Dr Nathan Watson-Haigh
Nathan has almost 15 years experience in the field of bioinformatics with expertise in genomics, transcriptomics, system biology, phylogenetics, bioinformatics training, Linux systems administration, 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 plays a pivotal role in the development and application of analytical approaches and pipelines to NGS-based wheat genomics data sets. He is responsible for the systems administration of Linux-based scientific computing infrastructure, including a large memory computer, storage and virtual machines.
|2016||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|
|2001 - 2004||University of York||United Kingdom||PhD|
|1997 - 2001||University of Bath||United Kingdom||M.Pharmacol.|
|2008 - 2011||OCE Postoctoral Fellow||Commonwealth Scientific and Industrial Research Organisation (CSIRO)||Australia|
|2005 - 2008||Postdoctoral Fellow||University of Sheffield||United Kingdom|
|2017||Revote, J., Watson-Haigh, N., Quenette, S., Bethwaite, B., McGrath, A. & Shang, C. (2017). Development of a cloud-based Bioinformatics Training Platform. Briefings in Bioinformatics, 18, 3, 537-544.
|2017||Watson-Haigh, N., Revote, J., Suchecki, R., Tyagi, S., Corley, S., Shang, C. & McGrath, A. (2017). Towards an open, collaborative, reusable framework for sharing hands-on bioinformatics training workshops. Briefings in Bioinformatics, 18, 2, 348-355.
|2017||Schneider, M. V., Griffin, P. C., Tyagi, S., Flannery, M., Dayalan, S., Gladman, S. ... Lonie, A. (2017). Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Briefings in Bioinformatics, -.
|2017||Jiménez, R., Kuzak, M., Alhamdoosh, M., Barker, M., Batut, B., Borg, M. ... Leskošek, B. (2017). Four simple recommendations to encourage best practices in research software. F1000Research, 6, 876-876.
|2016||Amarasinghe, S., Watson-Haigh, N., Gilliham, M., Roy, S. & Baumann, U. (2016). The evolutionary origin of CIPK16: a gene involved in enhanced salt tolerance. Molecular Phylogenetics and Evolution, 100, 135-147.
|2016||Schneider, M. V., Griffin, P. C., Williams, J., Jimenez, R., Flicek, P., Bonazzi, V. ... McConville, M. (2016). Bioinformatics in Australia: a snapshot. Briefings in Bioinformatics, -.|
|2015||Liu, H., Searle, I., Watson-Haigh, N., Baumann, U., Mather, D., Able, A. & Able, J. (2015). Genome-wide identification of microRNAs in leaves and the developing head of four durum genotypes during water deficit stress. PLoS One, 10, 11, e0142799-1-e0142799-30.
|2014||Byrt, C., Xu, B., Krishnan, M., Lightfoot, D., Athman, A., Jacobs, A. ... Gilliham, M. (2014). The Na⁺ transporter, TaHKT1;5-D, limits shoot Na⁺ accumulation in bread wheat. The Plant Journal, 80, 3, 516-526.
|2013||McDowall, M., Watson-Haigh, N., Edwards, N., Kadarmideen, H., Nattrass, G., McGrice, H. & Hynd, P. (2013). Transient treatment of pregnant Merino ewes with modulators of cortisol biosynthesis coinciding with primary wool follicle initiation alters lifetime wool growth. Animal Production Science, 53, 10, 1101-1111.
|2013||Watson-Haigh, N., Shang, C., Haimel, M., Kostadima, M., Remco, L., Deshpande, N. ... Schneider, M. (2013). Next-generation sequencing: A challenge to meet the increasing demand for training workshops in Australia. Briefings in Bioinformatics, 14, 5, 563-574.
|2013||Stanley, D., Watson-Haigh, N., Cowled, C. & Moore, R. (2013). Genetic architecture of gene expression in the chicken. BMC Genomics, 14, 1, 13-1-13-9.
|2012||Watson-Haigh, N., O'Neill, C. & Kadarmideen, H. (2012). Proximity loggers: data handling and classification for quality control. IEEE Sensors Journal, 12, 5, 1611-1617.
|2012||Kadarmideen, H. & Watson-Haigh, N. (2012). Building gene co-expression networks using transcriptomics data for systems biology investigations: comparison of methods using microarray data. Bioinformation, 8, 18, 855-861.
|2012||Ajawatanawong, P., Atkinson, G., Watson-Haigh, N., MacKenzie, B. & Baldauf, S. (2012). SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments. Nucleic Acids Research, 40, W1, W340-W347.
|2011||Kogelman, L., Byrne, K., Vuocolo, T., Watson-Haigh, N., Kadarmideen, H., Kijas, J. ... Tellam, R. (2011). Genetic architecture of gene expression in ovine skeletal muscle. BMC Genomics, 12, 1, 607-1-607-17.
|2011||Kadarmideen, H., Watson-Haigh, N. & Andronicos, N. (2011). Systems biology of ovine intestinal parasite resistance: disease gene modules and biomarkers. Molecular Biosystems, 7, 1, 235-246.
|2011||Kadarmideen, H., Watson-Haigh, N. & Andronicos, N. (2011). Erratum: Systems biology of ovine intestinal parasite resistance: Disease gene modules and biomarkers (Molecular BioSystems (2011) DOI: 10.1039/C0MB00190B). Molecular BioSystems, 7, 12, 3376-.
|2010||Watson-Haigh, N., Kadarmideen, H. & Reverter, A. (2010). PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches. Bioinformatics, 26, 3, 411-413.
|2010||Goodswen, S., Gondro, C., Watson-Haigh, N. & Kadarmideen, H. (2010). FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. BMC Bioinformatics, 11, 1, 311-1-311-9.
|2009||Kunin, W., Vergeer, P., Kenta, T., Davey, M., Burke, T., Woodward, F. ... Butlin, R. (2009). Variation at range margins across multiple spatial scales: environmental temperature, population genetics and metabolomic phenotype. Proceedings of the Royal Society B: Biological Sciences, 276, 1661, 1495-1506.
|2008||Kenta, T., Gratten, J., Watson-Haigh, N. S., Hinten, G. N., Slate, J., Butlin, R. K. & Burke, T. (2008). Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method. Molecular Ecology Resources, 8, 6, 1230-1238.
|2007||Morrison, N., Bearden, D., Bundy, J., Collette, T., Currie, F., Davey, M. ... Viant, M. (2007). Standard reporting requirements for biological samples in metabolomics experiments: Environmental context. Metabolomics, 3, 3, 203-210.
|2010||Kadarmideen, H. N., Watson-Haigh, N., Kijas, J. W., Vuocolo, T., Byrne, K., Gondro, C. ... Telam, R. L. (2010). Genetics of global gene expression patterns and gene networks affecting muscling in sheep. World Congress on Genetics Applied to Livestock Production. Leipzig, Germany.|
|2010||O'Neill, C. J., Watson-Haigh, N., Goodswen, S., Williams, P. & Kadarmideen, H. N. (2010). The Use of Contact Loggers to Study Social and Oestrus Activity in Brahman and Composite Beef Heifers under Field Conditions. Animal Production in Australia. Armidale, Australia.|
|2009||Kadarmideen, H., McDowall, M., Nattrass, G., McGrice, H., Hynd, P. & Watson-Haigh, N. (2009). Weighted co-expression networks shed light on the molecular mechanism of action of metyrapone on wool follicle development. Conference of the Association for the Advancement of Animal Breeding and Genetics (AAABG). Barossa Valley.|
|2009||Kadarmideen, H. N., Andronicos, N. & Watson-Haigh, N. (2009). Systems genetics analysis reveals gene modules and heritable biomarkers for sheep intestinal parasite resistance. 18th Conference of the Association for the Advancement of Animal Breeding and Genetics. Barossa Valley, South Australia.|
|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;|