Prof Andrew Lonie

Top publications focussed on development and implementation of bioinformatics and computational biology methodologies and platforms.             

1. M Hong, G Macintyre, D Wedge, P Van Loo, S Lunke, L Alexandrov, C Sloggett, M Cmero, K Patel, F Marass, D Tsui, S Mangiola, A Lonie, H Naeem, N Sapre, P Phal, N Kurganovs, X Chin, M Kerger, N Rosenfeld, J Pedersen, A Ryan, I Haviv, A Costello, N Corcoran, C Hovens (2015). Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer. Nature Communications (accepted Jan 2015)
2. A Patch, E Christie, D Etemadmoghadam, DW. Garsed, J George, S Fereday,…, A Lonie,…, and D Bowtell (2015). Whole–genome characterization of chemoresistant ovarian cancer. Nature, 2015; 521 (7553): 489
3. D Park, K Tao, F Le Calvez-Kelm, T Nguyen-Dumont, N Robinot, F Hammet, F Odefrey, H Tsimiklis, Z Teo, L Thingholm, E Young, C Voegele, A Lonie, B Pope, T Roane, R Bell, H Hu, Shankaracharya, C Hu, J Ellis, J Li, I Makunin, E John, I Andrulis, M Terry, M Daly, S Buys, C Snyder, H Lynch, P Devilee, G Giles, J Hopper, B Feng, F Lesueur, S Tavtigian, M Southey and D Goldgar (2014). Rare mutations in RINT1 predispose carriers to breast and Lynch Syndrome-spectrum cancers. Cancer Discov. 2014 Jul;4(7):804-15.
4. Campos TD, Young ND1, Korhonen PK, Hall RS, Mangiola S, Lonie A, Gasser RB (2014). Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics. Parasite Vectors. 2014 May 27;7:242. doi: 10.1186/1756-3305-7-242.
5. Y Kuo, A Lonie, A Pearce and L Sonenberg (2014) “Mining Surprising Patterns and Their Explanations in Clinical Data”. Applied Artificial Intelligence 28(2),111-138
6. G Severi, M Southey, D English, C Jung, A Lonie, C McLean, H Tsimiklis, J Hopper, G Giles, L Baglietto (2014). Epigenome-wide methylation in DNA from peripheral blood as a marker of risk for breast cancer. Breast Cancer Research and Treatment Vol 148, Issue 3, pp 665-673
7. Pope, BJ, Nguyen-Dumont, T, Odefrey, F, Bell, R, Tavtigian, SV, Goldgar, DE, Lonie, A, Southey, MC, Park DJ. (2013). FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets. BMC Bioinformatics 2013, 14:65.
8. Elyas, M; Maynard, SB; Ahmad, A; Lonie, A (2014). Towards a Systematic Framework for Digital Forensics Readiness. Journal of Computer Information Systems. 54(3):97-105.
9. DJ Park, F Lesueur, T Nguyen-Dumont, M Pertesi, F Odefrey, F Hammet, SL Neuhausen, EM John, IL Andrulis, MB Terry, M Daly, S Buys, F Le Calvez-Kelm, A Lonie, BJ Pope, H Tsimiklis, C Voegele, FM Hilbers, N. Hoogerbrugge, A Barroso, A Osorio, BCFR, kConFab, GG Giles, P Devilee, J Benitez, JL Hopper, SV Tavtigian, DE Goldgar, MC Southey (2012). Rare mutations in XRCC2 confer increased risk of breast cancer. American Journal of Human Genetics. 90 (4): 734–739
10. PJ Harris, S Manos, ME Hibbert, E Kazmierczak, A Lonie (2010). VPH Clinical Data Integration, Life Sciences Computational Research and Outreach at the University of Melbourne. Virtual Physiological Human Annual Conference 2010 Brussels, Belgium
11. Miller H, Clarke S, Lane S, Lonie A, Lazaridis D, Petrovski S and Jones O. 2009. Predicting customer behaviour: The University of Melbourne’s KDD Cup report.  Proceedings of the KDD Cup 2009 – Accepted for publication in Journal of Machine Learning Research: Workshop and Conference Proceedings Volume 7: Proceedings of KDD-Cup 2009 competition.Other publications, papers, reports …
12. ZL Teo, DJ Park, F Odefrey, F Hammet, T Nguyen-Dumont, H Tsimiklis, BJ Pope, A Lonie, I Winship, GG Giles, ABCFS, JL Hopper and MC Southey. 2012. Expanded genetic analysis of a PALB2 c.3113G>A mutation carrying multiple-case breast cancer family via exome sequencing. (2012). Hereditary Cancer in Clinical Practice 2012, 10(Suppl 2):A92 doi:10.1186/1897-4287-10-S2-A92
13. MC Southey, DJ Park, F Lesueur, F Odefrey, T Nguyen-Dumont, F Hammet, SL Neuhausen, EM John, IL Andrulis, G Chenevix-Trench, L Baglietto, F Le Calvez-Kelm, M Pertesi, A Lonie, B Pope, O Sinilnikova, H Tsimiklis, GG Giles, JL Hopper, SV Tavtigian and DE Goldgar, MCCS, BCFR, kConFab. Identification of new breast cancer predisposition genes via whole exome sequencing. (2012) Hered Cancer Clin Pract. 2012; 10(Suppl 2): A40. Published online 2012 April 12. doi:  10.1186/1897-4287-10-S2-A40
14. Lonie, A (2012). In life sciences research today, resistance to computation is not an option. Australasian Biotechnology, Vol. 22, No. 3, Dec 2012: 14-15
15. PJ Harris, S Manos, ME. Hibbert, E Kazmierczak, A Lonie. 2010. VPH Clinical Data Integration, Life Sciences Computational Research and Outreach at the University of Melbourne. Virtual Physiological Human Annual Conference 2010 Brussels, Belgium
16. Tao Z, Lonie A & Nath G. 2009. A Data Clustering Approach To Discriminating Impersonating Devices In Wi-Fi Networks. Security Comm. Networks. 2010; 3:44–57
17. Chu X., Lonie A., Harris P., Thomas S.R. & Buyya R (2008). “A Service-Oriented Grid Environment for Integration of Distributed Kidney Models and Resources” Concurrency and Computation: Practice and Experience 2008; 20(9): 1095-111
18. Kuo Y, Lonie A., Paizis K. & Sonenberg E. “Domain Ontology Driven Data Mining – A Medical Case Study” Proceedings of the International Workshop on Domain Driven Data Mining 2007 pp.11-17
19. Yen-Ting Kuo, Liz Sonenberg & Andrew Lonie. 2008. Finding Explanations for Assisting Pattern Interpretation. 2008 IEEE/WIC/ACM International Conference on Web Intelligence. 48-51. California, United States: IEEE Computer Society
20. Tao Z, Nath G & Lonie A. 2008. An Optimal Sensor Architecture for Wi-Fi Intrusion Detection. International Journal of Computer Science and Network Security. 8 (2): 10-19.
21. Tao Z, Nath G & Lonie A. 2008. X-Mode: A Real Time Approach of Discriminating Wi-Fi network Impersonators. Proceedings of the 4th International Conference on Next Generation Web Services Practices. 151-158. California, United States: IEEE Computer Society.
22. Thomas R, Layton , Harris P, Lonie A, Moore . 2005. Towards a web resource for quantitative renal physiology. Journal of Physiology – London. 565P (0): 98.
23. Cowan PJ, Shinkel, TA, Fisicaro, N, Godwin JH, Bernabéu C, Almendro N, Rius C, Lonie AJ, Nottle MB, Wigley PL, Paizis K, Pearse MJ, and d’Apice AJ. 2003   Targeting Gene Expression to Endothelium in Transgenic Animals: A Comparison of the Human ICAM-2, PECAM-1 and Endoglin Promoters. Xenotransplantation. May;10(3):223-31.
24. Cowan PJ., Shinkel TA., Aminian A., Romanella M., Wigley PL., Lonie A., Nottle MB., Pearse MJ., d’Apice AJ. 1998.  High-level co-expression of complement regulators on vascular endothelium in transgenic mice: CD55 and CD59 provide greater protection from human complement-mediated injury than CD59 alone. Xenotransplantation Aug;5(3):184-90
25. Tearle RG, Tange MJ, Zannettino ZL, Katerelos M, Shinkel TA, Van Denderen BJ, Lonie A, Lyons I, Nottle MB, Cox T, Becker C, Peura AM, Wigley PL, Crawford RJ, Robins AJ, Pearse MJ, d’Apice AJ 1996 The alpha-1,3-galactosyltransferase knockout mouse. Implications for xenotransplantation. Transplantation Jan 15;61(1):13-9
26. Lonie A, D’Andrea R, Paro R, Saint R 1994.  Molecular characterisation of the Polycomblike gene of Drosophila melanogaster, a trans-acting negative regulator of homeotic gene expression. Development Sep;120(9):2629-36