Conferences and publications

Presentations from Lorne Genome and the Microsoft Campus Connections Summit, plus publications on a new algorithm for long read alignment, a psychosocial longitudinal study and more

KCCG researchers at Lorne for the 2019 Lorne Genome conference

29 April 2019

A number of KCCG researchers attended the Lorne Genome conference from 17-19 February.

Dr Mahdi Zeraati presented his work on the visualisation and genome-wide mapping of i-Motif DNA structure. I-Motif structures are tangled knots of DNA that are thought to play a crucial role in gene regulation, and their discovery was detailed in a Nature Chemistry publication last year.

James Ferguson had a poster on SquiggleKit – an open-source toolkit for manipulating Nanopore sequencing data that simplifies the steps of file handling, data extraction, visualisation and signal processing.

Tansel Ersavas presented a poster on deep convolutional neural networks for Nanopore signal processing – a strategy to improve the yield and accuracy of demultiplexed reads.

Genomic Technologies team leader Dr Martin Smith was invited to speak at a workshop on the applications of Nanopore long-read sequencing in translational research.

Outside of Lorne, Dr Smith was also invited to speak at:

  • Dissecting RNA biology, one molecule at a time, Otago Symposium on Oxford Nanopore Technology Symposium at the University of Otago, Dunedin in New Zealand.
  • Genomics beyond the base-pair: Harnessing real-time sequencing for precision medicine, at the Ste-Justine Hospital Research Centre (CR-CHUSJ) in Montreal, Canada
  • Nanopore long-read sequencing in clinical genomics: a current affair at the Montreal Clinical Research Institute (IRCM)
  • Going beyond the basepair with nanopores at the Queensland Brain Institute in Brisbane

KCCG Clinical and Scientific Heads Mary-Anne Young and Associate Professor Sarah Kummerfeld presented at the Young Presidents Organisation (YPO) Education Event in March 2019. Their presentation explored current challenges and opportunities in genomics research.  YPO is the global platform for chief executives to engage, learn and grow.

Garvan’s Chief of Informatics and KCCG Informatics Team Lead, Dr Warren Kaplan, was invited to present at the Microsoft Campus Connections Summit in Redmond, USA from 5-8 February. Presenting on Genomics and our journey to the cloud, Dr Kaplan described how genomics powers all of Garvan’s research themes, and how Garvan is computing on-premise, at the NCI in Canberra, as well as on commercial clouds like Microsoft Azure.


Team Leader of Genomic Technologies Dr Martin Smith and KCCG visiting student Hasindu Gamaarachchi had a paper published in Scientific Reports in March 2019, on Featherweight long read alignment using partitioned reference indexes.

The paper describes a technique for reducing the memory requirements of long read alignment to the human genome, through a combination of parameter optimisation, reference genome partitioning and multi-index merging. The team demonstrated that long reads can be aligned on a system with as little as 2GB RAM, with negligible impact on accuracy. This makes it possible for genomic analysis to be performed remotely, using the computational memory of a device as small as a smartphone.

Dr Martin Smith and Dr Kirston Barton, also from the Genomic Technologies team, were authors on an additional paper published in Nature Communications in March 2019: Chiral DNA sequences as commutable references standards for clinical genomics.

Genome Informatics Senior Research Officer Dr Mark McCabe was first author on Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases, published in Cold Spring Harbour Molecular Case Studies in April 2019.

Dr Kishore Kumar, KCCG Research Fellow, was senior author on High degree of genetic heterogeneity for hereditary cerebellar ataxias in Australia, published in The Cerebellum in February 2019.

Bronwyn Terrill, Education and Engagement Team Leader, was an author on Australians’ views and experience of personal genomic testing: survey findings from the Genioz study, published in the European Journal of Human Genetics in January 2019. This is the third paper from Genioz – the first large scale Australian study exploring attitudes towards personal genomic tests.  

KCCG Clinical Head Mary-Anne Young was an author on three papers: