I'm a computational biologist and began my scientific career as a software developer building biological databases in the UK. I returned to Australia to take up a position at the South Australian Partnership for Advanced Computing (SAPAC) as a Bioinformatics Specialist. This involved a close association with the Australian Centre for Plant Function Genomics (ACPFG) which in turn lead to a Ph.D and post-doctoral position at the ACPFG and the ARC CoE for Plant Cell Walls. My interests are in protein family evolution, coevolution networks and recently biological applications for machine learning.
My Ph.D research focused on the evolutionary history and dynamics of the cellulose synthase superfamily in the angiosperms (flowering plants). This aimed to explore how a family of proteins have evolved to produce the diversity of carbohydrates we consume for food, fuel and materials. We reconstructed molecular sequence evolution to infer when protein families evolved and how natural selection has shaped this process. The association of this snippet of evolution with other observed changes such as morphology and protein structural elements can now be used to predict protein function and other characteristics of a stubbornly inscrutable protein superfamily.
As a postdoctoral researcher at the ARC Centre of Excellence in Plant Cell Walls, my present research focuses on understanding the synthesis and interactions of cell wall carbohydrates and their evolution in the context of plant survival strategies and interactions with fungal pathogens. I use computational methods related to phylogenetics, genomics, transcriptomics, and homology modeling. My currents projects include:
- Plant genome assembly
- Phylogenetics of cell wall associated enzyme pathway
- Reconstructing the sequences of ancestral proteins
- Coevolution network analysis
- Applications of machine learning methodologies to phenotyping
|2017||Chowdhury,J, Lück,S, Rajaraman,J, Douchkov,D, Shirley,N, Schwerdt,J, Schweizer,P, Fincher,G, Burton,R, Little,A et al, 2017, Altered expression of genes implicated in xylan biosynthesis affects penetration resistance against powdery mildew, Frontiers in Plant Science, 8, 445-1-445-12 10.3389/fpls.2017.00445|
|2016||Paull,R, Chen,N, Ming,R, Wai,C, Shirley,N, Schwerdt,J, Bulone,V, 2016, Carbon Flux and Carbohydrate Gene Families in Pineapple, Tropical Plant Biology, 9, 3, 200-213 10.1007/s12042-016-9176-1|
|2016||Dimitroff,G, Little,A, Lahnstein,J, Schwerdt,J, Srivastava,V, Bulone,V, Burton,R, Fincher,G, 2016, (1,3;1,4)-β-glucan biosynthesis by the CSLF6 enzyme: position and flexibility of catalytic residues influence product fine structure, Biochemistry, 55, 13, 2054-2061 10.1021/acs.biochem.5b01384|
|2016||Marcotuli,I, Houston,K, Schwerdt,J, Waugh,R, Fincher,G, Burton,R, Blanco,A, Gadaleta,A, 2016, Genetic diversity and genome wide association study of β-glucan content in tetraploid wheat grains, PLoS One, 11, 4, e0152590-1-e0152590-15 10.1371/journal.pone.0152590|
|2016||Sato,K, Yamane,M, Yamaji,N, Kanamori,H, Tagiri,A, Schwerdt,J, Fincher,G, Matsumoto,T, Takeda,K, Komatsuda,T et al, 2016, Alanine aminotransferase controls seed dormancy in barley, Nature Communications, 7, - 10.1038/ncomms11625|
|2015||Ermawar,R, Collins,H, Byrt,C, Henderson,M, O'Donovan,L, Shirley,N, Schwerdt,J, Lahnstein,J, Fincher,G, Burton,R et al, 2015, Genetics and physiology of cell wall polysaccharides in the model C₄ grass, Setaria viridis spp, BMC Plant Biology, 15, 1, 236-1-236-18 10.1186/s12870-015-0624-0|
|2015||Ermawar,R, Collins,H, Byrt,C, Betts,N, Henderson,M, Shirley,N, Schwerdt,J, Lahnstein,J, Fincher,G, Burton,R et al, 2015, Distribution, structure and biosynthetic gene families of (1,3;1,4)-β-glucan in Sorghum bicolor, Journal of Integrative Plant Biology, 57, 4, 429-445 10.1111/jipb.12338|
|2015||Schwerdt,J, MacKenzie,K, Wright,F, Oehme,D, Wagner,J, Harvey,A, Shirley,N, Burton,R, Schreiber,M, Halpin,C et al, 2015, Evolutionary dynamics of the cellulose synthase gene superfamily in grasses, Plant Physiology, 168, 3, 968-983 10.1104/pp.15.00140|
|2015||Wong,S, Shirley,N, Little,A, Khoo,K, Schwerdt,J, Fincher,G, Burton,R, Mather,D, 2015, Differential expression of the HvCslF6 gene late in grain development may explain quantitative differences in (1,3;1,4)-β-glucan concentration in barley, Molecular Breeding, 35, 1, 20-1-20-12 10.1007/s11032-015-0208-6|
|2014||Schreiber,M, Wright,F, MacKenzie,K, Hedley,P, Schwerdt,J, Little,A, Burton,R, Fincher,G, Marshall,D, Waugh,R et al, 2014, The barley genome sequence assembly reveals three additional members of the CslF (1,3;1,4)-β-glucan synthase gene family, PLoS One, 9, 3, e90888-1-e90888-9 10.1371/journal.pone.0090888|
|2008||Jones,C, Schwerdt,J, Bretag,T, Baumann,U, Brown,A, 2008, GOSLING: a rule-based protein annotator using BLAST and GO, Bioinformatics, 24, 22, 2628-2629 10.1093/bioinformatics/btn486|
2008 - Grains Research & Development Corporation GRS Post-graduate scholarship.
2010 to present, Master of Plant Biotechnology (bioinformatics course)
The sequencing and assembly of Plantago ovata. Pastor Juliian, 2014 Honours project
The de novo sequencing, assembly and annotation of a draft genome of the marine microalga, Tetraselmis cordiformis. Jake Parker, 2013 Honours project.