Publications List

Refereed journal articles

2016

Lasham, A., Mehta, S., Fitzgerald, S., Woolley, A., Hearn, J., Hurley, D.G., Ruza, I., Algie, M., Sullivan, R., Shelling, A., Braithwaite, A., Print, C.G. A novel EGR-1 dependent mechanism for YB-1 modulation of paclitaxel response in a triple negative breast cancer cell line. Int J Cancer (accepted)

Jaudal, M., Zhang, L., Che, C., Hurley, D.G., Thomson, G., Wen, J., Mysore, K., Putterill, J. MtVRN2 is a Polycomb VRN2-like gene which represses the transition to flowering in the model legume Medicago truncatula. The Plant Journal (accepted).

Cursons J., Angel C.E., Hurley D.G., Dunbar P.R., Jacobs M.D., Crampin E.J. (2015) Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis. GigaScience 4 (1), 1-6

James, J., Hurley D.G., Gamage, T., Zhang, T., Vather, R., Prantham, P., Murti, P., Chamley, L., Isolation and Characterisation of a Novel Trophoblast Side-Population from First Trimester Placentae. Reproduction (accepted).

2015

Cursons J., Gao J., (Joint first authorship). Hurley D.G., Dunbar P.R., Jacobs M.D., Crampin E.J. Regulation of ERK-MAPK signaling in human epidermis. BMC Syst Biol. 2015;9(1):41.

Budden, D. M., Hurley, D. G., & Crampin, E. J. (2015). Modelling the conditional regulatory activity of methylated and bivalent promoters. Epigenetics & Chromatin 2015;8: 21. doi:10.1186/s13072-015-0013-9

2014

Hurley, D. G., Budden, D. M., & Crampin, E. J. (2014). Virtual Reference Environments: a simple way to make research reproducible. Briefings in Bioinformatics, bbu043. doi:10.1093/bib/bbu043

Hurley, D. G., Cursons, J., Wang, Y. K., Budden, D. M., Print, C. G., & Crampin, E. J. (2014). NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks. Bioinformatics, 31(2), 277–278. doi:10.1093/bioinformatics/btu612

Budden, D. M., Hurley, D. G., & Crampin, E. J. (2014). Predictive modelling of gene expression from transcriptional regulatory elements. Briefings in Bioinformatics, bbu034. doi:10.1093/bib/bbu034

Budden, D. M., Hurley, D. G., Cursons, J., Markham, J. F., Davis, M. J., & Crampin, E. J. (2014). Predicting expression: the complementary power of histone modification and transcription factor binding data. Epigenetics & Chromatin, 7(1), 1–12.

Hunter, F. W., Jaiswal, J. K., Hurley, D. G., Liyanage, H. D., McManaway, S. P., Gu, Y., … others. (2014). The flavoprotein FOXRED2 reductively activates nitro-chloromethylbenzindolines and other hypoxia-targeting prodrugs. Biochemical Pharmacology, 89(2), 224–235.

Jansson, D., Rustenhoven, J., Feng, S., Hurley, D., Oldfield, R. L., Bergin, P. S., … Dragunow, M. (2014). A role for human brain pericytes in neuroinflammation. Journal of Neuroinflammation, 11(1), 104.

2013

Wang, Y. K., Hurley, D. G., Schnell, S., Crampin, E. J., others, & Print, C. G. (2013). Integration of Steady-State and Temporal Gene Expression Data for the Inference of Gene Regulatory Networks. PLOS ONE, 8(8), e72103.

Wang, J., Guise, C. P., Hsu, H.-L., Hurley, D., Wilson, W. R., & Patterson, A. V. (2013). Identification of reductases capable of metabolic activation of hypoxia targeting prodrug SN30000 and hypoxia marker EF5. In Cancer Research (Vol. 73, pp. 2111–2111).

Blenkiron, C., Hurley, D. G., Fitzgerald, S., Lasham, A., others, & Print, C. G. (2013). Links between the Oncoprotein YB-1 and Small Non-Coding RNAs in Breast Cancer. PLOS ONE, 8(11), e80171. doi:10.1371/journal.pone.0080171

2012

Hurley, D., Araki, H., Tamada, Y., Dunmore, B., Sanders, D., Humphreys, S., … Print, C. G. (2012). Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Research, 40(6), 2377–2398. doi:10.1093/nar/gkr902

Grace, P. P. M., Hurley, D., Barratt, D. T. D., Tsykin, A., Watkins, L. R., Rolan, P. E., & Hutchinson, M. R. (2012). Harnessing pain heterogeneity and RNA transcriptome to identify blood-based pain biomarkers: a novel correlational study design and bioinformatics approach in a graded chronic constriction injury model. Journal of Neurochemistry, 122(5), 976–994. doi:10.1111/j.1471-4159.2012.07833.x

Wang, L., Hurley, D. G., (Joint first authorship),Watkins, W., Araki, H., Tamada, Y., Muthukaruppan, A., … Print, C. G. (2012). Cell cycle gene networks are associated with melanoma prognosis. Plos One, 7(4), e34247. doi:10.1371/journal.pone.0034247

2011

Araki, H., Hurley, D., Crampin, E., Print, C., & Kuhara, S. (2011). Gene Network Analysis and Application. Biophysics (Seibutsu Butsuri), 51(4), 182–185.

Thesis

Hurley DG. Gene network inference and application. The University of Auckland. 2011.

Book chapters

Ellett, S., Ferguson, I. R., Shuotun, Z., Karunasinghe, N., Marlow, G., Hurley, D. G., … Ferguson, L. R. (2013). Foodomics to Study Efficacy of Human Dietary Interventions. In Nutrigenomics and Nutrigenetics in Functional Foods and Personalized Nutrition (pp. 269–280). CRC Press.

Other

Invited talks

Hurley, D. Networks in Computational Biology. Winter School in Mathematical and Computational Biology, The University of Queensland Institute for Molecular Bioscience, Brisbane, July 2-6, 2013.

Hurley, D. Network Methods in Systems Biology. Winter School in Mathematical and Computational Biology, The University of Queensland Institute for Molecular Bioscience, Brisbane, July 2-6, 2012.

Hurley, D. Applications of Network Methods in Systems Biology . Queensland Institute of Medical Research, Brisbane, July 8, 2012.

Hurley, D. Gene network inference and Systems Biology. Winter School in Mathematical and Computational Biology, The University of Queensland Institute for Molecular Bioscience, Brisbane, July 4-8, 2011.

Hurley, D. Gene Networks for Cancer Research, Bioinformatics Institute seminar series, University of Auckland. September 2010

Other talks

Hurley, D., Wang, L. Cell cycle gene networks are associated with melanoma prognosis. Submitted talk, Cancer Biology satellite meeting of the Queenstown Research Week 2012, Queenstown, New Zealand.

Hurley, D. A Rapid Development Toolkit for GenePattern, Auckland Bioengineering Institute departmental seminar, University of Auckland. October 2010

Hurley, D. Systems Biology, Gene Networks and Human Health, Auckland Bioengineering Institute PhD Completion seminar, University of Auckland. September 2010.