A5045805444- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Aquaculture disease management and microbiota
- Algal biology and biofuel production
- Marine and coastal ecosystems
- Genomics and Chromatin Dynamics
- Microbial Community Ecology and Physiology
- Coral and Marine Ecosystems Studies
- Aquatic Ecosystems and Phytoplankton Dynamics
- Marine Biology and Ecology Research
- Epigenetics and DNA Methylation
- interferon and immune responses
- Neuroinflammation and Neurodegeneration Mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Machine Learning and Data Classification
- Mitochondrial Function and Pathology
- Ocean Acidification Effects and Responses
- Invertebrate Immune Response Mechanisms
- Cell Image Analysis Techniques
- Marine and coastal plant biology
- Alzheimer's disease research and treatments
University of Tasmania
2021-2024
Garvan Institute of Medical Research
2014-2023
University of Technology Sydney
2019-2022
St Vincent's Clinic
2016-2021
UNSW Sydney
2016-2021
University of Waikato
2017
Allan Wilson Centre
2015
University of Otago
2015
Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with comprehensive, manually curated reference database 287 lncRNAs that described independently scientific literature. In addition to capturing great recent literature describing functions individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater...
Abstract Motivation The branchpoint element is required for the first lariat-forming reaction in splicing. However current catalogues of human branchpoints remain incomplete due to difficulty experimentally identifying these splicing elements. To address this limitation, we have developed a machine-learning algorithm—branchpointer—to identify elements solely from gene annotations and genomic sequence. Results Using branchpointer, annotate 85% introns with sensitivity (61.8%) specificity...
Machine learning is a modern approach to problem-solving and task automation. In particular, machine concerned with the development applications of algorithms that can recognize patterns in data use them for predictive modeling. Artificial neural networks are particular class models evolved into what now described as deep learning. Given computational advances made last decade, be applied massive sets innumerable contexts. Therefore, has become its own subfield context biological research,...
The Symbiodiniaceae are a taxonomically and functionally diverse family of marine dinoflagellates. Their symbiotic relationship with invertebrates such as scleractinian corals has made them the focus decades research to resolve underlying biology regulating their sensitivity stressors, particularly thermal stress. Research to-date suggests that stress is governed by complex interplay between phylogenetic dependent independent traits (diversity characteristics species). Consequently, there...
ABSTRACT ORF prediction in de-novo assembled transcriptomes is a critical step for RNA-Seq analysis and transcriptome annotation. However, current approaches do not appropriately account factors such as strand-specificity incompletely transcripts. Strand-specific libraries should produce transcripts the correct orientation, therefore ORFs only be annotated on sense strand. Additionally, start site selection more complex than appreciated sequences upstream of first codon need to correctly 5’...
Abstract Cellular responses to stimuli are rapid and continuous yet the vast majority of investigations transcriptional during developmental transitions typically use long interval time courses; limiting available interpretive power. Moreover, such experiments focus on protein-coding transcripts, ignoring important impact noncoding RNAs. We therefore evaluated coding expression dynamics at unprecedented temporal resolution (6-hourly) in differentiating mouse embryonic stem cells report new...
Quality control checks are the first step in RNA-Sequencing analysis, which enable identification of common issues that occur sequenced reads. Checks for sequence quality, contamination, and complexity commonplace, allow users to implement steps downstream can account these issues. Strand-specificity reads is frequently overlooked often unavailable even published data, yet when unknown or incorrectly specified have detrimental effects on reproducibility accuracy analyses.To address issues,...
The integrity of coral reef ecosystems worldwide rests on a fine-tuned symbiotic interaction between an invertebrate and dinoflagellate microalga from the family Symbiodiniaceae. Recent advances in bottom-up shotgun proteomic approaches availability vast amounts genetic information about Symbiodiniaceae have provided unique opportunity to better understand molecular mechanisms underpinning interactions coral-Symbiodiniaceae. However, resilience this cell wall, as well presence polyanionic...
ABSTRACT Background The branchpoint element is required for the first lariat-forming reaction in splicing. However due to difficulty experimentally mapping at a genome-wide scale, current catalogues are incomplete. Results We have developed machine-learning algorithm trained with empirical human annotations identify elements from primary genome sequence alone. Using this approach, we can accurately locate branchpoints 85% of introns gene annotations. Consistent as basal genetic elements,...
The mitochondrial genome (mtDNA) is distinct from the nuclear and known to play a significant role in several disease phenotypes, such as longevity fertility. Here we characterize complete genomes (∼16 590 bp), extent of within between strain variation for 27 adult zebrafish, representing five commonly used laboratory strains (AB, TL, HL, WIK, SJD) one line acquired local pet shop. These data were subsequently analyzed determine phylogenetic relationships ascertain if positive selection...
Background: The branchpoint element is required for the first lariat-forming reaction in splicing. However due to difficulty experimentally mapping at a genome-wide scale, current catalogues are incomplete. Results: We have developed machine-learning algorithm trained with empirical human annotations identify elements from primary genome sequence alone. Using this approach, we can accurately locate branchpoints 85% of introns gene annotations. Consistent as basal genetic elements, find our...
Neurons are central to lifelong learning and memory, but ageing disrupts their morphology function, leading cognitive decline. Although epigenetic mechanisms known play crucial roles in neuron-specific genome-wide maps into old age remain scarce, often being limited whole-brain homogenates confounded by glial cells. Here, we mapped H3K4me3, H3K27ac, H3K27me3 mouse neurons across lifespan. This revealed stable H3K4me3 global losses of H3K27ac age. We observed patterns synaptic function gene...
ABSTRACT Quality control checks are the first step in RNA-Sequencing analysis, which enable identification of common issues that occur sequenced reads. Checks for sequence quality, contamination, and complexity commonplace, allow users to implement steps downstream can account these issues. Strand-specificity reads is frequently overlooked often unavailable even published data, yet when unknown or incorrectly specified have detrimental effects on reproducibility accuracy analyses. We present...
Abstract Investigations of transcriptional responses during developmental transitions typically use time courses with intervals that are not commensurate the timescales known biological processes. Moreover, such experiments focus on protein-coding transcripts, ignoring important impact long noncoding RNAs. We evaluated coding and expression dynamics at high temporal resolution (6-hourly) in differentiating mouse embryonic stem cells report effects increased characterization underlying...
Abstract Fluorescence-Activated Cell Sorting (FACS) is a powerful method with many applications in microalgal research, especially for screening and selection of cells improved phenotypes. However, the technology requires further investigation to determine phenotypic stability sorted populations. Phaeodactylum tricornutum were using FACS excitation/emission parameters targeted towards favouring industrially-relevant carotenoid fucoxanthin. The resulting cultures showed significantly higher...