Dr Nathan Watson-Haigh

Nathan Watson-Haigh
Research Fellow in Bioinformatics
School of Agriculture, Food and Wine
Faculty of Sciences

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.

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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.

Appointments

Date Position Institution name
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

Education

Date Institution name Country Title
2001 - 2004 University of York United Kingdom PhD
1997 - 2001 University of Bath United Kingdom M.Pharmacol.

Postgraduate Training

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

Research Interests

Bioinformatics, Bioinformatics Software, Distributed and Grid Systems, Distributed Computing, Genomics, Operating Systems, Phylogeny and Comparative Analysis, Programming Languages

Journals

Year Citation
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.
10.1093/bib/bbw032
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.
10.1093/bib/bbw013
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, -.
10.1093/bib/bbx071
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.
10.12688/f1000research.11407.1
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.
10.1016/j.ympev.2016.03.031
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.
10.1371/journal.pone.0142799
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.
10.1111/tpj.12651
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.
10.1071/AN12193
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.
10.1093/bib/bbt022
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.
10.1186/1471-2164-14-13
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.
10.1109/JSEN.2011.2175215
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.
10.6026/97320630008855
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.
10.1093/nar/gks561
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.
10.1186/1471-2164-12-607
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.
10.1039/C0MB00190B
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-.
10.1039/C1MB90044G
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.
10.1093/bioinformatics/btp674
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.
10.1186/1471-2105-11-311
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.
10.1098/rspb.2008.1767
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.
10.1111/j.1755-0998.2008.02190.x
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.
10.1007/s11306-007-0067-1

Conference Papers

Year Citation
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.

Datasets

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;

PhD Co-supervisor for:

Memberships

Date Role Membership Country
2011 - 2013 President Bioinformatics Interest Group for South Australia (BIG SA) Australia

Committee Memberships

Date Role Committee Institution Country
2014 - 2014 Member Student Management Committee ACPFG Australia
Position
Research Fellow in Bioinformatics
Phone
83132046
Campus
Waite
Building
Plant Genomics Centre
Room Number
2 05
Org Unit
School of Agriculture, Food and Wine

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