Research Projects

Professor Marc Wilkins

We develop and use ‘omics technology in our  investigations of molecular systems biology. We have extensive expertise in proteomics and in next-gen sequencing, and the bioinformatics analysis of resulting data. We use networks to contextualise and interpret data, to understand the biology of model organisms and mammalian cells. We have extensive experience in transcriptomics and genomics. I have two labs that work together in the Systems Biology Initiative.

Google scholar profile

Bioinformatics lab

Projects in data analysis and integration include:

• the PG Nexus – a platform for proteogenomic identification of ORFs in genomes and for the confirmation of splice variants from RNA-seq and proteomic data
• PTMoracle – a Cytoscape app for the co-analysis of protein PTMs and structural features with protein-protein interaction networks
• Understanding the network basis of drug synergy in S. cerevisiae and Cryptococcus

Projects in genomics and transcriptomics include:

• Assembly and annotation of the Koala genome
• Assembly and annotation of fungal and bacterial genomes
• Transcriptomic analysis of cancer cachexia, of Williams–Beuren syndrome, of transcription factors in stem cell development, in epithelial cells on invasion by Campylobacter, in behavioural changes in the Australian black cricket

Proteomics lab

The focus of the proteomics lab is to understand the role of post-translational modifications in protein-protein interaction networks. Our overarching hypothesis is that modifications are used extensively to modulate interactions, and in doing so regulate function. We are exhaustively studying the role of protein methylation in this regard.

Projects include:

• Proteome-scale analyses of protein methylation and investigation of function
• Discovery of new eukaryotic protein methyltransferases and defining their sites of methylation on substrate proteins
• the Protein interaction code – showing how combinations of protein modifications modulate the specificity of their interactions with partners
• the Conditional two-hybrid system – a unique means of measuring how the modifications of proteins affect their protein-protein interactions