Publications List

This is our current list of publications by date.

Table of Contents

2015

Cursons J., Gao J., Hurley D.G., Dunbar P.R., Jacobs M.D., Crampin EJ. Regulation of ERK-MAPK signaling in human epidermis. BMC Syst Biol. 2015;9(1):41. doi: 10.1186/s12918-015-0187-6

Cursons, J., Leuchowius, K.-J., Waltham, M., Tomaskovic-Crook, E., Foroutan, M., Bracken, C. P., … Davis, M. J. (2015). Stimulus-dependent differences in signalling regulate epithelial-mesenchymal plasticity and change the effects of drugs in breast cancer cell lines. Cell Communication and Signaling, 13(1), 26.

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

Siekmann, I. (2014). Bifurcation analysis of individual-based models in population dynamics. Ecological Complexity. doi:10.1016/j.ecocom.2014.06.002

Siekmann, I., Sneyd, J., & Crampin, E. J. (2014). Statistical analysis of modal gating in ion channels. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 470(2166), 20140030–20140030. doi:10.1098/rspa.2014.0030

Martin, J., Wang, X., Simpson, C., & Siekmann, I. (2014). PyTrA: ultra-fast transient absorption data analysis software. International Journal of Nanotechnology, 11(5/6/7/8), 601. doi:10.1504/IJNT.2014.060582

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.

Siekmann, I. (2013). On competition in ecology, epidemiology and eco-epidemiology. Ecological Complexity, 14, 166–179. doi:10.1016/j.ecocom.2013.01.003

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.