Mr Budi Permana
Bioinformatics Research Assistant
UQ Centre for Clinical Research
Journal Articles
Wen, Sophie C. H., Harris, Patrick N. A., Forde, Brian, Permana, Budi, Chatfield, Mark D., Lau, Colleen L., Spurling, Geoffrey, Bauer, Michelle J., Balch, Ross, Chambers, Henry, Schlapbach, Luregn J., Clark, Julia E., Dougherty, Sonia, Blyth, Christopher C., Britton, Philip N., Clifford, Vanessa, Haeusler, Gabrielle M., McMullan, Brendan, Wadia, Ushma, Paterson, David L., Irwin, Adam D., on behalf of the PAEDS network, Carr, Jeremy, Vasilunas, Nan, Francis, Joshua R., Macartney, Kristine, Crawford, Nigel W., Wood, Nicholas, Buttery, Jim ... Glover, Catherine (2024). Characterization of gram-negative bloodstream infections in hospitalised Australian children and their clinical outcomes. Clinical Infectious Diseases, 79 (3), 734-743. doi: 10.1093/cid/ciae341
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
Permana, Budi, Harris, Patrick N. A., Roberts, Leah W., Cuddihy, Thom, Paterson, David L., Beatson, Scott A. and Forde, Brian M. (2024). HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data. Microbial Genomics, 10 (2) 001200. doi: 10.1099/mgen.0.001200
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
Shafiq, Muhammad, Bilal, Hazrat, Permana, Budi, Xu, Danhong, Cai, Gengzhong, Li, Xin, Zeng, Mi, Yuan, Yumeng, Jiao, Xiaoyang and Yao, Fen (2023). Characterization of antibiotic resistance genes and mobile elements in extended-spectrum β-lactamase-producing Escherichia coli strains isolated from hospitalized patients in Guangdong, China. Journal of Applied Microbiology, 134 (7) lxad125, 1-12. doi: 10.1093/jambio/lxad125
Permana, Budi, Beatson, Scott A. and Forde, Brian M. (2023). GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach. BMC Bioinformatics, 24 (1) 209, 1-9. doi: 10.1186/s12859-023-05332-x
Permana, Budi, Harris, Patrick N. A., Runnegar, Naomi, Lindsay, Margaret, Henderson, Belinda C., Playford, E. G., Paterson, David L., Beatson, Scott A. and Forde, Brian M. (2023). Using genomics to investigate an outbreak of vancomycin-resistant Enterococcus faecium ST78 at a large tertiary hospital in Queensland. Microbiology Spectrum, 11 (3) e0420422, 1-10. doi: 10.1128/spectrum.04204-22
Shafiq, Muhammad, Zeng, Mi, Permana, Budi, Bilal, Hazrat, Huang, Jinhu, Yao, Fen, Algammal, Abdelazeem Mohamed, Li, Xin, Yuan, Yumeng and Jiao, Xiaoyang (2022). Coexistence of blaNDM–5 and tet(X4) in international high-risk Escherichia coli clone ST648 of human origin in China. Frontiers in Microbiology, 13 1031688, 1031688. doi: 10.3389/fmicb.2022.1031688
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
Conference Papers
Aslan, Abdullah Tarik, Demir, Mervenur, Tanriverdi, Elif Seren, Permana, Budi, Izuagbe, Rhys, Ramsay, Kay A., Forde, Brian, Otlu, Baris, Paterson, David L., Harris, Patrick, Akova, Murat and Hazirolan, Gulsen (2024). Loss of OmpK35 and Glycine-aspartic acid Duplication in ompK36 Negatively Affect the in vitro Synergy of Meropenem in Combination with Piperacillin/tazobactam or Imipenem Against OXA-48-like Carbapenemase-producing Klebsiella pneumoniae. 33rd International Congress of Antimicrobial Chemotherapy (ICC), Istanbul, Turkey, 3-6 November 2024. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.jgar.2024.10.019
Gassiep, Ian, Burnard, Delaney, Permana, Budi, Bauer, Michelle J., Cuddihy, Thom, Forde, Brian M., Chatfield, Mark D., Ling, Weiping, Mayer-Coverdale, Johanna, Norton, Robert and Harris, Patrick N.A. (2024). The molecular epidemiology of Burkholderia pseudomallei in North Queensland. Pathology Update 2024, Adelaide, VIC, Australia, 1 - 3 March 2024. Oxford, United Kingdom: Elsevier. doi: 10.1016/j.pathol.2023.12.133