Speaker: Dr Ira Cooke

Title: Using whole genome sequencing to understand the recent evolutionary history of corals and their symbionts on the Great Barrier Reef

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Abstract: A major climate shift at the end of the last ice-age reshaped many coastal landscapes and marine ecosystems including coral reefs. On the Great Barrier Reef (GBR) sea-level rise associated with this event flooded a vast shelf creating a distinct inshore region which now harbours extensive coral assemblages despite being subject to relatively high turbidity, freshwater input and thermal fluctuations. Genetic signatures caused by adaptation to these events are of particular interest because they could help understand how coral populations will respond to major climate change now underway due to anthropogenic activity. To understand the post-glacial evolutionary history of the reef building coral Acropora tenuis in the inshore GBR we sequenced its genome and then resequenced 150 individual colonies from 5 reefs. In this talk I will describe the recent evolutionary, demographic and ecological history of these corals and their symbionts that emerges from an analysis of this data. 
About the speaker: Ira Cooke is a Senior Lecturer at James Cook University
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Speaker: Professor Melanie Bahlo

Title: TBtyper: determining TB strain composition in TB whole genome sequencing data

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Abstract: Whole genome sequencing (WGS) is increasingly being used to profile the pathogens that have infected patients in infectious diseases such as malaria, Covid-19 and TB. Many chronic infectious diseases have the challenge that previous infections can become re-activated after sometimes considerable periods of dormancy as well as well as causing new infections with patients potentially being host to multiple strains.  Since different strains of infections can have very different profiles in terms of disease course and drug resistance it is important to know the repertoire of strains a patient may be host to, not just the most frequent, or actively disease causing strain. Deep WGS sequencing data enables the determination of the composition of strains. We have developed a new method, called TBTyper, that can tease apart strains in WGS data from patients with higher specificity and sensitivity than previously possible, whilst also phylotyping the strains that comprise the mixture.
About the speaker: Melanie Bahlo is a laboratory head at Walter and Eliza Hall Institute of Medical Research
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Speaker: Dr Derek Sarovich

Title: Comprehensive antibiotic resistance detection from whole-genome sequence data

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Abstract: Antimicrobial resistance (AMR) is emerging as a major threat to human health worldwide. Whole-genome sequencing (WGS) holds great potential for rapidly and accurately detecting AMR from genomic data in the diagnostic laboratory setting. We present an improved tool for Antibiotic Resistance Detection and Prediction (ARDaP) from WGS data. ARDaP was designed with three priorities: 1) to accurately identify a wide range of AMR genetic determinants (i.e. horizontally-acquired gene gain, single-nucleotide polymorphisms, insertions-deletions, copy-number variation, and functional gene loss); 2) to predict enigmatic AMR determinants based on novel mutants with moderate-or high-consequence impacts in known AMR-conferring genes, and 3) to detect minor AMR allelic determinants in mixed (e.g. metagenomic) sequence data. ARDaP performance has been so far tested on two major pathogens, Burkholderia pseudomallei and Pseudomonas aeruginosa, with greatly improved performance in comparison to current software.
About the speaker: Derek Sarovich is a senior research fellow at the University of the Sunshine Coast
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Speaker: Professor Jean Yang

Title: Characterisation of cell communication in COVID19 patients

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Abstract: COVID-19 patients suffer from a wide range of disease progression, varied largely from no symptoms, moderate, severe, and critical symptoms with high mortality risk. We will discuss our workflow for identifying cells that are differentially interacting across patients under different disease progression. We applied the workflow on public single-cell RNA-seq datasets (Chua et al., Liao et al., Wilks et al. and Zhang et al.), including nasopharyngeal, bronchial,  bronchoalveolar lavage fluid and PBMC samples from COVID19 patients under moderate and critical conditions and from healthy controls. Here, we reannotated the cell types into subgroups, and characterised the cell-type interaction patterns between epithelial and immune cells for all patients. Our results illustrate diverse communication patterns across different groups of patients, which leads to the identification of drug targetable subgroups with more active cell-cell interaction during disease progression.
About the speaker: Jean Yang is a Professor at The University of Sydney
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Speaker: Dr Jac Charlesworth

Title: Detecting rare variants for complex disease

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Abstract: Genome-wide association studies have been highly successful at identifying common risk loci for many complex diseases, but the translation of these findings has mostly led to a better understanding of risk (in some populations) and the development of polygenic risk scores, rather than gene identification or drug discovery. The impact of rare variants on these conditions is more difficult to determine. Dr Charlesworth will discuss the use of family studies and individualised genomics methods on her quest for complex disease relevant rare variants.
About the speaker: Jac Charlesworth is a Senior Research Fellow at Menzies Institute for Medical Research
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Speaker: Professor Shoba Ranganathan

Title: Benchmarking de novo genome assembly methods

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Abstract: Genome sequencing has become routine, with 57144 genomes now available. This data tsunami has also spurred the development of a multitude of tools for assembly and analysis of genomes. Benchmarking has been done for bacterial genomes and some sequencing technologies. Here is a comprehensive benchmark of 20 assembly and 8 polishing tools for eukaryotic genome construction from the sequencing trinity: Illumina, Nanopore and PacBio, as well as coverage effects, for two gold standard model organisms, C. elegans and D. melanogaster.
About the speaker: Shoba Ranganathan is a Professor at Macquarie University
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