogo applies maximal dependence decomposition (MDD) cluster aligned signal into subgroups containing...
Summary Hepatitis C virus ( HCV ) transmission is high in prisons. This study investigated trends incidence and associated factors among a cohort of prisoners with history injecting drug use New South Wales, Australia. Data were available from the Incidence Transmission Study—prisons HITS ‐p) 2005 to 2014. Temporal evaluated. Factors time seroconversion people ongoing was assessed using Cox proportional hazards. Among 320 antibody‐negative participants (mean age 26; 72% male), 62% (n=197)...
Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in intracellular signal transduction. Due to the difficulty performing high-throughput mass spectrometry-based experiment, there is a desire predict sites using computational methods. However, previous studies regarding silico prediction of plant lack consideration kinase-specific data. Thus, we are motivated propose new method that investigates different substrate specificities sites. Experimentally verified data...
Abstract Aims To document the relationships between injecting drug use, imprisonment and hepatitis C virus ( HCV ) infection. Design Prospective cohort study. Setting Multiple prisons in New South Wales, A ustralia. Participants seronegative prisoners with a life‐time history of use IDU were enrolled followed prospectively n = 210) by interview antibody RNA testing 6–12‐monthly for up to 4 years when prison. Measurements incidence was calculated using person‐years method. Cox regression used...
Introduction We conducted a detailed analysis of trends in new HIV diagnoses Australia by country birth, to understand any changes epidemiology, relationship migration patterns and implications for public health programs. Methods Poisson regression analyses were performed, comparing the age-standardised diagnosis rates per 100,000 estimated resident population between 2006–2010 2011–2015 region with stratification exposure (male-to-male sex, heterosexual sex–males females). Correlation...
Protein O-GlcNAcylation, involving the β-attachment of single N-acetylglucosamine (GlcNAc) to hydroxyl group serine or threonine residues, is an O-linked glycosylation catalyzed by O-GlcNAc transferase (OGT). Molecular level investigation basis for OGT's substrate specificity should aid understanding how contributes diverse cellular processes. Due increasing number O-GlcNAcylated peptides with site-specific information identified mass spectrometry (MS)-based proteomics, we were motivated...
Abstract Hepatitis C virus (HCV) is predominantly transmitted between persons who inject drugs. For this population, global prevalence of HCV infection high and incarceration common an independent risk factor for acquisition. To explore transmission dynamics in incarcerated populations, we integrated sequences with behavior spatiotemporal data analyzed clusters among prisoners Australia. We detected 3 recent consisting 4 likely in-custody events involving source/recipient pairs located the...
Viruses infect humans and progress inside the body leading to various diseases complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication inhibition normal host-cell functions. Due its biological importance, there is a desire identify protein sites on human viruses. However, use mass spectrometry-based experiments proven be expensive labor-intensive. Furthermore, previous studies which have identified viruses do not...
Abstract Background and aims Australia is currently on track to meet the World Health Organization (WHO) global hepatitis C virus (HCV) elimination goals by 2030, reflecting universal subsidized access testing direct‐acting antiviral (DAA) treatment. In New South Wales, DAA treatment in prisons has scaled‐up substantially, with 1000 prisoners treated 2017. However, HCV prevalence incidence this setting high, which could undermine efforts. This study aimed test preventative effects of...
The phosphorylation of virus proteins by host kinases is linked to viral replication. This leads an inhibition normal host-cell functions. Further elucidation in required order aid drug design and treatment. However, only a few studies have investigated substrate motifs identifying sites. Additionally, existing bioinformatics tool do not consider potential that may initiate the protein.329 experimentally verified fragments on 111 were collected from virPTM. These clustered into subgroups...
Introduction Correctional facilities are high-priority settings for coordinated public health responses to the COVID-19 pandemic. These at high risk of disease transmission due close contacts between people in prison and with wider community. People also vulnerable severe given their burden co-morbidities. Methods We developed a mathematical model evaluate effect various interventions, including vaccination, on mitigation outbreaks, applying it prisons Australia Canada. Results found that,...
In eukaryotes, ubiquitin-conjugation is an important mechanism underlying proteasome-mediated degradation of proteins, and as such, plays essential role in the regulation many cellular processes. ubiquitin-proteasome pathway, E3 ligases play roles by recognizing a specific protein substrate catalyzing attachment ubiquitin to lysine (K) residue. As more experimental data on conjugation sites become available, it becomes possible develop prediction models that can be scaled big data. However,...
Carboxylation is a modification of glutamate (Glu) residues which occurs post-translation that catalyzed by γ-glutamyl carboxylase in the lumen endoplasmic reticulum. Vitamin K critical co-factor post-translational conversion Glu to γ-carboxyglutamate (Gla) residues. It has been shown process carboxylation involved blood clotting cascade, bone growth, and extraosseous calcification. However, studies this field have limited difficulty experimentally studying substrate site specificity...
Regulation of pre-mRNA splicing is achieved through the interaction RNA sequence elements and a variety RNA-splicing related proteins (splicing factors). The machinery in humans not yet fully elucidated, partly because factors have been exhaustively identified. Furthermore, experimental methods for factor identification are time-consuming lab-intensive. Although many computational proposed RNA-binding proteins, there exists no development that focuses on so far. Therefore, we motivated to...
Correctional centres (termed here ‘prisons’) are at high risk of COVID-19 and have featured major outbreaks worldwide. Inevitable close contacts, frequent inmate movements, a disproportionate burden co-morbidities mean these environments need to be prioritised in any public health response respiratory pathogens such as COVID-19. We developed an individual-based SARS-CoV-2 transmission model for the prison system New South Wales, Australia ‐ incorporating all 33 correctional centres, 13,458...
Forecasting pharmaceutical stock inventory is a complex problem affecting the healthcare industry across globe. South Australia no different. This prompted SA Pharmacy to collaborate with team of researchers at University explore ways projecting for their state-wide services. In this paper, we utilised industry-supplied time-series data train prediction models using linear regression, exponential smoothing, Holt Winters Seasonal Additive, and Additive + damped algorithms. Among these models,...
The Danish healthcare system is often hailed as a pioneer in quality health services and initiatives. However, there are still gaps this despite an impressive effort by stakeholders. To address this, it essential to identify specify unmet needs space. biodesign process of innovation well-documented multi-disciplinary approach used produce sustainable solutions fit for society. Adopting concept, the BioMedical Design Novo Nordisk Foundation Fellowship programme has been established Denmark...
Abstract Correctional facilities are at high risk of COVID-19 outbreaks due to the inevitable close contacts in environment. Such a priority public health response epidemic. We developed user-friendly Excel spreadsheet model (building on previously Recidiviz model) analyze correctional and potential impact prevention strategies - Incarceration Model. The requires limited inputs can be used by non-modelers. outbreak mitigation is illustrated for an example prison setting.
Protein phosphorylation in viruses plays crucial regulatory roles enhancing progression, replication, and inhibition of host cell functions.Due to the difficulty mass spectrometry-based identification viral sites, we are motivated develop a new method investigate substrate motifs identify protein sites on viruses.The experimentally verified data were extracted from public resource recursively statistical is applied cluster whole set phosphorylated sequences into subgroups containing...