A5040511420- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA modifications and cancer
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- Microbial Metabolic Engineering and Bioproduction
- Amyotrophic Lateral Sclerosis Research
- Allergic Rhinitis and Sensitization
- Cancer-related gene regulation
- Food Allergy and Anaphylaxis Research
- Advanced Proteomics Techniques and Applications
- RNA Interference and Gene Delivery
- Neurogenesis and neuroplasticity mechanisms
- Wnt/β-catenin signaling in development and cancer
- Machine Learning in Bioinformatics
- Advanced biosensing and bioanalysis techniques
- MicroRNA in disease regulation
- Bioinformatics and Genomic Networks
- Machine Learning and ELM
- Plant Molecular Biology Research
- Asthma and respiratory diseases
- T-cell and B-cell Immunology
- vaccines and immunoinformatics approaches
- Neuroinflammation and Neurodegeneration Mechanisms
The University of Queensland
2013-2020
Queensland Eye Institute
2014
Bioinformatics Institute
2010-2013
Agency for Science, Technology and Research
2010-2013
Institute for Infocomm Research
2006-2007
Recent advances in next-generation sequencing technology allow high-throughput cDNA (RNA-Seq) to be widely applied transcriptomic studies, particular for detecting differentially expressed genes between groups. Many software packages have been developed the identification of (DEGs) treatment groups based on RNA-Seq data. However, there is a lack consensus how approach an optimal study design and choice suitable analysis. In this comparative we evaluate performance three most frequently used...
Abstract Background Tea is the most popular non-alcoholic health beverage in world. The tea plant ( Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process enhance its freezing tolerance winter. Changes that occur at molecular level response low temperatures are poorly understood plants. To elucidate mechanisms of acclimation, we employed RNA-Seq and digital gene expression (DGE) technologies study genome-wide profiles during Results Using Illumina sequencing platform,...
Wnt proteins are secreted post-translationally modified that signal locally to regulate development and proliferation. The production of bioactive Wnts requires a number dedicated factors in the secreting cell whose coordinated functions not fully understood. A screen for small molecules identified inhibitors vacuolar acidification as potent secretion. Inhibition V-ATPase or disruption pH gradients by diverse drugs potently inhibited Wnt/β-catenin signaling both cultured human cells vivo,...
Abstract Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterised by the loss of upper and lower motor neurons. ALS exhibits high phenotypic variability including age site onset, duration. To uncover epigenetic transcriptomic factors that may modify an phenotype, we used cohort Australian monozygotic twins (n = 3 pairs) triplets 1 set) are discordant for represent sporadic two most common types familial ALS, linked to C9orf72 SOD1 . Illumina Infinium...
The activity of neural precursor cells in the adult hippocampus is regulated by various stimuli; however, whether these stimuli regulate same or different populations remains unknown. Here, we developed a novel cell-sorting protocol that allows purification to homogeneity neurosphere-forming precursors from mouse and examined responsiveness individual using clonal assay. We show within Hes5-GFP + /Nestin-GFP /EGFR cell population, which comprises majority precursors, there are two distinct...
Abstract Recent advances in next-generation sequencing technology allow high-throughput cDNA (RNA-Seq) to be widely applied transcriptomic studies, particular for detecting differentially expressed genes between groups. Many software packages have been developed the identification of (DEGs) treatment groups based on RNA-Seq data. However, there is a lack consensus how approach an optimal study design and choice suitable analysis. In this comparative we evaluate performance three most...
Assessment of potential allergenicity and patterns cross-reactivity is necessary whenever novel proteins are introduced into human food chain. Current bioinformatic methods in allergology focus mainly on the prediction allergenic proteins, with no information among known allergens. In this study, we present AllerTool, a web server essential tools for assessment predicted as well published The analysis include graphical representation allergen information; local sequence comparison tool that...
Transcriptome-wide expression profiling of neurons has provided important insights into the underlying molecular mechanisms and gene patterns that transpire during learning memory formation. However, there is a paucity tools for stimulus-induced RNA within specific neuronal cell populations. A bioorthogonal method to chemically label nascent (i.e., newly transcribed) in cell-type-specific temporally controlled manner, which also amenable bioconjugation via click chemistry, was recently...
HLA-C locus products are poorly understood in part due to their low expression at the cell surface. Recent data indicate that these molecules serve as major restriction elements for human immunodeficiency virus type 1 (HIV-1) cytotoxic T lymphocyte (CTL) epitopes. We report here a structure-based technique prediction of peptides binding Cw*0401. The models were rigorously trained, tested and validated using experimentally verified Cw*0401 non-binding obtained from biochemical studies. A new...
Abstract Background Computational comparison of two protein structures is the starting point many methods that build on existing knowledge, such as structure modeling (including complexes and conformational changes), molecular replacement, or annotation by structural similarity. In a commonly used strategy, significant effort invested in matching sets atoms. complementary approach, global descriptor assigned to overall structure, thus losing track substructures within. Results Using small...
deconSTRUCT webserver offers an interface to a protein database search engine, usable for general purpose detection of similar (sub)structures. Initially, it deconstructs the query structure into its secondary elements (SSEs) and reassembles match target by requiring (tunable) degree similarity in direction sequential order SSEs. Hierarchical organization judicious use information about enables achieve sensitivity specificity established engines at orders magnitude increased speed, without...
In this work, belonging to the field of comparative analysis protein sequences, we focus on detection functional specialization residue level. As input, take a set sequences divided into groups orthologues, each group known be responsible for different function. This provides two independent pieces information: within conservation and overlap in amino acid type across groups. We build our discussion around scoring functions that keep separated source signal easy trace back its source....
Cube-DB is a database of pre-evaluated results for detection functional divergence in human/vertebrate protein families. The analysis organized around the nomenclature associated with human proteins, but based on all currently available vertebrate genomes. Using full genomes enables us, through mutual-best-hit strategy, to construct comparable taxonomical samples paralogues under consideration. Functional specialization scored residue level according two models behavior after divergence:...
When comparing sequences of similar proteins, two kinds questions can be asked, and the related inference made. First, one may ask to what degree they are similar, then, how differ. In first case tentatively conclude that conserved elements common all central importance protein's function. latter regions specialization discriminative function or binding partners across subfamilies proteins. Experimental efforts - mutagenesis pharmacological intervention then pointed in either direction,...