A5090797394- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Polyomavirus and related diseases
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Single-cell and spatial transcriptomics
- Evolution and Genetic Dynamics
- Bioinformatics and Genomic Networks
- Genomics and Rare Diseases
- Chromosomal and Genetic Variations
- History and advancements in chemistry
- Full-Duplex Wireless Communications
- Advanced Polymer Synthesis and Characterization
- Chemistry and Stereochemistry Studies
- Mitochondrial Function and Pathology
- Genetic factors in colorectal cancer
- Environmental DNA in Biodiversity Studies
- Gene expression and cancer classification
- Nutrition, Genetics, and Disease
- RNA and protein synthesis mechanisms
The University of Melbourne
2020-2025
Melanoma Institute Australia
2015-2023
The University of Sydney
2015-2023
RMIT University
2023
Stem Cells Australia
2020
University of Tasmania
2015-2018
Australian Antarctic Division
2015-2018
Abstract Merkel cell carcinoma (MCC) is an uncommon, but highly malignant, cutaneous tumor. polyoma virus (MCV) has been implicated in a majority of MCC tumors; however, viral-negative tumors have reported to be more prevalent some geographic regions subject high sun exposure. While the impact MCV and viral T-antigens on development extensively investigated, little known about etiology tumors. We performed targeted capture massively parallel DNA sequencing 619 cancer genes compare gene...
Long-read single-cell RNA sequencing (scRNA-seq) enables the quantification of isoforms in individual cells. However, long-read scRNA-seq using Oxford Nanopore platform has largely relied upon matched short-read data to identify cell barcodes. We introduce BLAZE, which accurately and efficiently identifies 10x barcodes only nanopore data. BLAZE outperforms existing tools provides an accurate representation cells present when compared short reads. simplifies while improving results, is...
// Anja Heinemann 1, 2, 3 , Carleen Cullinane 4 Ricardo De Paoli-Iseppi 5 James S. Wilmott Dilini Gunatilake Jason Madore Dario Strbenac 6 Jean Y. Yang Kavitha Gowrishankar 2 Jessamy C. Tiffen Rab K. Prinjha 7 Nicholas Smithers Grant A. McArthur Peter Hersey Stuart J. Gallagher 1 Melanoma Research Group, Kolling Institute of Medical Research, University Sydney, St Leonards NSW, Australia Australia, North Immunology and Oncology Centenary Institute, Camperdown, Translational Laboratory,...
Age structure is a fundamental aspect of animal population biology. strongly related to individual physiological condition, reproductive potential and mortality rate. Currently, there are no robust molecular methods for age estimation in birds. Instead, individuals must be ringed as chicks establish known-age populations, which labour-intensive expensive process. The chronological using DNA methylation (DNAm) emerging approach mammals including humans, mice some non-model species. Here, we...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read cDNA sequencing in vitro human primate infection models study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA upregulates earlier than TRS-independent sgRNA. An abundant class of consisting a portion open reading frame 1ab (ORF1ab) containing nsp1 joins ORF10, the 3′ untranslated region...
Abstract Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such can be challenging due the high sequence error and small library sizes, which decreases quantification accuracy reduces power for statistical testing. Here, we report two nanopore RNA-seq datasets with goal obtaining gene- isoform-level differential expression information. A dataset synthetic, spliced, spike-in RNAs (‘sequins’) as well a...
ABSTRACT The RNA modification N6-methyladenosine (m6A) is highly abundant in the human brain and implicated neuropsychiatric neurodegenerative disorders. However, most techniques for studying m6A cannot resolve modifications within isoforms we lack an isoform-level map of sites brain. Profiling therefore a critical step towards understanding complex mechanisms that underpin function disease. Oxford Nanopore direct sequencing (DRS) can quantify isoform expression, polyA tail lengths, enabling...
The marsupial moles are arguably Australia’s most enigmatic marsupials. Almost indistinguishable from placental (eutherian) moles, they provide a striking example of convergent evolution. Exploring the genome southern mole, we insights into its unusual biology. We show definitively by retrophylogenomic analysis that closely related to bandicoots and bilbies (order Peramelemorphia). find evidence marked decline in mole effective population size, likely preceding arrival humans regions near...
The diagnosis of Mendelian disorders following uninformative exome and genome sequencing remains a challenging often unmet need. Following family quartet including two siblings with suspected mitochondrial disorder, RNA (RNAseq) was pursued in one sibling. Long-read amplicon used to determine quantify transcript structure. Immunoblotting studies quantitative proteomics were performed demonstrate functional impact. Differential expression analysis RNAseq data identified significantly...
Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections are imperative help understand and prevent this disease. Here we implemented RNA-sequencing (RNA-seq) using Oxford Nanopore Technologies (ONT) long-reads measure differential host gene expression, transcript polyadenylation isoform usage within various epithelial cell lines permissive non-permissive for SARS-CoV-2 infection. SARS-CoV-2-infected mock-infected...
Abstract Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds genomic variants that alter expression and/or products (isoforms) made by genes. However, how these genes contribute disease onset through altered RNA splicing is not well understood. Combining our new bioinformatic pipeline IsoLamp with nanopore long-read amplicon sequencing, we deeply profiled isoform repertoire 31 high-confidence neuropsychiatric in human...
Abstract Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Making sense of the plethora known novel isoforms being identified by transcriptomic approaches requires a user-friendly way to visualize gene how they content, expression levels potential Here we introduce IsoVis, freely available webserver that accepts user-supplied data visualizes expressed clear, intuitive manner. IsoVis contains numerous features,...
Abstract Oxford Nanopore direct RNA sequencing (DRS) is capable of complete molecules and accurately measuring gene isoform expression. However, as DRS designed to profile intact RNA, expression quantification may be more heavily dependent upon integrity than alternative methodologies. It currently unclear how degradation impacts or whether it can corrected for. To assess the impact on DRS, we performed a time series using SH-SY5Y neuroblastoma cells. Our results demonstrate that significant...
Most seabirds do not have any outward identifiers of their chronological age, so estimation seabird population age structure generally requires expensive, long-term banding studies. We investigated the potential to use a molecular biomarker estimate in short-tailed shearwaters (Ardenna tenuirostris). quantified DNA methylation several A. tenuirostris genes that shown age-related changes mammals. In birds ranging from chicks 21 years bisulphite treated blood and feather was sequenced levels...
Abstract Single-cell RNA sequencing (scRNA-seq) has revolutionised our ability to profile gene expression. However, short-read (SR) scRNAseq methodologies such as 10x are restricted the 3’ or 5’ ends of transcripts, providing accurate expression but little information on isoforms expressed in each cell. Newly developed long-read (LR) scRNA-seq enables quantification individual cells LR using Oxford Nanopore platform largely relied upon matched data identify cell barcodes and allow single...
Abstract The growth factor Neuregulin-1 (NRG1) has pleiotropic roles in proliferation and differentiation of the stem cell niche different tissues. It been implicated gut, brain muscle development repair. Six isoform classes NRG1 over 28 protein isoforms have previously described. Here we report a new class NRG1, designated NRG1-VII to denote that these arise from myeloid-specific transcriptional start site (TSS) uncharacterized. Long-read sequencing was used identify eight high-confidence...
A nuclease flush can be used to recover blocked pores on Oxford Nanopore Technologies (ONT) flow cells maximise overall sequencing output. The Flow Cell Wash Kit (EXP-WSH004/EXP-WSH004-XL) was developed remove blockages DNA cells, but does not restore their RNA counterparts. This short protocol describes a simple modification the Flush enable pore recovery in cells. uses two RNases digest blockage-causing nucleic acids: RNase CocktailTM Enzyme Mix and H. contains endoribonucleases T1, which...
This protocol details how to design primers for a target gene and carry-out long-range PCR subsequent Nanopore long-read amplicon sequencing (LSK114). It outlines the resources, tools settings we use amplify entire annotated CDS of gene, capturing as many alternative RNA isoforms possible, make these ready multiplexed library. should reliably result in amplicons 1 - 11 kb range. Amplicons resulting from this be specific transcripts interest with minimal or no off-targets ensuring efficient targets.