A5052404494- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- Mesenchymal stem cell research
- Genetics, Bioinformatics, and Biomedical Research
- Cancer Cells and Metastasis
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Cell Image Analysis Techniques
- Lymphatic System and Diseases
- Metabolomics and Mass Spectrometry Studies
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Research Data Management Practices
- Gene Regulatory Network Analysis
- Cancer Genomics and Diagnostics
- Machine Learning in Bioinformatics
- Biomedical and Engineering Education
- Immune cells in cancer
- Sepsis Diagnosis and Treatment
- Scientific Computing and Data Management
- Congenital heart defects research
- RNA Research and Splicing
- Occupational and environmental lung diseases
Peter MacCallum Cancer Centre
2022-2023
The University of Melbourne
2016-2023
Monash University
2020-2023
The Alfred Hospital
2023
Australian Regenerative Medicine Institute
2023
Stem Cells Australia
2020
The University of Queensland
2015-2016
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...
During development, the lymphatic vasculature forms as a second network derived chiefly from blood vessels. The transdifferentiation of embryonic venous endothelial cells (VECs) into (LECs) is key step in this process. Specification, differentiation and maintenance LEC fate are all driven by transcription factor Prox1, yet downstream mechanisms remain to be elucidated. We here present single-cell transcriptomic atlas lymphangiogenesis zebrafish, revealing new markers hallmarks over four...
Mesenchymal stromal cells (MSC) are widely used for the study of mesenchymal tissue repair, and increasingly adopted cell therapy, despite lack consensus on identity these cells. In part this is due to specificity MSC markers. Distinguishing from other such as fibroblasts particularly difficult using standard analysis surface proteins, there an urgent need improved classification approaches. Transcriptome profiling commonly describe compare different types; however, efforts identify specific...
Stemformatics is an established gene expression data portal containing over 420 public datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem community, it has a major focus on pluripotency, tissue cells, staged differentiation. includes curated 'collections' of relevant to reprogramming, as well hematopoiesis leukaemia. Rather than simply rehosting they appear in repositories, uses stringent set quality control metrics its own...
Stromal support is critical for lung homeostasis and the maintenance of an effective epithelial barrier. Despite this, previous studies have found a positive association between number mesenchymal stromal cells (MSCs) isolated from alveolar compartment human diseases associated with dysfunction. We hypothesised that bronchoalveolar lavage derived MSCs (BAL-MSCs) are dysfunctional distinct resident tissue (LT-MSCs). In this study, we comprehensively interrogated phenotype transcriptome...
Gene expression atlases have transformed our understanding of the development, composition and function human tissues. New technologies promise improved cellular or molecular resolution, led to identification new cell types, better defined states. But as emerge, information derived on old platforms becomes obsolete. We demonstrate that it is possible combine a large number different profiling experiments summarised from dozens laboratories representing hundreds donors, create an integrated...
Abstract Background Diseases are complex phenotypes often arising as an emergent property of a non-linear network genetic and epigenetic interactions. To translate this resulting state into causal relationship with subset regulatory features, many experiments deploy array laboratory assays from multiple modalities. Often, each these datasets is large, heterogeneous, noisy. Thus, it non-trivial to unify interpretable phenotype. Although recent methods address problem varying degrees success,...
Despite the volume of experiments performed and data available, complex biology coronavirus SARS-COV-2 is not yet fully understood. Existing molecular profiling studies have focused on analysing functional omics a single type, which captures changes in small subset perturbations caused by virus. As logical next step, results from multiple such analysis may be aggregated to comprehensively interpret mechanisms SARS-CoV-2. An alternative approach integrate simultaneously parallel fashion...
<ns4:p>Data from multiple omics layers of a biological system is growing in quantity, heterogeneity and dimensionality. Simultaneous multi-omics data integration immense interest to researchers as it has potential unlock previously hidden biomolecular relationships leading early diagnosis, prognosis, expedited treatments. Many tools for are developed. However, these often restricted highly specific experimental designs, types data, formats. A major limitation the field lack pipeline that can...
Phenotypes are driven by regulated gene expression, which in turn mediated complex interactions between diverse biological molecules. Protein-DNA such as histone and transcription factor binding well studied, along with RNA-RNA short RNA silencing of genes. In contrast, lncRNA-protein interaction (LPI) mechanisms comparatively unknown, likely the difficulties studying LPI. However, LPI emerging key epigenetic mechanism, playing a role development disease. Their importance is further...
Abstract The emerging field of Genome-NLP (Natural Language Processing) aims to analyse biological sequence data using machine learning (ML), offering significant advancements in data-driven diagnostics. Three key challenges exist Genome-NLP. First, long biomolecular sequences require “tokenisation” into smaller subunits, which is non-trivial since many “words” remain unknown. Second, ML methods are highly nuanced, reducing interoperability and usability. Third, comparing models reproducing...
During development, the lymphatic vasculature forms as a second, new vascular network derived from blood vessels. The transdifferentiation of embryonic venous endothelial cells (VECs) into (LECs) is first step in this process. Specification, differentiation and maintenance LEC fate are all driven by transcription factor Prox1, yet downstream mechanisms remain to be elucidated. We present single cell transcriptomic atlas lymphangiogenesis zebrafish revealing markers hallmarks over four...
Mesenchymal stromal cells (MSC) are widely used, isolated from a variety of tissues and increasingly adopted for cell therapy, but the identity these is poorly defined commonalities between MSC different sources controversial. Here we undertook comprehensive review all public expression studies to assess whether derived shared any common molecular attributes. In doing so, discovered an over-arching transcriptional phenotype by wide MSC, freshly or cultured cells, under growth conditions. We...
ABSTRACT Gene expression atlases have transformed our understanding of the development, composition and function human tissues. New technologies promise improved cellular or molecular resolution, led to identification new cell types, better defined states. But as emerge, information derived on old platforms becomes obsolete. We demonstrate that it is possible combine a large number different profiling experiments summarised from dozens laboratories representing hundreds donors, create an...
<ns3:p>Data from multiple omics layers of a biological system is growing in quantity, heterogeneity and dimensionality. Simultaneous multi-omics data integration field research as it has strong potential to unlock information on previously hidden relationships leading early diagnosis, prognosis expedited treatments. Many tools for are being developed. However, these often restricted highly specific experimental designs, types data. While some general methods do exist, they require formats...