A5088175231- Neurobiology and Insect Physiology Research
- Congenital heart defects research
- Circadian rhythm and melatonin
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Congenital Heart Disease Studies
- Cardiovascular Issues in Pregnancy
- RNA modifications and cancer
- Genomics and Rare Diseases
- Photoreceptor and optogenetics research
- Gene expression and cancer classification
- Environmental DNA in Biodiversity Studies
- Sleep and Wakefulness Research
- Extracellular vesicles in disease
- Genetics, Bioinformatics, and Biomedical Research
- RNA Research and Splicing
- Scientific Computing and Data Management
- Plant and Biological Electrophysiology Studies
- Neuroscience and Neuropharmacology Research
- Coronary Artery Anomalies
- Biomimetic flight and propulsion mechanisms
- Mitochondrial Function and Pathology
- Aortic Disease and Treatment Approaches
- Software Testing and Debugging Techniques
- Cardiovascular, Neuropeptides, and Oxidative Stress Research
Victor Chang Cardiac Research Institute
2016-2025
UNSW Sydney
2018-2025
The University of Queensland
2012-2023
Griffith University
2019
The University of Sydney
2016
Norwegian Institute of Marine Research
2012
Most existing dimensionality reduction and clustering packages for single-cell RNA-seq (scRNA-seq) data deal with dropouts by heavy modeling computational machinery. Here, we introduce CIDR (Clustering through Imputation Dimensionality Reduction), an ultrafast algorithm that uses a novel yet very simple implicit imputation approach to alleviate the impact of in scRNA-seq principled manner. Using range simulated real data, show improves standard principal component analysis outperforms...
Sleep is a dynamic process comprising multiple stages, each associated with distinct electrophysiological properties and potentially serving different functions. While these phenomena are well described in vertebrates, it unclear if invertebrates have sleep stages. We perform local field potential (LFP) recordings on flies spontaneously sleeping, compare their brain activity to induced using either genetic activation of sleep-promoting circuitry or the GABAA agonist Gaboxadol. find...
Spontaneous coronary artery dissection (SCAD) is a cause of acute syndrome that predominantly affects women. Its pathophysiology remains unclear but connective tissue disorders (CTD) and other vasculopathies have been observed in many SCAD patients. A genetic component for increasingly appreciated, although few genes robustly implicated. We sought to clarify the using targeted genome-wide methods cohort sporadic cases identify both common rare disease-associated variants.
Abstract Congenital heart disease (CHD) is the most common class of human birth defects, with a prevalence 0.9% births. However, two-thirds cases have an unknown cause, and many these are thought to be caused by in utero exposure environmental teratogens. Here we identify potential teratogen causing CHD mice: maternal iron deficiency (ID). We show that ID mice causes severe cardiovascular defects offspring. These likely arise from increased retinoic acid signalling embryos. The can prevented...
Larval zebrafish innately perform a suite of behaviors that are tightly linked to their evolutionary past, notably escape from threatening stimuli and pursuit capture prey. These have been carefully examined in the but mostly with regard movements trunk tail larvae. Here, we employ kinematics analyses describe pectoral fins during predatory behavior. In accord previous studies, find roles for slow swimming immediately after striking We novel long-latency, not short-latency C-bends. also...
Sleep is a dynamic process in most animals, involving distinct stages that probably perform multiple functions for the brain. Before sleep can be initiated, it likely behavioral responsiveness to outside world needs reduced, even while animal still awake. Recent work Drosophila has uncovered switch dorsal fan-shaped body (dFB) of fly’s central brain, but not known whether these sleep-promoting neurons also govern acute need ignore salient stimuli environment during transitions. We found...
Most existing dimensionality reduction and clustering packages for single-cell RNA-Seq (scRNA-Seq) data deal with dropouts by heavy modelling computational machinery. Here we introduce CIDR (Clustering through Imputation Dimensionality Reduction), an ultrafast algorithm which uses a novel yet very simple ‘implicit imputation’ approach to alleviate the impact of in scRNA-Seq principled manner. Using range simulated real data, have shown that improves standard principal component analysis...
Background Spontaneous coronary artery dissection (SCAD) is an increasingly recognized cause of acute syndrome or sudden cardiac death, primarily affecting relatively young women (median age, 51 years) without typical cardiovascular risk factors. SCAD has a genetic component, with genome‐wide association studies identifying multiple loci. Thoracic aortic (type A) shares some overlap SCAD, suggesting potential common predispositions. Methods We performed screening whole‐genome sequencing 17...
General anesthetics cause a profound loss of behavioral responsiveness in all animals. In mammals, general anesthesia is induced part by the potentiation endogenous sleep-promoting circuits, although "deep" understood to be more similar coma (Brown et al., 2011). Surgically relevant concentrations anesthetics, such as isoflurane and propofol, have been shown impair neural connectivity across mammalian brain (Mashour Hudetz, 2017; Yang 2021), which presents one explanation why animals become...
Abstract Summary Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current analysis tools are not specifically designed to efficiently process scRNA-seq data due their limited scalability. Here we introduce Falco, cloud-based framework enable paralellization existing processing pipelines using big technologies Apache Hadoop and Spark for performing massively parallel large scale transcriptomic data. Using two public datasets popular...
The dopamine ontogeny hypothesis for schizophrenia proposes that transient dysregulation of the dopaminergic system during brain development increases likelihood this disorder in adulthood. To test a high throughput animal model, we have transiently manipulated signaling developing fruit fly Drosophila melanogaster and examined behavioral responsiveness adult flies. We found either increase neuron activity or decrease receptor expression permanently impairs adults. A screen impaired revealed...
Mitochondrial DNA (mtDNA) mutations contribute to human disease across a range of severity, from rare, highly penetrant causal for monogenic disorders with milder contributions phenotypes. mtDNA variation can exist in all copies or percentage and be detected levels as low 1%. The large number the possibility multiple alternative alleles at same nucleotide position make task identifying allelic very challenging. In recent years, specialized variant calling algorithms have been developed that...
Mutations in the presynaptic protein syntaxin1A modulate general anesthetic effects vitro and vivo. Coexpression of a truncated confers resistance to volatile intravenous anesthetics, suggesting target mechanism distinct from postsynaptic inhibitory receptor processes. Hypothesizing that recovery anesthesia may involve component, authors tested whether mutations facilitated isoflurane Drosophila melanogaster.A construct was expressed neurons. The compared on induction versus mutant animals...
The most common cyanotic congenital heart disease (CHD) requiring management as a neonate is transposition of great arteries (TGA). Clinically, up to 50% TGA patients develop some form neurodevelopmental disability (NDD), thought have significant genetic component. A "ciliopathy" and links with laterality disorders been proposed. This first report whole genome sequencing in TGA, sought identify clinically relevant variants contributing heart, brain defects.Initial analyses on 100 focussed...
Abstract Motivation In silico prediction tools are essential for identifying variants which create or disrupt cis-splicing motifs. However, there limited options genome-scale discovery of splice-altering variants. Results We have developed Spliceogen, a highly scalable pipeline integrating predictions from some the individually best performing models splice motif prediction: MaxEntScan, GeneSplicer, ESRseq and Branchpointer. Availability implementation Spliceogen is available as command line...
Testing of bioinformatics software often suffers from the oracle problem, especially when testing that analyses human genome sequencing data. Metamorphic has been proposed to alleviate problem. Nonetheless, smaller research or clinical centres may be challenged by complexity and resources required implement a suitable metamorphic framework in practice. This paper presents case study on how cloud-based can applied widely used genomic pipeline, discusses future implementing large-scale...
Abstract Summary Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current analysis tools are not specifically designed to efficiently process scRNA-seq data due their limited scalability. Here we introduce Falco, cloud-based framework enable paralellisation existing processing pipelines using big technologies Apache Hadoop and Spark for performing massively parallel large scale transcriptomic data. Using two public sets popular...