Research Fellow in Bioinformatics
School of Biological Sciences
Faculty of Sciences
Nathan has over 15 years experience in the field of bioinformatics with expertise in genomics, transcriptomics, system biology, phylogenetics, bioinformatics training, Linux systems administration, pipeline development, high-performance and cloud computing.
Nathan's background was first in biology, by undergraduate training, and then in bioinformatics by PhD. During his PhD he investigated the location of the root, the oldest part, of the eukaryotic tree of life. It was here where he learned about phylogenetics and molecular sequence analysis. At this time he was also exposed to high-performance computing infrastructure and the Linux operating system. In addition, he became involved in Open Source projects with contributions to BioPerl in the form of writing unit tests.
Following his PhD he took up a bioinformatics postdoctoral position on a project looking at the range margins of Arabidopsis lyrata ssp. petraea. It was here where Nathan was first exposed to the 'omics. His principle role was to analyse microarray data as well as to integrate datasets coming from transcriptomics, metabolomics, proteomics, population genetics and ecological studies. During this time, Nathan was responsible for the systems administration of several Linux machines and was first exposed to metabolomics data analysis.
Nathan then joined CSIRO as a postdoctoral research fellow using system biology approaches to investigate complex production traits in livestock species. Nathan drew on his prior experiences with microarrays and developed his knowledge in reproducible research and high-performance computing in the analysis of co-expression networks.
Nathan got his first taste of Next Generation Sequencing (NGS) data when he joined the Australian Wine Research Institute (AWRI) as a senior bioinformatician. It was here where he led efforts to assemble a grapevine genome, spearheaded efforts to establish an unincorporated bioinformatics interest group in South Australia (BIG SA) and led the establishment of a cloud-based Bioinformatics Training Platform (BTP) in collaboration with Bioplatforms Australia (BPA), CSIRO Bioinformatics Core and the European Bioinformatics Institute (EBI).
Nathan joined the ACPFG in the School of Ag, Food & Wine in late 2013. He played a pivotal role in the development and application of analytical approaches and pipelines to NGS-based wheat genomics data sets. He was responsible for setting up and managing the Linux-based scientific computing infrastructure, including several large memory compute nodes configured as a Slurm cluster, 100's TBytes of clustered filesystem storage and around 2 dozen virtual machines.
Date Position Institution name 2018 Researcher in Bioinformatics, Bioinformatics Hub University of Adelaide 2016 - 2018 Research Fellow in Bioinformatics University of Adelaide 2012 - 2016 Research Fellow in Bioinformatics The Australian Centre for Plant Functional Genomics (ACPFG) 2011 - 2012 Senior Bioinformatician Australian Wine Research Institute 1999 - 2000 Research Assistant Bayer
Date Institution name Country Title 2001 - 2004 University of York United Kingdom PhD 1997 - 2001 University of Bath United Kingdom M.Pharmacol.
Date Title Institution Country 2008 - 2011 OCE Postoctoral Fellow Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia 2005 - 2008 Postdoctoral Fellow University of Sheffield United Kingdom
Year Citation 2015 Liu, H., Searle, I., Watson-Haigh., Baumann., Mather, D. E., Able, A. J., & Able, J. A. (2015). Genome-wide identification of differentially expressed microRNAs in leaves and the developing head of four durum genotypes during water deficit stress.
- Exploring genetic diversity to identify new heat tolerance genes in wheat (LP150100694; $680k) ARC - Linkage Projects (2016-2020)
- Next Generation Enhancement of the South Australian Regional Facility for Molecular Ecology and Evolution (LE130100065; $370k). ARC - Linkage Infrastructure, Equipment and Facilities (2013-2014)
- Improving bioinformaticians productivity through Software Carpentry ($10k). Australian Bioinformatics Network (2013).
Current Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2020 Principal Supervisor Identifying Gene Expression Changes Associated with Autophagic Response Regulation in Individuals with Alzheimer's Disease Master of Philosophy Master Full Time Ms Wenjun Liu 2019 Co-Supervisor Global Analysis of Seed Development during Mucilage Production in Plantago Ovata Doctor of Philosophy Doctorate Full Time Mrs Lina Herliana 2019 Co-Supervisor Defining the Role of Vacuolar Pyrophosphatase (OVP) Genes in Abiotic Stress Tolerance in Rice Doctor of Philosophy Doctorate Full Time Mr Aaron Layne Phillips 2019 Co-Supervisor GABA Signalling in Cereals Doctor of Philosophy Doctorate Full Time Miss Na Sai 2019 Co-Supervisor The Role of RNA Modifications in Endosperm Development Doctor of Philosophy Doctorate Full Time Miss Huong Thi Thuy Ta
Past Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2014 - 2018 Co-Supervisor Defining Transcriptional Networks Associated with Plant Salinity Tolerance Doctor of Philosophy Doctorate Full Time Ms Shanika Lakmini Amarasinghe
Date Role Committee Institution Country 2014 - 2014 Member Student Management Committee ACPFG Australia
Date Role Membership Country 2011 - 2013 President Bioinformatics Interest Group for South Australia (BIG SA) Australia
Date Role Editorial Board Name Institution Country 2019 - ongoing Associate Editor Plant Methods BioMed Central United Kingdom
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