A5074585985- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- Service-Oriented Architecture and Web Services
- Bioinformatics and Genomic Networks
- Semantic Web and Ontologies
- Genetic factors in colorectal cancer
- Colorectal Cancer Treatments and Studies
- Alzheimer's disease research and treatments
- Biomedical Text Mining and Ontologies
- Colorectal Cancer Screening and Detection
- Business Process Modeling and Analysis
- Gene expression and cancer classification
- Cholinesterase and Neurodegenerative Diseases
- Environmental Monitoring and Data Management
- Amyotrophic Lateral Sclerosis Research
- Advanced Software Engineering Methodologies
- Scientific Computing and Data Management
- Machine Learning in Bioinformatics
- Advanced Computational Techniques and Applications
- Viral Infectious Diseases and Gene Expression in Insects
- Kawasaki Disease and Coronary Complications
- Genetic Neurodegenerative Diseases
- Biomedical Research and Pathophysiology
- Text and Document Classification Technologies
Macquarie University
2011-2024
Australian Genome Research Facility
2013-2023
Commonwealth Scientific and Industrial Research Organisation
2009-2011
Data61
2010
Multiple testing corrections are a useful tool for restricting the FDR, but can be blunt in context of low power, as we demonstrate by series simple simulations. Unfortunately, proteomics experiments power common, driven proteomics-specific issues like small effects due to ratio compression, and few replicates reagent high cost, instrument time availability other issues; such situations, most multiple methods, if used with conventional thresholds, will fail detect any true positives even...
The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation peak areas. Reference can be generated locally through information dependent acquisition, or obtained from community data repositories commonly studied organisms. However, there have been no studies to systematically evaluate how repository-based affect performance proteomic studies. To...
Abstract Even in the setting of optimal resuscitation high-income countries severe sepsis and septic shock have a mortality 20–40%, with antibiotic resistance dramatically increasing this risk. To develop reference dataset enabling identification common bacterial targets for therapeutic intervention, we applied standardized genomic, transcriptomic, proteomic metabolomic technological framework to multiple clinical isolates four sepsis-causing pathogens: Escherichia coli , Klebsiella...
Abstract Understanding the mechanisms that drive TDP-43 pathology is integral to combating amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD) and other neurodegenerative diseases. Here we generated a longitudinal quantitative proteomic map of cortex from cytoplasmic rNLS8 mouse model ALS FTLD, developed complementary open-access webtool, TDP-map ( https://shiny.rcc.uq.edu.au/TDP-map/ ). We identified distinct protein subsets enriched for diverse biological pathways...
One of the most significant challenges in colorectal cancer (CRC) management is use compliant early stage population-based diagnostic tests as adjuncts to confirmatory colonoscopy. Despite near curative nature clinical surgical resection, mortality remains unacceptably high-as majority patients diagnosed by faecal haemoglobin followed colonoscopy occur at latter stages. Additionally, current screens reliant on fecal occult blood test (FOBT) have low compliance (~ 40%) and suffer...
We propose a system, called EVolution of Long-term Composed Services (Ev-LCS), to address the change management issues in long-term composed services (LCSs). An LCS is dynamic collaboration between autonomous web that collectively provide value-added service. It has commitment its users. first present formal model, which provides grounding semantics support automation management. set operators allow specify precise and manner. then enactment strategy actually implements changes. develop...
Rice crops are often subject to multiple abiotic stresses simultaneously in both natural and cultivated environments, resulting yield reductions beyond those expected from single stress. We report physiological changes after a 4 day exposure combined drought, salt extreme temperature treatments, following 2 salinity pre-treatment two rice genotypes-Nipponbare (a paddy rice) IAC1131 (an upland landrace). Stomata closed days of stresses, causing intercellular CO2 concentrations assimilation...
We propose a service-oriented approach to generate and manage mashups. The proposed is realized using the Mashup Services System (MSS), novel platform support users create, use, mashups with little or no programming effort. relieves from programming-intensive, error-prone, largely nonreusable output process for creating maintaining describe overall design of MSS discuss evaluate its main enabling technologies.
Amyloid β (Aβ) accumulation and its aggregation is characteristic molecular feature of the development Alzheimer's disease (AD). More recently, Aβ has been suggested to be associated with retinal pathology AD, glaucoma drusen deposits in age related macular degeneration (AMD). In this study, we investigated proteins biochemical networks that are affected by amyloid 661W photoreceptor cells culture. Time dose dependent effects on were determined utilising tandem mass tag (TMT) labelling-based...
XML has become the universal data format for a wide variety of information systems. The large number documents existing on web and in other storage systems makes classification an important task. As typical type semistructured data, have both structures contents. Traditional text learning techniques are not very suitable document as considered. This paper presents novel complete framework classification. We first present knowledge representation method which is based typed higher order logic...
Abstract COVID-19 has infected more than 275 million worldwide (at the beginning of 2022). Children appear less susceptible to and present with milder symptoms. Cases children developing clinical features Kawasaki-disease have been described. Here we utilise Mass Spectrometry proteomics determine plasma proteins expressed in healthy pre-pandemic, multisystem inflammatory syndrome (MIS-C) induced ARDS. Pathway analyses were performed affected pathways. 76 are differentially across groups, 85...
We describe a useful workflow for characterizing proteomics experiments incorporating many conditions and abundance data using the popular weighted gene correlation network analysis (WGCNA) approach functional annotation with PloGO2 R package, latter of which we have extended made available to Bioconductor. The can use quantitative from labeled or label-free was developed handle multiple files stemming partition pairwise comparisons. WGCNA similarly produce potentially large number clusters...
Extracellular deposits of the amyloid-beta peptide (Aβ) are known as main pathological hallmark Alzheimer's disease. In disease, neurons injured and die throughout brain, a process in which Aβ neurotoxicity is considered to play an important role. However, molecular mechanisms underlying toxicity that lead neurodegeneration not clearly established. Here we have elucidated pathways networks impacted by using SH-SY5Y human neuroblastoma cells model. These were treated with Aβ1–42 peptides...
Credible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). In this proof-of-concept study, we employed mixture selected recombinant DDA libraries to subsequently identify (not quantify) cancer-associated SWATH/DIA. The exemplar protein spectral library (rPSL) was derived tryptic digestion 36 that had been previously implicated as possible cancer biomarkers both our...
Large-scale peptide mass spectrometry (MS)/MS reference libraries are essential for the comprehensive analysis of data-independent acquisition (DIA) MS datasets, providing a set spectra identification and quantification proteins. We have developed novel web-based R-package (iSwathX) combining that is compatible with different DIA software. This open-source web GUI automates process normalization combination spectral provides user-friendly method performing library format conversions,...
Protein quantification using data-independent acquisition methods such as SWATH-MS most commonly relies on spectral matching to a reference MS/MS assay library. To enable deep proteome coverage and efficient use of existing data, in silico approaches have been described archived or publicly available large libraries for matching. Since implicit the larger is increasing likelihood false-discoveries, new workflows are needed ensure high confidence protein under these conditions. We present...
Proteomics and genomics discovery experiments generate increasingly large result tables, necessitating more researcher time to convert the biological data into new knowledge. Literature review is an important step in this process can be tedious for scale experiments. An informed strategic decision about which biomolecule targets should pursued follow-up thus remains a considerable challenge. To streamline formalise of literature retrieval analysis based ‘omics as decision-facilitating...
A standardized procedure for label-free nano-LC-SRM analysis of 32 high-medium abundance proteins from nondepleted human plasma was established and SRM data were acquired on 45 separate days a control sample that independently prepared 39 distinct dates over an 18-month period (542 days). This case study enabled us to assess quantitative variance associated with analysis, mimicking experimental conditions would be experienced clinical trial biomarker studies. We assessed preparation...
Web services composition is an emerging paradigm for enabling application integration within and across organizational boundaries. Effectively verifying service to comply with the requirements challenging. Verifying composed against certain properties discussed in this paper. TLA (Temporal Logic of Actions) introduced enable effective verification. In particular, algorithms transforming from OWL-S are proposed. We then show that automatically behaviours can be achieved by using TLC (TLA...