Publications

2017

J. Cursons, M. J. Davis. Determining the Significance of Protein Network Features and Attributes Using Permutation Testing. Methods in Molecular Biology 2017 1549 199-208

M. Foroutan, J. Cursons, S. Hediyeh-Zadeh, E. W. Thompson, M. J. Davis. A Transcriptional Program for Detecting TGFbeta-induced EMT in Cancer. Molecular Cancer Research 2017. DOI: 10.1158/1541-7786.MCR-16-0313

P. J. Gawthrop. Bond-Graph Modelling and Causal Analysis of Biomolecular Systems
in Bond Graphs for Modelling, Control and Fault Diagnosis of Engineering Systems, pp587-623. 03 January 2017, Springer

2016

M.C. Andrews, J. Cursons, D.G. Hurley, M. Anaka, J.S. Cebon, A. Behren, E.J. Crampin. Systems analysis identifies miR-29b regulation of invasiveness in melanoma. Molecular Cancer 2016 15:72 http://dx.doi.org/10.1186/s12943-016-0554-y

D.M. Budden, E.J. Crampin. Distributed gene expression modelling for exploring variability in epigenetic function. BMC Bioinformatics 2016 17:446 http://dx.doi.org/10.1186/s12859-016-1313-1 https://arxiv.org/abs/1507.05720

D.M. Budden, E.J. Crampin. Information theoretic inference of biological networks from continuous-valued data. BMC Systems Biology 10:89 http://dx.doi.org/10.1186/s12918-016-0331-y

J. Cui, M. Faria, M. Björnmalm, Y. Ju, T. Suma, S.T. Gunawan, J.J. Richardson, S. Bals, E.J. Crampin, F. Caruso. A framework to account for sedimentation and diffusion in particle-cell interactions. Langmuir 2016 http://dx.doi.org/10.1021/acs.langmuir.6b01634

P.J. Gawthrop, E.J. Crampin. Modular Bond-graph Modelling and Analysis of Biomolecular Systems. IET Systems Biology 2016 http://dx.doi.org/10.1049/iet-syb.2015.0083

J.M. Jarosz, S. Ghosh, L. Delbridge, A. Petzer, A. Hickey, E.J. Crampin, E.G. Hansen, V. Rajagopal. Changes in mitochondrial morphology and organisation can enhance energy supply from mitochondrial oxidative phosphorylation in diabetic cardiomyopathy. American Journal of Physiology – Cell Physiology 2016 http://dx.doi.org/10.1152/ajpcell.00298.2016

I. Siekmann, M. Fackrell, E.J. Crampin, P. Taylor (2016). Modelling modal gating of ion channels with hierarchical Markov models. Proc. R. Soc. A 472: 20160122 http://dx.doi.org/10.1098/rspa.2016.0122

K. Tran, J.-C. Han, A. Taberner, C. Barrett, E.J. Crampin, and D. Loiselle. Myocardial energetics is not compromised during compensated hypertrophy in the Dahl salt-sensitive rat model of hypertension. AJP – Heart and Circulatory Physiology 2016 http://dx.doi.org/10.1152/ajpheart.00396.2016

Yenkai Lim, Yunxia Wan, Dimitrios Vagenas, Dmitry A. Ovchinnikov, Chris F. L. Perry, Melissa J. Davis, Chamindie Punyadeera. Salivary DNA methylation panel to diagnose HPV-positive and HPV-negative head and neck cancers. BMC Cancer 2016 16:749 DOI: 10.1186/s12885-016-2785-0

Anne C. Rios, Nai Yang Fu, Joseph Cursons, Geoffrey J. Lindeman and Jane E. Visvader. The complexities and caveats of lineage tracing in the mammary gland. Breast Cancer Research 2016 18:116. DOI: 10.1186/s13058-016-0774-5

Dagmar Waltemath, Jonathan R Karr, Frank T Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K Aranganathan, Kambiz Baghalian, Arne T Bittig, Paulo E Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S Costa, Joseph Cursons, Tobias Czauderna, Arthur P Goldberg, Harold F Gómez, Jens Hahn, Tuure Hameri, Daniel F Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knuepfer, Matthias Koenig, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Toure, Jannis Uhlendorf, Thawfeek M Varusai, Leandro H Watanabe, Florian Wendland, Markus Wolfien, James T Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber. Toward Community Standards and Software for Whole-Cell Modeling. IEEE Transactions on Biomedical Engineering 2016 63 (10) 2007-2014. doi: 10.1109/TBME.2016.2560762

Tristan McCaughey, Paul G Sanfilippo, George EC Gooden, David M Budden, Li Fan, Eva Fenwick, Gwyneth Rees, Casimir MacGregor, Lei Si, Christine Chen, Helena Hai Liang, Timothy Baldwin, Alice Pébay, Alex W Hewitt. A Global Social Media Survey of Attitudes to Human Genome Editing. Cell Stem Cell 18 May 5, 569-572, 2016. http://dx.doi.org/10.1016/j.stem.2016.04.011

I. Siekmann, H. Malchow. Fighting Enemies and Noise: Competition of Residents and Invaders in a Stochastically Fluctuating Environment. Mathematical Modelling of Natural Phenomena. Vol. 11, No. 5, 2016, pp. 137-157 http://doi.org/10.1051/mmnp/201611509

Annette Lasham, Sunali Y. Mehta, Sandra J. Fitzgerald, Adele G. Woolley, James I. Hearn, Daniel G. Hurley, Igor Ruza, Michael Algie, Andrew N. Shelling, Antony W. Braithwaite, Cristin G. Print. A novel EGR-1 dependent mechanism for YB-1 modulation of paclitaxel response in a triple negative breast cancer cell line. International Journal of Cancer 2016 Volume 139, Issue 5 Pages 1157–1170. DOI: 10.1002/ijc.30137

Mauren Jaudal, Lulu Zhang, Chong Che, Daniel G. Hurley, Geoffrey Thomson, Jiangqi Wen, Kirankumar S. Mysore, Joanna Putterill. MtVRN2 is a Polycomb VRN2-like gene which represses the transition to flowering in the model legume Medicago truncatula. The Plant Journal (2016) 86, 145–160. doi: 10.1111/tpj.13156

Shannon Fenn, Alexandre Mendes, David M. Budden. Addressing the non-functional requirements of computer vision systems: a case study. Machine Vision and Applications 2016, Volume 27, Issue 1, pp 77–86. DOI: 10.1007/s00138-015-0726-6

2015

I. Siekmann, P. Cao, J. Sneyd, E.J. Crampin (2015). Data-Driven Modelling Of The Inositol-Trisphosphate Receptor (IP3R) And Its Role In IP3-Dependent Calcium-Induced Calcium Release (ICICR). In M.D. Pitta and H. Berry (Eds.), Computational Glioscience (Chapter 2). Springer. http://arxiv.org/abs/1507.06064

M.L. Neal, B.E. Carlson, C.T. Thompson, R.C. James, K.G. Kim, K. Tran, E.J. Crampin, D.L. Cook, J.H. Gennari (2015). Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. PLoS ONE 10(12): e0145621. http://dx.doi.org/10.1371/journal.pone.0145621

J. Cursons, C.E. Angel, D.G. Hurley, C.G. Print, P.R. Dunbar, M.D. Jacobs, E.J. Crampin (2015). Spatially-transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis. GigaScience.2015, 4:63. http://dx.doi.org/10.1186/s13742-015-0102-5
Supporting data for “Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis”. GigaScience Database. http://dx.doi.org/10.5524/100168

S. Detchokul, A. Elangovan, E.J. Crampin, M.J. Davis, A.G. Frauman (2015). Network analysis of an in vitro model of androgen-resistance in prostate cancer. BMC Cancer 15:883. http://dx.doi.org/10.1186/s12885-015-1884-7

P.J. Gawthrop, J. Cursons, E.J. Crampin (2015). Hierarchical Bond Graph Modelling of Biochemical Networks. Proc Roy Soc Lond A 471 2184 20150642
http://dx.doi.org/10.1098/rapha.2015.0642

J. Cursons, J. Gao, D.G. Hurley, C.G. Print, P.R. Dunbar, M.D. Jacobs, E.J. Crampin (2015). Regulation of ERK-MAPK Signalling in Human Epidermis. BMC Systems Biology 9:41 http://dx.doi.org/10.1186/s12918-015-0187-6

K.T. Sharp, E.J. Crampin, J. Sneyd (2015). A spatial model of fluid recycling in the airways of the lung. Journal of Theoretical Biology 382 198-215 http://dx.doi.org/10.1016/j.jtbi.2015.06.050

V. Rajagopal, G. Bass, C. Walker, D. Crossman, A. Petzer, I. Siekmann, A. Hickey, M. Hoshijima, M. Ellisman, E.J. Crampin, C. Soeller (2015). Examination of the effects of heterogeneous organization of RyR clusters, myofibrils and mitochondria on Ca2+ release patterns in cardiomyocytes. PLoS Computational Biology 11(9): e1004417 http://dx.doi.org/10.1371/journal.pcbi.1004417

K. Tran, D. Loiselle, E.J. Crampin (2015). Regulation of cardiac cellular bioenergetics: mechanisms and consequences. Physiological Reports, 3 (7), e12464 http://dx.doi.org/10.14814/phy2.12464

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

J. Cursons, K.-J. Leuchowius, M. Waltham, E. Tomascovik-Crook, M. Foroutan, C. Bracken, A. Redfern, E.J. Crampin, I. Street, M.J. Davis, E.W. Thompson (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 13:26 http://dx.doi.org/10.1186/s12964-015-0106-x

A. Shah, D. Chen, A. R. Boda, L. J. Foster, M. J. Davis, M. M. Hill. RaftProt: mammalian lipid raft proteome database. Nucleic Acids Research 2015 43 (D1): D335-D338 DOI: https://doi.org/10.1093/nar/gku1131

M. Flannery, D. M. Budden, A. Mendes. FlexDM: Simple, parallel and fault-tolerant data mining using WEKA. Source Code for Biology and Medicine 2015 10:13 DOI: 10.1186/s13029-015-0045-3

2014

D.M. Budden, D.G. Hurley, J. Cursons, J.F. Markham, M.J. Davis, E.J. Crampin (2014). Predicting expression: The complementary power of histone modification and transcription factor binding data. Epigenetics & Chromatin, 7:36 1-12 http://dx.doi.org/10.1186/1756-8935-7-36

D.G. Hurley, D.M. Budden, E.J. Crampin (2014). Virtual reference environments: A simple way to make research reproducible. Briefings in Bioinformatics bbu043 http://dx.doi.org/10.1093/bib/bbu043

D.G. Hurley, J. Cursons, Y. Wang, C.G. Print, E.J. Crampin (2015). NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks. Bioinformatics 31(2) 277-8 http://dx.doi.org/10.1093/bioinformatics/btu612

D.M. Budden, D.G. Hurley, E.J. Crampin (2015). Predictive modeling of gene expression from transcriptional regulatory elements. Briefings in Bioinformatics 16 (4): 616-628
http://dx.doi.org/10.1093/bib/bbu034

P.J. Gawthrop, E.J. Crampin (2014). Energy-based analysis of biochemical cycles using bond graphs. Proc. R. Soc. A. 470 20140459 http://dx.doi.org/10.1098/rspa.2014.0459

J. Sneyd, E.J. Crampin, D. Yule (2014). Multiscale Modelling of Saliva Secretion. Mathematical Biosciences 257 69-79 http://dx.doi.org/10.1016/j.mbs.2014.06.017

I. Siekmann, L. Wagner, D. Yule, J. Sneyd, E.J. Crampin (2014). Statistical analysis of modal gating in ion channels. Proc R Soc A 2014 470:20140030 http://dx.doi.org/10.1098/rspa.2014.0030

P. Gawthrop, I. Loram, H. Gollee, M. Lakie. Intermittent control models of human standing: similarities and differences. Biological Cybernetics 2014, Volume 108, Issue 2, pp 159–168 doi:10.1007/s00422-014-0587-5

2013

Y. K. Wang, D. G. Hurley, S. Schnell, C. G. Print, E. J. Crampin (2013) Integration of Steady-State and Temporal Gene Expression Data for the Inference of Gene Regulatory Networks. PLoS ONE 8(8): e72103. doi:10.1371/journal.pone.0072103

Y. K. Wang, C. Print, E. J. Crampin (2013). Biclustering reveals breast cancer tumour subgroups with common clinical features and improves prediction of disease recurrence. BMC Genomics (2013), 14:102. doi:10.1186/1471-2164-14-102