The University of Queensland

Purification protocols for extracellular vesicles

Lane, Rebecca E., Korbie, Darren, Trau, Matt and Hill, Michelle M. (2017). Purification protocols for extracellular vesicles. In Winston Patrick Kuo and Shidong Jia (Ed.), Extracellular vesicles: methods and protocols (pp. 111-130) New York, United States: Humana Press. doi:10.1007/978-1-4939-7253-1_10

Methods used for noncoding RNAs analysis

Askarian-Amiri, Marjan E., Korbie, Darren J., Sarkar, Debina and Finlay, Graeme (2016). Methods used for noncoding RNAs analysis. Molecular pathology in cancer research. (pp. 151-175) edited by Sunil R. Lakhani and Stephen B. Fox. New York, U.S.A.: Springer . doi: 10.1007/978-1-4939-6643-1_8

Transcriptional comparison of testicular adrenal rest tumors with fetal and adult tissues

Schröder, Mariska A M, Sweep, Fred C G J, van Herwaarden, Antonius E., Mitchell, Rod T., Eliveld, Jitske, van Pelt, Ans M M, Rowan, Alan E., Korbie, Darren, Stikkelbroeck, Nike M M L, Claahsen-van der Grinten, Hedi L. and Span, Paul N. (2022). Transcriptional comparison of testicular adrenal rest tumors with fetal and adult tissues. European Journal of Endocrinology, 187 (5), 607-615. doi: 10.1530/EJE-22-0143

Modelling clinical DNA fragmentation in the development of universal PCR-based assays for bisulfite-converted, formalin-fixed and cell-free DNA sample analysis

Johnston, Andrew D., Lu, Jennifer, Korbie, Darren and Trau, Matt (2022). Modelling clinical DNA fragmentation in the development of universal PCR-based assays for bisulfite-converted, formalin-fixed and cell-free DNA sample analysis. Scientific Reports, 12 (1) 16051, 1-18. doi: 10.1038/s41598-022-18196-7

Next-Generation Molecular Discovery: From Bottom-Up In Vivo and In Vitro Approaches to In Silico Top-Down Approaches for Therapeutics Neogenesis

Kenny, Sophie E., Antaw, Fiach, Locke, Warwick J., Howard, Christopher B., Korbie, Darren and Trau, Matt (2022). Next-Generation Molecular Discovery: From Bottom-Up In Vivo and In Vitro Approaches to In Silico Top-Down Approaches for Therapeutics Neogenesis. Life, 12 (3) 363, 1-24. doi: 10.3390/life12030363

Opportunities for early cancer detection: the rise of ctDNA methylation-based pan-cancer screening technologies

Constantin, Nicolas, Sina, Abu Ali Ibn, Korbie, Darren and Trau, Matt (2022). Opportunities for early cancer detection: the rise of ctDNA methylation-based pan-cancer screening technologies. Epigenomes, 6 (1) 6. doi: 10.3390/epigenomes6010006

Dynamic monitoring of EMT in CTCs as an indicator of cancer metastasis

Zhang, Zhen, Wuethrich, Alain, Wang, Jing, Korbie, Darren, Lin, Lynlee L. and Trau, Matt (2021). Dynamic monitoring of EMT in CTCs as an indicator of cancer metastasis. Analytical Chemistry, 93 (50) acs.analchem.1c03167, 16787-16795. doi: 10.1021/acs.analchem.1c03167

Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod

Mayne, Benjamin, Espinoza, Thomas, Roberts, David, Butler, Gavin L., Brooks, Steven, Korbie, Darren and Jarman, Simon (2021). Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod. Molecular Ecology Resources, 21 (7) 13440, 2324-2332. doi: 10.1111/1755-0998.13440

Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships

Schwaber, Jessica L., Korbie, Darren, Andersen, Stacey, Lin, Erica, Chrysanthopoulos, Panagiotis K., Trau, Matt and Nielsen, Lars K. (2021). Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships. PLoS ONE, 16 (2 ) e0246107, e0246107. doi: 10.1371/journal.pone.0246107

A DNA methylation age predictor for zebrafish

Mayne, Benjamin, Korbie, Darren, Kenchington, Lisa, Ezzy, Ben, Berry, Oliver and Jarman, Simon (2020). A DNA methylation age predictor for zebrafish. Aging, 12 (24), 24817-24835. doi: 10.18632/aging.202400

Regulation of canonical oncogenic signaling pathways in cancer via DNA methylation

Lu, Jennifer, Wilfred, Premila, Korbie, Darren and Trau, Matt (2020). Regulation of canonical oncogenic signaling pathways in cancer via DNA methylation. Cancers, 12 (11) 3199, 1-29. doi: 10.3390/cancers12113199

Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing

Raftery, Lyndon J., Howard, Christopher B., Grewal, Yadveer S., Vaidyanathan, Ramanathan, Jones, Martina L., Anderson, Will, Korbie, Darren, Duarte, Tania, Duc Cao, Minh, Nguyen, Son Hoang, Coin, Lachlan JM, Mahler, Stephen M and Trau, Matt (2019). Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing. Lab on a Chip, 19 (24), 4083-4092. doi: 10.1039/c9lc00978g

Optimizing size exclusion chromatography for extracellular vesicle enrichment and proteomic analysis from clinically relevant samples

Lane, Rebecca E., Korbie, Darren, Trau, Matt and Hill, Michelle M. (2019). Optimizing size exclusion chromatography for extracellular vesicle enrichment and proteomic analysis from clinically relevant samples. Proteomics, 19 (8) 1800156, 1800156. doi: 10.1002/pmic.201800156

PrimerROC: accurate condition-independent dimer prediction using ROC analysis

Johnston, Andrew D., Lu, Jennifer, Ru, Ke-lin, Korbie, Darren and Trau, Matt (2019). PrimerROC: accurate condition-independent dimer prediction using ROC analysis. Scientific Reports, 9 (1) 209, 209. doi: 10.1038/s41598-018-36612-9

Tracking antigen specific T-cells: technological advancement and limitations

Dey, Shuvashis, Kamil Reza, K., Wuethrich, Alain, Korbie, Darren, Ibn Sina, Abu Ali and Trau, Matt (2019). Tracking antigen specific T-cells: technological advancement and limitations. Biotechnology Advances, 37 (1), 145-153. doi: 10.1016/j.biotechadv.2018.11.010

Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker

Sina, Abu Ali Ibn, Carrascosa, Laura G., Liang, Ziyu, Grewal, Yadveer S., Wardiana, Andri, Shiddiky, Muhammad J. A., Gardiner, Robert A., Samaratunga, Hemamali, Gandhi, Maher K., Scott, Rodney J., Korbie, Darren and Trau, Matt (2018). Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker. Nature Communications, 9 (1) 4915, 4915. doi: 10.1038/s41467-018-07214-w

A SERS microfluidic platform for targeting multiple soluble immune checkpoints

Reza, K. Kamil, Sina, Abu Ali Ibn, Wuethrich, Alain, Grewal, Yadveer S., Howard, Christopher B., Korbie, Darren and Trau, Matt (2018). A SERS microfluidic platform for targeting multiple soluble immune checkpoints. Biosensors and Bioelectronics, 126, 178-186. doi: 10.1016/j.bios.2018.10.044

MiR-29b-1-5p is altered in BRCA1 mutant tumours and is a biomarker in basal-like breast cancer

Milevskiy, Michael J. G., Sandhu, Gurveen K., Wronski, Anna, Korbie, Darren, Brewster, Brooke L., Shewan, Annette, Edwards, Stacey L., French, Juliet D. and Brown, Melissa A. (2018). MiR-29b-1-5p is altered in BRCA1 mutant tumours and is a biomarker in basal-like breast cancer. Oncotarget, 9 (71), 33577-33588. doi: 10.18632/oncotarget.26094

Parallel profiling of cancer cells and proteins using a graphene oxide functionalized ac-EHD SERS immunoassay

Reza, K. Kamil, Dey, Shuvashis, Wuethrich, Alain, Sina, Abu Ali Ibn, Korbie, Darren, Wang, Yuling and Trau, Matt (2018). Parallel profiling of cancer cells and proteins using a graphene oxide functionalized ac-EHD SERS immunoassay. Nanoscale, 10 (39), 18482-18491. doi: 10.1039/c8nr02886a

Extracellular vesicles as circulating cancer biomarkers: opportunities and challenges

Lane, R. E., Korbie, D., Hill, M. M. and Trau, M. (2018). Extracellular vesicles as circulating cancer biomarkers: opportunities and challenges. Clinical and Translational Medicine, 7 (1) 14, 14. doi: 10.1186/s40169-018-0192-7

A multiplex microplatform for the detection of multiple DNA methylation events using gold-DNA affinity

Ibn Sina, Abu Ali, Foster, Matthew Thomas, Korbie, Darren, Carrascosa, Laura G., Shiddiky, Muhammad J. A., Gao, Jing, Dey, Shuvashis and Trau, Matt (2017). A multiplex microplatform for the detection of multiple DNA methylation events using gold-DNA affinity. Analyst, 142 (19), 3573-3578. doi: 10.1039/c7an00611j

Detection of aberrant protein phosphorylation in cancer using direct gold-protein affinity interactions

Ahmed, Mostak, Carrascosa, Laura G., Ibn Sina, Abu Ali, Zarate, Ester Marina, Korbie, Darren, Ru, Ke-lin, Shiddiky, Muhammad J. A., Mainwaring, Paul and Trau, Matt (2017). Detection of aberrant protein phosphorylation in cancer using direct gold-protein affinity interactions. Biosensors and Bioelectronics, 91, 8-14. doi: 10.1016/j.bios.2016.12.012

Evaluation of different oligonucleotide base substitutions at CpG binding sites in multiplex bisulfite-PCR sequencing

Lu, Jennifer, Ru, Kelin, Candiloro, Ida, Dobrovic, Alexander, Korbie, Darren and Trau, Matt (2017). Evaluation of different oligonucleotide base substitutions at CpG binding sites in multiplex bisulfite-PCR sequencing. Scientific Reports, 7 (1) 45096, 45096. doi: 10.1038/srep45096

PrimerSuite: a high-throughput web-based primer design program for multiplex bisulfite PCR

Lu, Jennifer, Johnston, Andrew, Berichon, Philippe, Ru, Ke-lin, Korbie, Darren and Trau, Matt (2017). PrimerSuite: a high-throughput web-based primer design program for multiplex bisulfite PCR. Scientific Reports, 7 (1) 41328, 41328. doi: 10.1038/srep41328

Rapid molecular profiling of myeloproliferative neoplasms using targeted Exon Resequencing of 86 genes involved in JAK-STAT signaling and epigenetic regulation

Magor, Graham W., Tallack, Michael R., Klose, Nathan M., Taylor, Debra, Korbie, Darren, Mollee, Peter, Trau, Matt and Perkins, Andrew C. (2016). Rapid molecular profiling of myeloproliferative neoplasms using targeted Exon Resequencing of 86 genes involved in JAK-STAT signaling and epigenetic regulation. Journal of Molecular Diagnostics, 18 (5), 707-718. doi: 10.1016/j.jmoldx.2016.05.006

Phase II randomized preoperative window-of-opportunity study of the PI3K inhibitor pictilisib plus anastrozole compared with anastrozole alone in patients with estrogen receptor-positive breast cancer

Schmid, Peter, Pinder, Sarah E., Wheatley, Duncan, Macaskill, Jane, Zammit, Charles, Hu, Jennifer, Price, Robert, Bundred, Nigel, Hadad, Sirwan, Shia, Alice, Sarker, Shah-Jalal, Lim, Louise, Gazinska, Patrycja, Woodman, Natalie, Korbie, Darren, Trau, Matt, Mainwaring, Paul, Gendreau, Steven, Lackner, Mark R., Derynck, Mika, Wilson, Timothy R., Butler, Hannah, Earl, Gemma, Parker, Peter, Purushotham, Arnie and Thompson, Alastair (2016). Phase II randomized preoperative window-of-opportunity study of the PI3K inhibitor pictilisib plus anastrozole compared with anastrozole alone in patients with estrogen receptor-positive breast cancer. Journal of Clinical Oncology, 34 (17), 1987-1994. doi: 10.1200/JCO.2015.63.9179

MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing

Wong, Nicholas C., Pope, Bernard J., Candiloro, Ida L., Korbie, Darren, Trau, Matt, Wong, Stephen Q., Mikeska, Thomas, Zhang, Xinmin Z, Pitman, Mark, Eggers, Stefanie, Doyle, Stephen R and Dobrovic, Alexander (2016). MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing. BMC Bioinformatics, 17 (1) 98, 98.1-98.14. doi: 10.1186/s12859-016-0950-8

Germline polymorphisms in an enhancer of PSIP1 are associated with progression-free survival in epithelial ovarian cancer

French, Juliet D., Johnatty, Sharon E., Lu, Yi, Beesley, Jonathan, Gao, Bo, Kalimutho, Murugan, Henderson, Michelle J., Russell, Amanda J., Kar, Siddhartha, Chen, Xiaoging, Hillman, Kristine M., Kaufmann, S, Sivakumaran H., O'Reilly, Martin, Wang, Chen, Korbie, Darren J., Lambrechts, Diether, Despierre, Evelyn, Van Nieuwenhuysen, Els, Lambrechts, Sandra, Vergote, Ignace, Karlan, Beth, Lester, Jenny, Orsulic, Sandra, Walsh, Christine, Fasching, Peter A., Beckmann, Matthias W., Ekici, Arif B., Hein, Alexander ... MacGregor, Stuart (2016). Germline polymorphisms in an enhancer of PSIP1 are associated with progression-free survival in epithelial ovarian cancer. Oncotarget, 7 (6), 6353-6368. doi: 10.18632/oncotarget.7047

Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat

Wong, Nicholas C., Pope, Bernard J., Candiloro, Ida, Korbie, Darren, Trau, Matt, Wong, Stephen Q., Mikeska, Thomas, van Denderen, Bryce J. W., Thompson, Erik W., Eggers, Stefanie, Doyle, Stephen R. and Dobrovic, Alexander (2015). Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat. Gigascience, 4 (1) 55, 55.1-55.8. doi: 10.1186/s13742-015-0098-x

DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer

Stone, Andrew, Zotenko, Elena, Locke, Warwick J., Korbie, Darren, Millar, Ewan K. A., Pidsley, Ruth, Stirzaker, Clare, Graham, Peter, Trau, Matt, Musgrove, Elizabeth A., Nicholson, Robert I., Gee, Julia M. W. and Clark, Susan J. (2015). DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer. Nature Communications, 6 (1) 7758, 7758.1-7758.9. doi: 10.1038/ncomms8758

Observations of tunable resistive pulse sensing for exosome analysis: improving system sensitivity and stability

Anderson, Will, Lane, Rebecca, Korbie, Darren and Trau, Matt (2015). Observations of tunable resistive pulse sensing for exosome analysis: improving system sensitivity and stability. Langmuir, 31 (23), 6577-6587. doi: 10.1021/acs.langmuir.5b01402

Multiplex bisulfite PCR resequencing of clinical FFPE DNA

Korbie, Darren, Lin, Erica, Wall, David, Nair, Shalima S., Stirzaker, Clare, Clark, Sue J. and Trau, Matt (2015). Multiplex bisulfite PCR resequencing of clinical FFPE DNA. Clinical Epigenetics, 7 (28) 28, 1-11. doi: 10.1186/s13148-015-0067-3

Methylome sequencing in triple negative breast cancer reveals distinct methylation clusters with prognostic value

Stirzaker, Clare, Zotenko, Elena, Song, Jenny Z., Qu, Wenja, Nair, Shalima, Locke, Warwick J., Stone, Andrew Stone, Armstrong, Nicola J., Robinson, Mark D., Dobrovic, Alexander, Avery-Kiejda, Kelly A., Peters, Kate M., French, Juliet D., Stein, Sandra, Korbie, Darren J., Trau, Matt, Forbes, John F., Scott, Rodney J., Brown, Melissa A., Francis, Glenn D. and Clark, Susan J. (2015). Methylome sequencing in triple negative breast cancer reveals distinct methylation clusters with prognostic value. Nature Communications, 6 (5899) 5899, 1-11. doi: 10.1038/ncomms6899

Analysis of exosome purification methods using a model liposome system and tunable-resistive pulse sensing

Lane, Rebecca E., Korbie, Darren, Anderson, Will, Vaidyanathan, Ramanathan and Trau, Matt (2015). Analysis of exosome purification methods using a model liposome system and tunable-resistive pulse sensing. Scientific Reports, 5 (1) 7639, 7639.1-7639.7. doi: 10.1038/srep07639

Detecting exosomes specifically: a multiplexed device based on alternating current electrohydrodynamic induced nanoshearing

Vaidyanathan, Ramanathan, Naghibosadat, Maedeh, Rauf, Sakandar, Korbie, Darren, Carrascosa, Laura G., Shiddiky, Muhammad J. A. and Trau, Matt (2014). Detecting exosomes specifically: a multiplexed device based on alternating current electrohydrodynamic induced nanoshearing. Analytical Chemistry, 86 (22), 11125-11132. doi: 10.1021/ac502082b

MicroRNAs-140-5p/140-3p modulate leydig cell numbers in the developing mouse testis

Rakoczy, Joanna, Fernandez-Valverde, Selene L., Glazov, Evgeny A., Wainwright, Elanor N., Sato, Tempei, Takada, Shuji, Combes, Alexander N., Korbie, Darren J., Miller, David, Grimmond, Sean M., Little, Melissa H., Asahara, Hiroshi, Mattick, John S., Taft, Ryan J. and Wilhelm, Dagmar (2013). MicroRNAs-140-5p/140-3p modulate leydig cell numbers in the developing mouse testis. Biology of Reproduction, 88 (6) 143, 143. doi: 10.1095/biolreprod.113.107607

Expression of distinct RNAs from 3′ untranslated regions

Mercer, Tim R., Wilhelm, Dagmar, Dinger, Marcel E., Solda, Giulia, Korbie, Darren J., Glazov, Evgeny A., Truong, Vy, Schwenke, Maren, Simons, Cas, Matthaei, Klaus I., Saint, Robert, Koopman, Peter and Mattick, John S. (2011). Expression of distinct RNAs from 3′ untranslated regions. Nucleic Acids Research, 39 (6), 2393-2403. doi: 10.1093/nar/gkq1158

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

Mercer, Tim R., Dinger, Marcel E., Bracken, Cameron P., Kolle, Gabriel, Szubert, Jan M., Korbie, Darren J., Askarian-Amiri, Marjan E., Gardiner, Brooke B., Goodall, Gregory J., Grimmond, Sean M. and Mattick, John S. (2010). Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Research, 20 (12), 1639-1650. doi: 10.1101/gr.112128.110

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

Taft, Ryan, Simons, Cas, Nahkuri, Satu, Oey, Harald, Korbie, Darren J., Mercer, Timothy R., Holst, Jeff, Ritchie, William, Wong, Justin J-L., Rasko, John E. J., Rokhsar, Daniel S., Degnan, Bernard M. and Mattick, John S. (2010). Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nature Structural and Molecular Biology, 17 (8), 1030-1035. doi: 10.1038/nsmb.1841

Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data

Jung, Chol-Hee, Hansen, Martin A., Makunin, Igor V., Korbie, Darren J. and Mattick, John S. (2010). Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data. BMC Genomics, 11 (1 Article # 77) 77, 1-12. doi: 10.1186/1471-2164-11-77

Touchdown PCR for increased specificity and sensitivity in PCR amplification

Korbie, D. J. and Mattick, J. S. (2008). Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nature Protocols, 3 (9), 1452-1456. doi: 10.1038/nprot.2008.133

Molecular evolution of the HBII-52 snoRNA Cluster

Nahkuri, S., Taft, R. J., Korbie, D. J. and Mattick, J. S. (2008). Molecular evolution of the HBII-52 snoRNA Cluster. Journal of Molecular Biology, 381 (4), 810-815. doi: 10.1016/j.jmb.2008.06.057

Detecting Exosomes Specifically: a Microfluidic Approach Based on Alternating Current Electrohydrodynamic Induced Nanoshearing

Shiddiky, Muhammad J, Vaidyanathan, Ramanathan, Naghibosadat, Maedeh, Rauf, Sakandar, Korbie, Darren, Carrascosa, Laura G and Trau, Matt (2014). Detecting Exosomes Specifically: a Microfluidic Approach Based on Alternating Current Electrohydrodynamic Induced Nanoshearing. 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, San Antonio, TX United States, 26-30 October 2014. San Antonio, TX United States: MicroTAS.

Novel Strategies for the Prediction and Control of Advanced Breast Cancer via nanoscaled Epigenetic-Based Biosensors

Korbie, Darren (2013). Novel Strategies for the Prediction and Control of Advanced Breast Cancer via nanoscaled Epigenetic-Based Biosensors. National Breast Cancer Foundation. (Collection) doi: 10.14264/uql.2017.21

The identification and characterization of novel RNAs in the mouse transcriptome

Darren Korbie (2011). The identification and characterization of novel RNAs in the mouse transcriptome. PhD Thesis, Institute for Molecular Bioscience, The University of Queensland.