Dr Nicholas Hamilton

Snr Machine Learnining Consult

Research Computing Centre

Senior Research Fellow

Institute for Molecular Bioscience
n.hamilton@imb.uq.edu.au
+61 7 334 62033

Overview

Dr Nick Hamilton is the Institute Bio-Mathematician at the Institute for Molecular Bioscience (IMB) and holds a co-appointment with the Research Computing Centre at UQ. He gained a PhD in Pure Mathematics from the University of Western Australia in 1996 and was subsequently awarded Fellowships in Australia and Belgium. In 2002, Nick made the decision to change fields into the exciting new areas of computational biology and bioinformatics, returned to Australia, and subsequently took up a position within the ARC Centre of Excellence in Bioinformatics at UQ. In 2008 he was appointed as a Laboratory Head at IMB, and Institute Bio-Mathematician in 2014, where he continues to lead a group in bio-image informatics, mathematical modelling and data visualisation, developing methodologies to deal with the current deluge of data that new microscopy imaging technologies have enabled.

Research Interests

  • Bioinformatics
  • Bio-image informatics
  • Data visualisation
  • Mathematical modelling
  • Machine learning
  • GPU algorithms
  • High throughput bio-image analysis
  • Image processing
  • Graph clustering algorithms
  • Combinatorial computing
  • Finite geometry
  • Group theory
  • Algebra
  • Combinatorics
  • Formal methods for computing

Qualifications

  • PhD, The University of Western Australia
  • BSc, The University of Western Australia

Publications

View all Publications

Supervision

  • Doctor Philosophy

  • Doctor Philosophy

  • Doctor Philosophy

View all Supervision

Publications

Book Chapter

  • Condon, Nicholas D., Wall, Adam A., Yeo, Jeremy C., Hamilton, Nicholas A. and Stow, Jennifer L. (2017). Image-based analysis of phagocytosis: measuring engulfment and internalization. In Roberto Botelho (Ed.), Phagocytosis and phagosomes: methods and protocols (pp. 201-214) New York, NY, United States: Humana Press. doi:10.1007/978-1-4939-6581-6_13

  • Hamilton, N. and Huber, T. (2008). An Introduction to Protein contact Prediction. Bioinformatics. (pp. 87-104) edited by Jonathan M. Keith. USA: Humana Press. doi: 10.1007/978-1-60327-429-6-3

  • Hamilton, Nicholas, Kerr, Markus, Burrage, Kevin and Teasdale, Rohan D. (2007). Analyzing real-time video microscopy: the dyamics and geometry of vescicles and tubules in endocytosis. Current Protocols in Cell Biology. (pp. 4.16.1-1.16.11) edited by Bonifacio, J. S., Dasso, M., Harford, J. B., Lippincott-Schwartz, J. and Yamada K. M.. Hoboken, NJ United States: John Wiley & Sons. doi: 10.1002/0471143030.cb0416s35

  • Burrage, K., Burrage,P. M., Hamilton, N. and Tian, T (2006). Computer-intensive simulations for cellular models. Parallel Computing in Bioinformatics and Computational Biology. (pp. 79-119) edited by Albert Y Zomaya. New Jersey, USA: John Wiley & Sons. doi: 10.1002/0471756504.ch4

Journal Article

Conference Publication

  • Plisson, Fabien, Piggott, Andrew, Hamilton, Nicholas and Capon, Robert (2018). Predicting blood-brain barrier permeability of marine-derived kinase inhibitors. 256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond, Boston, MA, United States, 19-23 August 2018. Washington, DC, United States: American Chemical Society (ASC).

  • Combes, Alexander, Lefevre, James, Short, Kieran, Ju, Adler, Georgas, Kylie, Lamberton, Timothy, Cairncross, Oliver, Rumballe, Bree, McMahon, Andrew, Little, Melissa, Hamilton, Nicholas and Smyth, Ian (2017). An integrated cell, tissue and whole organ profile of kidney morphogenesis. 18th International Congress of Developmental Biology, Singapore Singapore, Jun 18-22, 2017. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.mod.2017.04.432

  • Budnar, S., Gomez, G., Naghibosidat, M., Wee, K., Gupta, S., Kambe, H., Verma, S., Hamilton, N., Neufeld, Z. and Yap, A. S. (2017). Anillin dependent stabilization of Rho signaling at adherens junctions influences cell extrusion and collective cell migration. ASCB/EMBO Meeting, Philadelphia Pa United States, 2-6 December 2017. Bethesda, MD United States: American Society for Cell Biology.

  • Priya, R., Gomez, G. A., Budnar, S., Verma, S., Hamilton, N. A. and Yap, A. S. (2015). Patterning Rho signaling at the epithelial Zonula Adherens: a tale of feedback loops. 2015 Cell Biology ASCB Annual Meeting, San Diego CA, United States, 12-16 December 2015. Bethesda, MD United States: American Society for Cell Biology.

  • Wu, S., Gomez, G. A., Michael, M., Verma, S., Cox, H., Lefevre, J. G., Parton, R. G., Hamilton, N. A. and Yap, A. S. (2014). Disruption of cortical tension patterning drives the outgrowth of oncogenic cells. EACR-23: 23rd Biennial Congress of the European Association for Cancer Research, Munich, Germany, 5-8 July 2014. OXFORD: ELSEVIER SCI LTD. doi: 10.1016/S0959-8049(14)50251-1

  • Follett, J., Norwood, S., Hamilton, N., Collins, B., Bugarcic, A. and Teasdale, R. D. (2014). Parkinson's Disease Causing Mutations Alters Retromer's Function. ASCB/IFCB Meeting, Philadelphia, PA United States, 06 - 10 December 2014. Bethesda, MD United States: American Society for Cell Biology.

  • Combes, A., Short, K., Lefevre, J., Ju, A., Georgas, K., Rumballe, B., Mcmahon, A., Hamilton, N., Smyth, I. and Little, M. (2013). An Integrated Cell, Tissue and Whole Organ Profile of Kidney Morphogenesis. 49th Annual Scientific Meeting of the Australian and New Zealand Society of Nephrology, Brisbane Australia, 9-11 September 2013. Richmond, Australia: Wiley-Blackwell Publishing Asia. doi: 10.1111/nep.12121

  • Belward, John A., Burrage, Kevin, Teasdale, Rohan D. and Hamilton, Nicholas A. (2011). Linear models for endocytic transformations from live cell imaging. CTAC2010 : 15th Biennial Computational Techniques and Applications Conference, Univeristy of New South Wales, Sydney, Australia, 28 November - 1 December 2010. Cambridge, United Kingdom: Cambridge University Press. doi: 10.0000/anziamj.v52i0.3801

  • Bustamam, Alhadi, Burrage, Kevin and Hamilton, Nicholas A. (2010). A GPU implementation of fast parallel Markov clustering in Bioinformatics using ELLPACK-R sparse data format. ACT 2010, Jakarta, Indonesia, 2 - 3 December, 2010. Los Alamitos, CA, U.S.A.: IEEE Computer Society Conference Publishing Services (CPS). doi: 10.1109/ACT.2010.10

  • Bustamam, Alhadi, Burrage, Kevin and Hamilton, Nicholas A. (2010). Fast parallel Markov clustering in bioinformatics using massively parallel graphics processing unit computing. Joint PDMC/HiBi Workshop 2010: International Workshop on High Performance Computational Systems Biology (2nd, HiBi, 2010); International Workshop on Parallel and Distributed Methods in Verification (9th, PDMC, 2010), Enschede, Netherlands, 30 September-1 October 2010. Piscataway, NJ, U.S.A.: Institute of Electrical and Electronic Engineers (IEEE). doi: 10.1109/PDMC-HiBi.2010.23

  • Bustamam, A., Sehgal, M. S., Hamilton, N. A., Wong, S., Ragan, M. A. and Burrage, K (2009). An efficient parallel implementation of Markov clustering algorithm for large-scale protein-protein interaction networks that uses MPI. 5th IMT-GT international conference on mathematics, statistics and their applications, Bukittinggi, Indonesia, 9 -11 June 2009. Indonesia: Department of Mathematics, Andalas University.

  • Hamilton, A, Pantelic, S, Hanson,, Fink, L, Karunaratne, M and Teasdale, R D (2006). Automated subcellar phenotype classification : An introduction and recent results. 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006), Hobart, Australia, 4/12/2006. Sydney, Australia: Australian Computer Society.

  • Hamilton, N., Burrage, K., Ragan, M. A. and Huber, T. (2004). Protein contact prediction using patterns of correlation. 29th Annual Lorne Conference on Protein Structure and Function, Lorne, Victoria, 8-12 February 2004.

  • Hamilton, N, Hazel, D, Kearney, P, Traynor, O and Wildman, L (1998). A complete formal development using Cogito. 21st Australasian Computer Science Conference (ACSC 98), Perth Australia, Feb 04-06, 1998. SINGAPORE: SPRINGER-VERLAG SINGAPORE PTE LTD.

Other Outputs

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor

    Other advisors: