Thomas Shafee
Research Data Specialist
Thomas is a specialist in research data ecosystems with a background across academia, industry, and scholarly publishing. His research background ranges from blue-skies evolutionary biochemistry and data science to highly applied medical and agricultural biotech. His work now focuses on how improved data sharing and coordination can bring together divergent expertise to solve multidisciplinary problems. He combines this with experience in advanced analytics and machine learning to get the most impact out of hard-won data. He is a long-standing contributor to linked open data and semantic knowledgebases, as well as the broader open knowledge movement through his work with the Wikimedia Foundation and Open Access Australasia.
As a lead for the Australian Dataspaces Hub with the Australian Research Data Commons (ARDC), he provides subject matter expertise and specialist capabilities to guide the strategy and deployment of dataspace projects across Australia to help increase national R&D productivity and effectiveness. He coordinates with the International Data Spaces Association to ensure Australian implementation is compatible with the broader international network and that Australian interests and perspectives are represented internationally.
At CeRDI, Thomas is applying the sovereign data governance and technical interoperability of dataspaces to our projects across environmental and earth sciences to improve data bridges between research, industry, and government. That organisational trust and confidence is vital for sharing sensitive data to best tackle cross-sector societal challenges.
Email: t.shafee@federation.edu.au
LinkedIn: linkedin.com/in/t-shafee 
ORCID: orcid.org/0000-0002-2298-7593
- Journal papers
Lampugnani, E. R., Ford, K., Ho, Y. Y., van de Meene, A., Lahnstein, J., Tan, H.-T., Burton, R. A., Fincher, G. B., Shafee, T., Bacic, A., et al. (2024). Glycosyl transferase GT2 genes mediate the biosynthesis of an unusual (1, 3; 1, 4)-β-glucan exopolysaccharide in the bacterium Sarcina ventriculi. Molecular Microbiology, 121(6), 1245–1261. doi.org/10.26181/30364840
Parisi, K., McKenna, J. A., Lowe, R., Harris, K. S., Shafee, T., Guarino, R., Lee, E., van der Weerden, N. L., Bleackley, M. R., & Anderson, M. A. (2024). Hyperpolarisation of mitochondrial membranes is a critical component of the antifungal mechanism of the plant defensin, Ppdef1. Journal of Fungi, 10(1), 54. doi.org/10.3390/jof10010054
Ashwood, L. M., Elnahriry, K. A., Stewart, Z. K., Shafee, T., Naseem, M. U., Szanto, T. G., van der Burg, C. A., Smith, H. L., Surm, J. M., Undheim, E. A. B., et al. (2023). Genomic, functional and structural analyses elucidate evolutionary innovation within the sea anemone 8 toxin family. BMC Biology, 21(1), 121. doi.org/10.1101/2022.12.08.518931
Ma, Y., Shafee, T., Mudiyanselage, A. M., Ratcliffe, J., MacMillan, C. P., Mansfield, S. D., Bacic, A., & Johnson, K. L. (2023). Distinct functions of FASCICLIN-LIKE ARABINOGALACTAN PROTEINS relate to domain structure. Plant Physiology, 192(1), 119–132. doi.org/10.1093/plphys/kiad097
Shafee, T., Mietchen, D., Lubiana, T., Jemielniak, D., & Waagmeester, A. (2023). Ten quick tips for editing Wikidata. PLOS Computational Biology, 19(7), e1011235. doi.org/10.1371/journal.pcbi.1011235
Nunn, J. S., Shafee, T., Chang, S., Stephens, R., Elliott, J., Oliver, S., John, D., Smith, M., Orr, N., Preston, J., et al. (2022). Standardised data on initiatives—STARDIT: Beta version. Research Involvement and Engagement, 8(1), 31. doi.org/10.31219/osf.io/w5xj6
Turki, H., Hadj Taieb, M. A., Shafee, T., Lubiana, T., Jemielniak, D., Aouicha, M. B., Labra Gayo, J. E., Youngstrom, E. A., Banat, M., Das, D., et al. (2022). Representing COVID-19 information in collaborative knowledge graphs: The case of Wikidata. Semantic Web, 13(2), 233–264. doi.org/10.26181/19469930
Turki, H., Jemielniak, D., Taieb, M. A. H., Labra Gayo, J. E., Aouicha, M. B., Banat, M., Shafee, T., Prud’hommeaux, E., Lubiana, T., Das, D., et al. (2022). Using logical constraints to validate statistical information about disease outbreaks in collaborative knowledge graphs: the case of COVID-19 epidemiology in Wikidata. PeerJ Computer Science, 8, e1085. doi.org/10.60692/5mkd9-hvz97
Nunn, J., & Shafee, T. (2021). Poster: Standardised data on initiatives and citizen science. In CitSciVirtual.
Bleackley, M. R., Vasa, S., Harvey, P. J., Shafee, T. M. A., Kerenga, B. K., Soares da Costa, T. P., Craik, D. J., Lowe, R. G. T., & Anderson, M. A. (2020). Histidine-rich defensins from the solanaceae and brasicaceae are antifungal and metal binding proteins. Journal of Fungi, 6(3), 145. doi.org/10.26181/13213451
Liu, E., MacMillan, C. P., Shafee, T., Ma, Y., Ratcliffe, J., Van de Meene, A., Bacic, A., Humphries, J., & Johnson, K. L. (2020). Fasciclin-like arabinogalactan-protein 16 (FLA16) is required for stem development in Arabidopsis. Frontiers in Plant Science, 11, 615392. doi.org/10.26181/13515464.v3
Norton, R. S., Mitchell, M. L., & Shafee, T. (2020). Correlations among sequence, physicochemical properties and function in peptide toxins. doi.org/10.1016/j.toxicon.2019.10.074
Pfeifer, L., Shafee, T., Johnson, K. L., Bacic, A., & Classen, B. (2020). Arabinogalactan-proteins of Zostera marina L. contain unique glycan structures and provide insight into adaption processes to saline environments. Scientific Reports, 10(1), 8232. doi.org/10.26181/5e8c491575d77
Shafee, T. (2020). A guided tour of the secret world behind Wikipedia. In Nerd Nite. doi.org/10.26181/5e3f86b37ec2e
Shafee, T., Bacic, A., & Johnson, K. (2020). Evolution of sequence-diverse disordered regions in a protein family: order within the chaos. Molecular Biology and Evolution, 37(8), 2155–2172. doi.org/10.1093/molbev/msaa096
Waagmeester, A., Stupp, G., Burgstaller-Muehlbacher, S., Good, B. M., Griffith, M., Griffith, O. L., Hanspers, K., Hermjakob, H., Hudson, T. S., Hybiske, K., et al. (2020). Wikidata as a knowledge graph for the life sciences. eLife, 9, e52614. doi.org/10.26181/13211342
Dash, T. S., Shafee, T., Harvey, P. J., Zhang, C., Peigneur, S., Deuis, J. R., Vetter, I., Tytgat, J., Anderson, M. A., & Craik, D. J. (2019). A centipede toxin family defines an ancient class of CSαβ defensins. Structure, 27(2), 315–326. doi.org/10.1016/j.str.2018.10.022
Harris, K. S., Anderson, M. A., Shafee, T. M. A., Durek, T., Jackson, M., & Craik, D. (2019). Generation of peptides. US Patent Application 15/762,433.
Kerenga, B. K., McKenna, J. A., Harvey, P. J., Quimbar, P., Garcia-Ceron, D., Lay, F. T., Phan, T. K., Veneer, P. K., Vasa, S., Parisi, K., et al. (2019). Salt-tolerant antifungal and antibacterial activities of the corn defensin ZmD32. Frontiers in Microbiology, 10, 795. doi.org/10.26181/13211579.v3
Mitchell, M. L., Shafee, T., Papenfuss, A. T., & Norton, R. S. (2019). Evolution of cnidarian trans-defensins: sequence, structure and exploration of chemical space. Proteins, 87(7), 551–560. doi.org/10.1002/prot.25679
Norton, R. S., Morales, R. A. V., Krishnarjuna, B., Mitchell, M. L., & Shafee, T. M. (2019). The ShK fold as an efficient scaffold for potent potassium channel blockade and other functions. Toxicon, 158, S25. doi.org/10.1016/j.toxicon.2018.10.092
Oehme, D. P., Shafee, T., Downton, M. T., Bacic, A., & Doblin, M. S. (2019). Differences in protein structural regions that impact functional specificity in GT2 family β-glucan synthases. PLoS ONE, 14(10), e0224442. doi.org/10.26181/13211357
Parisi, K., Shafee, T. M. A., Quimbar, P., van der Weerden, N. L., Bleackley, M. R., & Anderson, M. A. (2019). The evolution, function and mechanisms of action for plant defensins. Seminars in Cell & Developmental Biology, 88, 107–118. doi.org/10.26181/13213427.v1
Shafee, T., & Anderson, M. A. (2019). A quantitative map of protein sequence space for the cis-defensin superfamily. Bioinformatics, 35(5), 743–752. doi.org/10.26181/13213259.v2
Shafee, T., Mitchell, M. L., & Norton, R. S. (2019). Mapping the chemical and sequence space of the ShKT superfamily. Toxicon, 165, 95–102. doi.org/10.1016/j.toxicon.2019.04.008
Turki, H., Shafee, T., Taieb, M. A. H., Aouicha, M. B., Vrandečić, D., Das, D., & Hamdi, H. (2019). Wikidata: a large-scale collaborative ontological medical database. Journal of Biomedical Informatics, 99, 103292. doi.org/10.1016/j.jbi.2019.103292
Jackson, M. A., Gilding, E. K., Shafee, T., Harris, K. S., Kaas, Q., Poon, S., Yap, K., Jia, H., Guarino, R., Chan, L. Y., et al. (2018). Molecular basis for the production of cyclic peptides by plant asparaginyl endopeptidases. Nature Communications, 9(1), 2411. doi.org/10.26181/13211363
Shafee, T. (2018). The aims and scope of WikiJournal of Science. WikiJournal of Science, 1(1), 1–3. doi.org/10.26181/13211360
Das, D., Shafee, T., Masukume, G., & Haggstrom, M. (2017). WikiJournal – a new form of open access publishing. In Society for Information Science, 33, 8.
Harris, K., Anderson, M., Shafee, T., Durek, T., Jackson, M., & Craik, D. (2017). Generation of peptides. US Patent WO2017049362 A1.
Lowe, R., Shirley, N., Bleackley, M., Dolan, S., & Shafee, T. (2017). Transcriptomics technologies. PLoS Computational Biology, 13(5), e1005457. doi.org/10.1371/journal.pcbi.1005457
Shafee, T. M. A., Lay, F. T., Phan, T. K., Anderson, M. A., & Hulett, M. D. (2017). Convergent evolution of defensin sequence, structure and function. Cellular and Molecular Life Sciences, 74(4), 663–682. doi.org/10.1007/s00018-016-2344-5
Shafee, T., & Lowe, R. (2017). Eukaryotic and prokaryotic gene structure. WikiJournal of Medicine, 4(1), 2. doi.org/10.15347/wjm/2017.002
Shafee, T., Das, D., Masukume, G., & Häggström, M. (2017). WikiJournal of Medicine, the first Wikipedia-integrated academic journal. WikiJournal of Medicine, 4(1), 1. doi.org/10.26181/13211366.v1
Shafee, T., Mietchen, D., & Su, A. I. (2017). Academics can help shape Wikipedia. Science, 357(6351), 557–558. doi.org/10.1126/science.aao0462
Shafee, T., Masukume, G., Kipersztok, L., Das, D., Häggström, M., & Heilman, J. (2017). Evolution of Wikipedia’s medical content: past, present and future. Journal of Epidemiology and Community Health, 71(11), 1122–1129. doi.org/10.1136/jech-2016-208601
Shafee, T. (2017). Wikipedia-integrated publishing: a comparison of successful models. Health Informatics, 26, 2.
Bleackley, M. R., Payne, J. A. E., Hayes, B. M. E., Durek, T., Craik, D. J., Shafee, T. M. A., Poon, I. K. H., Hulett, M. D., van der Weerden, N. L., & Anderson, M. A. (2016). Nicotiana alata defensin chimeras reveal differences in the mechanism of fungal and tumor cell killing and an enhanced antifungal variant. Antimicrobial Agents and Chemotherapy, 60(10), 6302–6312. doi.org/10.1128/aac.01479-16
Masukume, G., Kipersztok, L., Das, D., Shafee, T. M. A., Laurent, M. R., & Heilman, J. M. (2016). Medical journals and Wikipedia: a global health matter. Lancet Global Health, 4(11), e791. doi.org/10.1016/s2214-109x(16)30254-6
Payne, J. A., Bleackley, M. R., Lee, T.-H., Shafee, T. M., Poon, I. K., Hulett, M. D., Aguilar, M.-I., van der Weerden, N. L., & Anderson, M. A. (2016). The plant defensin NaD1 introduces membrane disorder through a specific interaction with the lipid, phosphatidylinositol 4,5 bisphosphate. Biochimica et Biophysica Acta – Biomembranes. doi.org/10.26181/13515848.v2
Shafee, T. (2016). Wikipedia is already the world’s ‘Dr Google’—it’s time for doctors and researchers to make it better. The Conversation.
Shafee, T., Robinson, A., van der Weerden, N., & Anderson, M. (2016). Structural homology guided alignment of cysteine rich proteins. SpringerPlus, 5, 27. doi.org/10.1186/s40064-015-1609-z
Shafee, T. M. A., Lay, F. T., Hulett, M. D., & Anderson, M. A. (2016). The defensins consist of two independent, convergent protein superfamilies. Molecular Biology and Evolution, 33(9), 2345–2356. doi.org/10.1093/molbev/msw106
Shafee, T., & Cooke, I. (2016). AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments. BMC Bioinformatics, 17(1), 434. doi.org/10.1186/s12859-016-1300-6
Strugnell, J., Shafee, T., Wilson, N., Downey, R., Stevens, C., Shaw, J., & Baeseman, J. (2016). A step-change in the recognition of women in Antarctic science. Czech Polar Reports, 6(1), 119–120. doi.org/10.5817/CPR2016-1-9
Strugnell, J., Shafee, T., Wilson, N., Downey, R., Stevens, C., Shaw, J., & Baeseman, J. (2016). Profiles: Kudos for female Antarctic researchers. Nature, 536, 148. doi.org/10.26181/5e3a804247556
Shafee, T., Gatti-Lafranconi, P., Minter, R., & Hollfelder, F. (2015). Handicap-recover evolution leads to a chemically versatile, nucleophile-permissive protease. ChemBioChem, 16(13), 1866–1869. doi.org/10.1002/cbic.201500295
Shafee, T., Harris, K., & Anderson, M. (2015). Biosynthesis of cyclotides. Advances in Botanical Research, 76, 227–269. doi.org/10.26181/5e3a3d90e6328
Shafee, T. (2014). Evolvability of a viral protease: experimental evolution of catalysis, robustness and specificity. PhD thesis. doi.org/10.26181/5e4a097b2c2b8
Shafee, T., Gatti-Lafranconi, P., Minter, R., & Hollfelder, F. (2012). Experimental evolution of a viral protease to quantify evolvability. In SMBE, Dublin.
Zhang, A. T., Langley, A. R., Christov, C. P., Kheir, E., Shafee, T., Gardiner, T. J., & Krude, T. (2011). Dynamic interaction of Y RNAs with chromatin and initiation proteins during human DNA replication. Journal of Cell Science, 124(12), 2058–2069. doi.org/10.1242/jcs.086561