A5054811862- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Pregnancy and preeclampsia studies
- Epigenetics and DNA Methylation
- Gene Regulatory Network Analysis
- Cutaneous Melanoma Detection and Management
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Skin and Cellular Biology Research
- MicroRNA in disease regulation
- Cancer-related gene regulation
- Cellular Mechanics and Interactions
- RNA modifications and cancer
- Neuroinflammation and Neurodegeneration Mechanisms
- Barrier Structure and Function Studies
- Neonatal Respiratory Health Research
- Cancer, Hypoxia, and Metabolism
- Cancer-related molecular mechanisms research
- Network Security and Intrusion Detection
- Aquaculture disease management and microbiota
- Melanoma and MAPK Pathways
- Skin Protection and Aging
- Plant Molecular Biology Research
- melanin and skin pigmentation
- Marine Biology and Environmental Chemistry
University of Auckland
2011-2024
The University of Melbourne
2014-2018
Maurice Wilkins Centre
2014-2016
Melbourne School of Theology
2016
Data61
2015
East Carolina University
2009
New York State College of Veterinary Medicine
2005
Cornell University
2005
Brain inflammation plays a key role in neurological disease. Although much research has been conducted investigating inflammatory events animal models, potential differences human brain versus rodent models makes it imperative that we also study these phenomena cells and tissue. Primary cell cultures were generated from biopsy tissue of patients undergoing surgery for drug-resistant epilepsy. Cells treated with pro-inflammatory compounds IFNγ, TNFα, IL-1β, LPS, chemokines IP-10 MCP-1...
Abstract We have developed an efficient and inexpensive pipeline for streamlining large-scale collection genome sequencing of bacterial isolates. Evaluation this method involved a worldwide research collaboration focused on the model organism Salmonella enterica , 10KSG consortium. Following optimization logistics that shipping isolates as thermolysates in ambient conditions, project assembled diverse 10,419 from low- middle-income countries. The genomes were sequenced using LITE library...
Gene regulatory networks inferred from RNA abundance data have generated significant interest, but despite this, gene network approaches are used infrequently and often require input bioinformaticians. We assembled a suite of tools for analysing networks, we illustrate their use with microarray datasets in human endothelial cells. infer range based on this analysis discuss the strengths limitations inference data. welcome contact researchers interested using our visualization to answer...
The placenta is a vital fetal exchange organ connecting mother and baby. Specialised placental epithelial cells, called trophoblasts, are essential for adequate function. Trophoblasts transform the maternal vasculature to allow efficient blood flow facilitate nutrient uptake. Placental development in part regulated by epigenetic mechanisms. However, our understanding of how DNA methylation contributes human trophoblast differentiation limited. To better understand genome-wide differences...
The placenta is responsible for all nutrient and gas exchange between mother baby during pregnancy. differentiation of specialised placental epithelial cells called trophoblasts essential function, but we understand little about how these populations arise. Mouse trophoblast stem have allowed us to many the factors that regulate murine lineage development, human anatomically very different from mouse, it imperative isolate a cell development. Here developed novel methodology Hoechst...
The skin is largely comprised of keratinocytes within the interfollicular epidermis. Over approximately two weeks these cells differentiate and traverse thickness skin. stage differentiation therefore reflected in positions tissue, providing a convenient axis along which to study signaling events that occur situ during keratinocyte terminal differentiation, over this extended two-week timescale. canonical ERK-MAPK cascade (Raf-1, MEK-1/2 ERK-1/2) has been implicated controlling diverse...
Background The nucleic acid-binding protein YB-1, a member of the cold-shock domain family, has been implicated in progression breast cancer and is associated with poor patient survival. YB-1 sequence similarity to LIN28, another family member, which role regulation small noncoding RNAs (sncRNAs) including microRNAs (miRNAs). Therefore, investigate whether there an association between sncRNAs cancer, we investigated were bound by two cell lines (luminal A-like basal cell-like), abundance...
Predictive modelling of gene expression provides a powerful framework for exploring the regulatory logic underpinning transcriptional regulation. Recent studies have demonstrated utility such models in identifying dysregulation and miRNA associated with abnormal patterns transcription factor (TF) binding or nucleosomal histone modifications (HMs). Despite growing popularity approaches, comparative review various algorithms feature extraction methods is lacking. We define compare three...
Transcription factors (TFs) and histone modifications (HMs) play critical roles in gene expression by regulating mRNA transcription. Modelling frameworks have been developed to integrate high-throughput omics data, with the aim of elucidating regulatory logic that results from interactions DNA, TFs HMs. These models yielded an unexpected poorly understood result: HMs are statistically redundant explaining transcript abundance at a genome-wide level.We constructed predictive integrating...
Chemotherapy with taxanes such as paclitaxel (PTX) is a key component of triple negative breast cancer (TNBC) treatment. PTX used in combination other drugs both the adjuvant setting and advanced cancer. Because proportion patients respond poorly to or relapse after its use, greater understanding mechanisms conferring resistance required. One protein shown be involved drug Y-box binding 1 (YB-1). High levels YB-1 have previously been associated TNBCs. In this study, we aimed determine by...
Background Our understanding of the molecular pathways that underlie melanoma remains incomplete. Although several published microarray studies clinical melanomas have provided valuable information, we found only limited concordance between these studies. Therefore, took an in vitro functional genomics approach to understand pathways. Methodology/Principal Findings Affymetrix data were generated from A375 cells treated with siRNAs against 45 transcription factors and signaling molecules....
‘Reproducible research’ has received increasing attention over the past few years as bioinformatics and computational biology methodologies become more complex. Although reproducible research is progressing in several valuable ways, we suggest that recent increases internet bandwidth disk space, along with availability of open-source free-software licences for tools, enable another simple step to make reproducible. In this article, urge creation minimal virtual reference environments...
Optimising the timing of flowering contributes to successful sexual reproduction and yield in agricultural plants. FLOWERING LOCUS T (FT) genes, first identified Arabidopsis thaliana (Arabidopsis), promote universally, but upstream regulatory pathways can differ markedly among Flowering model legume, Medicago truncatula (Medicago) is accelerated by winter cold (vernalisation) followed long day (LD) photoperiods leading elevated expression floral activator, FT-like gene FTa1. However,...
In many cancers, microRNAs (miRs) contribute to metastatic progression by modulating phenotypic reprogramming processes such as epithelial-mesenchymal plasticity. This can be driven miRs targeting multiple mRNA transcripts, inducing regulated changes across large sets of genes. The miR-target databases TargetScan and DIANA-microT predict putative relationships examining sequence complementarity between mRNAs. However, it remains a challenge identify which miR-mRNA interactions are active at...
J. Neurochem . (2012) 122 , 976–994. Abstract A quantitative, peripherally accessible biomarker for neuropathic pain has great potential to improve clinical outcomes. Based on the premise that peripheral and central immunity contribute mechanisms, we hypothesized biomarkers could be identified from whole blood of adult male rats, by integrating graded chronic constriction injury (CCI), ipsilateral lumbar dorsal quadrant (iLDQ) transcriptomes, pathway analysis with behavior. Correlational...
We develop a new regression algorithm, cMIKANA, for inference of gene regulatory networks from combinations steady-state and time-series expression data. Using simulated datasets to assess the accuracy reconstructing networks, we show that data sets can successfully be combined identify interactions using algorithm. Inferring was found advantageous when noisy measurements collected with either lower sampling rates or limited number experimental replicates. illustrate our method by applying...
The wide variety of published approaches for the problem regulatory network inference makes using multiple algorithms complex and time-consuming. Network Analysis Inference Library (NAIL) is a set software tools to simplify range computational activities involved in inference. It uses modular approach connect different same visualization network-based analyses. NAIL technology-independent includes an interface layer allow easy integration components into other applications.NAIL implemented...
Phosphoprotein signalling pathways have been intensively studied in vitro, yet their role regulating tissue homeostasis is not fully understood. In the skin, interfollicular keratinocytes differentiate over approximately 2 weeks as they traverse epidermis. The extracellular signal-regulated kinase (ERK) branch of mitogen-activated protein (MAPK) pathway has implicated this process. Therefore, we examined ERK-MAPK activity within human epidermal situ. We used confocal microscopy and...
Motivation: Predictive modelling of gene expression is a powerful framework for the in silico exploration transcriptional regulatory interactions through integration high-throughput -omics data. A major limitation previous approaches their inability to handle conditional and synergistic that emerge when collectively analysing genes subject different mechanisms. This reduces overall predictive power thus reliability downstream biological inference. Results: We introduce an analytical...