A5031660373- Cancer Genomics and Diagnostics
- Erythrocyte Function and Pathophysiology
- Cancer Cells and Metastasis
- Bioinformatics and Genomic Networks
- Blood groups and transfusion
- Radiomics and Machine Learning in Medical Imaging
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Parasites and Host Interactions
- Helminth infection and control
- Pancreatic and Hepatic Oncology Research
- Epigenetics and DNA Methylation
- Pharmacogenetics and Drug Metabolism
- Genetic Mapping and Diversity in Plants and Animals
- Hemoglobinopathies and Related Disorders
- RNA modifications and cancer
- Parasite Biology and Host Interactions
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- Gene expression and cancer classification
- Breast Cancer Treatment Studies
- Folate and B Vitamins Research
- Single-cell and spatial transcriptomics
- Genetic Associations and Epidemiology
- Cancer-related molecular mechanisms research
Queensland University of Technology
2017-2025
Translational Research Institute
2017-2024
The University of Queensland
2013-2017
The University of Melbourne
2007-2015
Royal Women's Hospital
2015
Commonwealth Scientific and Industrial Research Organisation
2010-2012
Universitat Autònoma de Barcelona
2010
Cooperative Research Centre for Beef Genetic Technologies
2010
Macquarie University
2006-2008
Universitat Politècnica de València
2008
Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation DNA or protein sequences is a major requirement for successful application these approaches as information on gene products often key to interpretation experimental results. Therefore, there an increasing need bioinformatics resources which are able cope with large amount sequence data, produce valuable results easily accessible...
Abstract Motivation: Although transcription factors (TF) play a central regulatory role, their detection from expression data is limited due to low, and often sparse, expression. In order fill this gap, we propose impact factor (RIF) metric identify critical TF gene data. Results: To substantiate the generality of RIF, explore set experiments spanning wide range scenarios including breast cancer survival, fat, gonads sex differentiation. We show that strength RIF lies in its ability...
We describe a systems biology approach for the genetic dissection of complex traits based on applying gene network theory to results from genome-wide associations. The associations single-nucleotide polymorphisms (SNP) that were individually associated with primary phenotype interest, age at puberty in our study, explored across 22 related traits. Genomic regions surveyed genes harboring selected SNP. As result, an association weight matrix (AWM) was constructed as many rows and columns Each...
Harsh tropical environments impose serious challenges on poorly adapted species. In beef cattle, adaptation in the form of temperature and disease resistance, coupled with acclimatization to seasonal limited forage, comes at a cost production efficiency. Prominent among these costs is delayed onset puberty, challenging phenotype manipulate through traditional breeding mechanisms. Recently, system biology approaches, including gene networks, have been applied genetic dissection complex...
Third-stage larvae (L3) of the canine hookworm, Ancylostoma caninum, undergo arrested development preceding transmission to a host. Many mRNAs up-regulated at this stage are likely encode proteins that facilitate transition from free-living parasitic larva. The initial phase mammalian host invasion by A. caninum L3 (herein termed "activation") can be mimicked in vitro culturing serum-containing medium.The differentially transcribed between activated and non-activated were identified...
Summary Beef cattle breeds consist of three major genetic subdivisions. The taurine group is adapted to temperate environments, and the zebu Sanga groups are both tropical environments. With advent genotyping sequencing technologies in agriculture, genome‐wide exploration basis for differences adaptation has only just become possible. In this study, approximately 9000 single nucleotide polymorphism markers were genotyped on 317 animals a selection taurine, zebu, composite characterize any...
Abstract Oncogenesis and cancer can arise as a consequence of wide range genomic aberrations including mutations, copy number alterations, expression changes epigenetic modifications encompassing multiple omics layers. Integrating genomic, transcriptomic, proteomic epigenomic datasets via multi-omics analysis provides the opportunity to derive deeper holistic understanding development progression cancer. There are two primary approaches integrating data: multi-staged (focused on identifying...
Dynamic interconversions between transitional epithelial and mesenchymal states underpin the plasticity (EMP) seen in some carcinoma cell systems. We have delineated subpopulations existing within PMC42-LA breast cancer line by their EpCAM expression. These purified but phenotypically plastic states, EpCAMHigh (epithelial) EpCAMLow (mesenchymal), ability to regain phenotypic equilibrium of parental population (i.e., 80% 20% mesenchymal) over time, although rate reversion direction...
Cancer tissue-of-origin specific biomarkers are needed for effective diagnosis, monitoring, and treatment of cancers. In this study, we analyzed transcriptomics data from 37 cancer types provided by The Genome Atlas (TCGA) to identify gene expression signatures. We developed a deep neural network model classify cancers based on data. achieved predictive accuracy >97% across indicating the presence distinct interpreted using Shapley additive explanations signatures that significantly...
Targeted therapies have improved outcomes for certain cancer subtypes, but cytotoxic chemotherapy remains a mainstay triple-negative breast (TNBC). The epithelial-to-mesenchymal transition (EMT) is developmental program co-opted by cells that promotes metastasis and chemoresistance. There are no therapeutic strategies specifically targeting mesenchymal-like cells. We report the US Food Drug Administration (FDA)-approved chemotherapeutic eribulin induces ZEB1-SWI/SNF-directed chromatin...
Cancer has remarkable complexity at the molecular level, with multiple genes, proteins, pathways and regulatory interconnections being affected. We introduce a systems biology approach to study cancer that formally integrates available genetic, transcriptomic, epigenetic knowledge on and, as proof of concept, we apply it colorectal cancer. first classified all genes in human genome into cancer-associated non-cancer-associated based extensive literature mining. then selected set functional...
Measures of heifer fertility are economically relevant traits for beef production systems and knowledge candidate genes could be incorporated into future genomic selection strategies. Ten related to growth were measured in 890 Brangus heifers (3/8 Brahman × 5/8 Angus, from 67 sires). These were: BW hip height adjusted 205 365 d age, postweaning ADG, yearling assessment carcass (i.e., back fat thickness, intramuscular fat, LM area), as well pregnancy first service conception (FSC). collected...
We describe PGTools, an open source software suite for analysis and visualization of proteogenomic data. PGTools comprises applications, libraries, customized databases, tools mass-spectrometry data using combined proteomic genomic backgrounds. A single command is sufficient to search calculate false discovery rates, group annotate proteins, generate peptide databases from RNA-Seq transcripts, identify altered proteins associated with cancer, visualize genome scale sets sophisticated tools....
The analysis of expressed sequence tag (EST) datasets offers a rapid and cost-effective approach to elucidate the transcriptome an organism, but requiring several computational methods for assembly annotation. ESTExplorer is comprehensive workflow system EST data management analysis. pipeline uses 'distributed control approach' in which most appropriate bioinformatics tools are implemented over different dedicated processors. Species-specific repeat masking conceptual translation in-built....
Molecular mechanisms in skeletal muscle associated with anabolic steroid treatment of cattle are unclear and we aimed to characterize transcriptional changes. Cattle were chronically exposed (68 ± 20 days) a hormone implant containing 200 mg trenbolone acetate estradiol (Revalor-H). Biopsy samples from 48 (half treated) longissimus dorsi (LD) under local anesthesia collected. Gene expression levels profiled by microarray, covering 16,944 unique bovine genes: 121 genes differentially...
The human hookworm Necator americanus infects more than 400 million people worldwide, contributing substantially to the poverty in these regions. Adult stage N. live small intestine of host where they inject excretory/secretory (ES) products into mucosa. ES have been characterized at proteome level for a number animal species, but until now, difficulty obtaining sufficient has an obstacle characterizing secretome this important pathogen. Herein we describe and utilize information along with...
Abstract Background Activation and regulation of androgen receptor (AR) signaling the DNA damage response impact prostate cancer (PCa) treatment modalities deprivation therapy (ADT) radiotherapy. Here, we have evaluated a role for human single‐strand binding protein 1 (hSSB1/NABP2) in modulation cellular to androgens ionizing radiation (IR). hSSB1 has defined roles transcription maintenance genome stability, yet little is known about this PCa. Methods We correlated with measures genomic...
Background: Population genomic studies of individuals Indigenous ancestry have been extremely limited comprising <0.5% participants in international genetic databases and genome-wide association studies, contributing to a “genomic gap” that limits their access personalised medicine. While Australians face high burden chronic disease associated medication exposure, corresponding drug safety datasets are sorely lacking. Methods: To address this, we conducted pharmacogenomic study almost...