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Dr Nicholas Hamilton

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

Grants

View all Grants

Supervision

  • Deep learning methodologies for assistive diagnosis in skin cancer imaging

    Doctor Philosophy

  • Integrating multi-modal omics, single cell sequencing and histological imaging data with deep neural networks to study tissue heterogeneity

    Doctor Philosophy

  • Dynamics of SOX18 protein-protein interactions during the transcriptional control of endothelial cell differentiation

    Doctor Philosophy

View all Supervision

Publications

Book Chapter

  • Image-based analysis of phagocytosis: measuring engulfment and internalization

    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

  • An Introduction to Protein contact Prediction

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

  • Analyzing real-time video microscopy: the dyamics and geometry of vescicles and tubules in endocytosis

    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. In Bonifacio, J. S., Dasso, M., Harford, J. B., Lippincott-Schwartz, J. and Yamada K. M. (Ed.), Current Protocols in Cell Biology 35 ed. (pp. 4.16.1-1.16.11) Hoboken, NJ United States: John Wiley & Sons. doi:10.1002/0471143030.cb0416s35

  • Computer-intensive simulations for cellular models

    Burrage, K., Burrage,P. M., Hamilton, N. and Tian, T (2006). Computer-intensive simulations for cellular models. In Albert Y Zomaya (Ed.), Parallel Computing in Bioinformatics and Computational Biology 1 ed. (pp. 79-119) New Jersey, USA: John Wiley & Sons.

Journal Article

Conference Publication

  • Predicting blood-brain barrier permeability of marine-derived kinase inhibitors

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

  • An integrated cell, tissue and whole organ profile of kidney morphogenesis

    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. In: 18th International Congress of Developmental Biology, Singapore Singapore, (S152-S153). Jun 18-22, 2017. doi:10.1016/j.mod.2017.04.432

  • Anillin dependent stabilization of Rho signaling at adherens junctions influences cell extrusion and collective cell migration

    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. In: ASCB/EMBO Meeting, Philadelphia Pa United States, (). 2-6 December 2017.

  • Patterning Rho signaling at the epithelial Zonula Adherens: a tale of feedback loops

    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. In: Molecular Biology of the Cell. 2015 Cell Biology ASCB Annual Meeting, San Diego CA, United States, (). 12-16 December 2015.

  • Disruption of cortical tension patterning drives the outgrowth of oncogenic cells

    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. In: EACR-23: 23rd Biennial Congress of the European Association for Cancer Research, Munich, Germany, (S67-S67). 5-8 July 2014. doi:10.1016/S0959-8049(14)50251-1

  • Parkinson's Disease Causing Mutations Alters Retromer's Function

    Follett, J., Norwood, S., Hamilton, N., Collins, B., Bugarcic, A. and Teasdale, R. D. (2014). Parkinson's Disease Causing Mutations Alters Retromer's Function. In: ASCB Annual Meeting Abstracts. ASCB/IFCB Meeting, Philadelphia, PA United States, (). 06 - 10 December 2014.

  • An Integrated Cell, Tissue and Whole Organ Profile of Kidney Morphogenesis

    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. In: 49th Annual Scientific Meeting of the Australian and New Zealand Society of Nephrology, Brisbane Australia, (24-24). 9-11 September 2013. doi:10.1111/nep.12121

  • Linear models for endocytic transformations from live cell imaging

    Belward, John A., Burrage, Kevin, Teasdale, Rohan D. and Hamilton, Nicholas A. (2011). Linear models for endocytic transformations from live cell imaging. In: William McLean and Tony Roberts, Proceedings of the 15th Computational Techniques and Applications Conference. CTAC2010 : 15th Biennial Computational Techniques and Applications Conference, Univeristy of New South Wales, Sydney, Australia, (C156-C171). 28 November - 1 December 2010. doi:10.0000/anziamj.v52i0.3801

  • A GPU implementation of fast parallel Markov clustering in Bioinformatics using ELLPACK-R sparse data format

    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. In: Juan E. Guerrero, Proceedings of the 2nd International Conference on Advances in Computing, Control and Telecommunication Technologies. ACT 2010, Jakarta, Indonesia, (173-175). 2 - 3 December, 2010. doi:10.1109/ACT.2010.10

  • Fast parallel Markov clustering in bioinformatics using massively parallel graphics processing unit computing

    Bustamam, Alhadi, Burrage, Kevin and Hamilton, Nicholas A. (2010). Fast parallel Markov clustering in bioinformatics using massively parallel graphics processing unit computing. In: Joint PDMC+HiBi Workshop 2010: 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification; and Second International Workshop on High Performance Computational Systems Biology. Proceedings. 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, (116-125). 30 September-1 October 2010. doi:10.1109/PDMC-HiBi.2010.23

  • An efficient parallel implementation of Markov clustering algorithm for large-scale protein-protein interaction networks that uses MPI

    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. In: I. M. Arnawa, M. Muhafzan and S. Bahri, Proceedings of the 5th IMT-GT international conference on mathematics, statistics and their applications 2009 (ICMSA 2009). 5th IMT-GT international conference on mathematics, statistics and their applications, Bukittinggi, Indonesia, (94-101). 9 -11 June 2009.

  • Automated subcellar phenotype classification : An introduction and recent results

    Hamilton, A, Pantelic, S, Hanson,, Fink, L, Karunaratne, M and Teasdale, R D (2006). Automated subcellar phenotype classification : An introduction and recent results. In: Mikael Boden and Timothy Bailey, Conferences in research and practice in information technology online. 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006). 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006), Hobart, Australia, (67-72). 4/12/2006.

  • Protein contact prediction using patterns of correlation

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

  • A complete formal development using Cogito

    Hamilton, N, Hazel, D, Kearney, P, Traynor, O and Wildman, L (1998). A complete formal development using Cogito. In: McDonald, C, Proceedings of the 21st Australasian Computer Science Conference, Acsc'98. 21st Australasian Computer Science Conference (ACSC 98), Perth Australia, (319-330). Feb 04-06, 1998.

Other Outputs

PhD and MPhil Supervision

Current Supervision

  • Deep learning methodologies for assistive diagnosis in skin cancer imaging

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Integrating multi-modal omics, single cell sequencing and histological imaging data with deep neural networks to study tissue heterogeneity

    Doctor Philosophy — Associate Advisor

    Other advisors:

  • Dynamics of SOX18 protein-protein interactions during the transcriptional control of endothelial cell differentiation

    Doctor Philosophy — Associate Advisor

    Other advisors:

This staff member is a UQ Expert for media in the following fields:

Mathematical Modelling, Data Visualisation, Kidney Development, Bio-Imaging, Machine Learning, Cancer Imaging, Hacky Hour

They are happy to lend their expertise to your articles or broadcasts and share their research discoveries and insights with the community via media channels.

For additional assistance with story ideas, general advice and information or help with seeking further experts, please email the UQ Media Team or telephone (07) 3365 1120.

Links

ResearcherID: A-6033-2010

ORCID: 0000-0003-0331-3427

Scopus ID: 7101846142

Google Scholar ID: K6iJYakAAAAJ

Personal Profile: Link

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