Journal Articles
Permana, Budi, Falconer, Caitlin, Mayer-Coverdale, Johanna, Robson, Jennifer, Cuddihy, Thom, Schembri, Mark A., Paterson, David L., Harris, Patrick N. A. and Forde, Brian M. (2025). Snapshot genomic surveillance reveals insights into antimicrobial resistance and lineage diversity of uropathogens in older adults in Queensland. Open Forum Infectious Diseases, 12 (10) ofaf610, 1-8. doi: 10.1093/ofid/ofaf610
Walker, Lachlan L., Phan, Minh-Duy, Permana, Budi, Lian, Zheng Jie, Nhu, Nguyen Thi Khanh, Cuddihy, Thom, Peters, Kate M., Ramsay, Kay A., Stewart, Chelsea, Pfennigwerth, Niels, Kidd, Timothy J., Harris, Patrick N. A., Paterson, David L., Sweet, Matthew J., Forde, Brian M. and Schembri, Mark A. (2025). Emergence of a carbapenem-resistant atypical uropathogenic Escherichia coli clone as an increasing cause of urinary tract infection. Nature Communications, 16 (1) 8200, 1-10. doi: 10.1038/s41467-025-63477-0
Goodall, Emily C. A., Hodges, Freya, Kok, Weine, Permana, Budi, Cuddihy, Thom, Yang, Zihao, Kahler, Nicole, Shires, Kenneth, Pullela, Karthik, Torres, Von Vergel L., Rooke, Jessica L., Delhaye, Antoine, Collet, Jean-François, Bryant, Jack A., Forde, Brian M., Hemm, Matthew R. and Henderson, Ian R. (2025). PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes. Nucleic Acids Research, 53 (15) gkaf774, 1-16. doi: 10.1093/nar/gkaf774
Gassiep, Ian, Chatfield, Mark D., Permana, Budi, Burnard, Delaney, Bauer, Michelle J., Cuddihy, Thom, Forde, Brian M., Mayer-Coverdale, Johanna, Norton, Robert E. and Harris, Patrick N. A. (2024). The genomic epidemiology of clinical Burkholderia pseudomallei isolates in North Queensland, Australia. Pathogens, 13 (7) 584, 584. doi: 10.3390/pathogens13070584
Gassiep, Ian, Burnard, Delaney, Permana, Budi, Bauer, Michelle J., Cuddihy, Thom, Forde, Brian M., Chatfield, Mark D., Ling, Weiping, Norton, Robert and Harris, Patrick N. A. (2023). Melioidosis Queensland: an analysis of clinical outcomes and genomic factors. PLoS Neglected Tropical Diseases, 17 (10) e0011697, 1-13. doi: 10.1371/journal.pntd.0011697
Liu, Junyu, Maxwell, Michael, Cuddihy, Thom, Crawford, Theo, Bassetti, Madeline, Hyde, Cameron, Peigneur, Steve, Tytgat, Jan, Undheim, Eivind A.B. and Mobli, Mehdi (2023). ScrepYard: an online resource for disulfide-stabilised tandem repeat peptides. Protein Science, 32 (2) e4566, 1-12. doi: 10.1002/pro.4566
Bauer, Michelle J., Peri, Anna Maria, Lüftinger, Lukas, Beisken, Stephan, Bergh, Haakon, Forde, Brian M., Buckley, Cameron, Cuddihy, Thom, Tan, Patrice, Paterson, David L., Whiley, David M. and Harris, Patrick N. A. (2022). Optimized method for bacterial nucleic acid extraction from positive blood culture broth for whole-genome sequencing, resistance phenotype prediction, and downstream molecular applications. Journal of Clinical Microbiology, 60 (11) e01012-22, 1-11. doi: 10.1128/jcm.01012-22
Omaleki, Lida, Blackall, Patrick J., Cuddihy, Thom, White, Rhys T., Courtice, Jodi M., Turni, Conny, Forde, Brian M. and Beatson, Scott A. (2022). Phase variation in the glycosyltransferase genes of Pasteurella multocida associated with outbreaks of fowl cholera on free-range layer farms. Microbial Genomics, 8 (3) 000772. doi: 10.1099/mgen.0.000772
Cuddihy, Thom, Harris, Patrick N. A., Permana, Budi, Beatson, Scott A. and Forde, Brian M. (2022). CATHAI: cluster analysis tool for healthcare-associated infections. Bioinformatics Advances, 2 (1) vbac040, vbac040. doi: 10.1093/bioadv/vbac040
Omaleki, Lida, Blackall, Patrick J., Cuddihy, Thom, Beatson, Scott A., Forde, Brian M. and Turni, Conny (2020). Using genomics to understand inter- and intra- outbreak diversity of Pasteurella multocida isolates associated with fowl cholera in meat chickens. Microbial Genomics, 6 (3) 000346, 1-8. doi: 10.1099/mgen.0.000346
Setoh, Yin Xiang, Amarilla, Alberto A., Peng, Nias Y. G., Griffiths, Rebecca E., Carrera, Julio, Freney, Morgan E., Nakayama, Eri, Ogawa, Shinya, Watterson, Daniel, Modhiran, Naphak, Nanyonga, Faith Elizabeth, Torres, Francisco J., Slonchak, Andrii, Periasamy, Parthiban, Prow, Natalie A., Tang, Bing, Harrison, Jessica, Hobson-Peters, Jody, Cuddihy, Thom, Cooper-White, Justin, Hall, Roy A., Young, Paul R., Mackenzie, Jason M., Wolvetang, Ernst, Bloom, Jesse D., Suhrbier, Andreas and Khromykh, Alexander A. (2019). Determinants of Zika virus host tropism uncovered by deep mutational scanning. Nature Microbiology, 4 (5), 876-887. doi: 10.1038/s41564-019-0399-4
Conference Papers
Cuddihy, Thom, Forde, Brian, Rhodes, Nicholas, Paterson, David, Gorse, Dominique, Beatson, Scott and Harris, Patrick (2019). SRA down under: cache and analysis platform for infectious disease. Australian national conference for Health Informatics (HIC 2019), Melbourne, Australia, 12-14 August 2019. Amsterdam, Netherlands: IOS Press. doi: 10.3233/SHTI190776
Haynes, K. H., Cuddihy, T., Le Cao, K., Bradbury, L., Brown, M. A. and Thomas, G. P. (2014). Rna Sequencing in Ankylosing Spondylitis Identifies a Novel Disease-Specific Transcriptome and Splice Variants. 9th International Cogress on Spondyloarthritis, Gent, Belgium, 23-25 October 2014. Ospedaletto, Italy: Pacini Editore SpA.