Publications

Overview

WALTER, T., SHATTUCK, D., BALDOCK, R., BASTIN, M., CARPENTER, A.E., DUCE, S., ELLENBERG, J., FRASER, A., HAMILTON, N.A., PIEPER, S., RAGAN, M.A., SCHNEIDER, J., TOMANCAK, P., and HERICHE, J-K. (2010). Visualization of image data from cells to organisms. Nature Methods 7: S26-S41.

BURRAGE, K., HOOD, L. and RAGAN, M.A. (2006). Advanced computing for systems biology. Briefings in Bioinformatics 7: 390-398.

MARSH, B.J. (2006). Toward a "Visible Cell"... and beyond. Australian Biochemist 37:5-10.

TEASDALE, R.D. and HAMILTON, N. (2006). Imaging the future: managing the exponential growth in cell image data. Australian Biochemist 37: 16-20.

HUNTER, J., RAGAN, M.A., and LITTLE, S. Position Paper for Semantic Web Life Sciences Workshop, 27 Oct. 2004, Available online here.

Experimental Data

NOSKE, A.B., COSTIN, A.J., MORGAN, G.P., and MARSH, B.J. (2008). Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets. Journal of Structural Biology 161: 298–313.

MARSH, B.J. (2006). Reconstructing mammalian membrane architecture by large area cellular tomography. Methods in Cell Biology 79C:193-220.

VAN DER HEIDE, P., XU, X., MARSH, B.J., HANEIN, D., and VOLKMANN, N. (2007). Efficient automatic noise reduction of electron tomographic reconstructions based on iterative median filtering. Journal of Structural Biology 158: 196-204.

RICHTER, T., FLOETENMEYER, M., FERGUSON, C., GALEA, G., GOH, J., LINDSAY, M.R., MORGAN, G.P., MARSH, B.J., and PARTON, R.G. (2008). High-resolution 3D quantitative analysis of caveolar ultrastructure and caveola- cytoskeleton interactions. Traffic 9: 893-909.

Ontologies and Data Management/Integration

FINK, J.L., ATURALIYA, R.N., DAVIS, M.J., ZHANG, F., HANSON, K., TEASDALE, M.S., KAI, C., KAWAI, J., CARNINCI, P., HAYASHIZAKI, Y. & TEASDALE, R.D. (2006). LOCATE: A mouse protein subcellular localization database. Nucleic Acids Research 34(Database issue): D213-7.

ATURALIYA, R.N., FINK, J.L., DAVIS, M.J., TEASDALE, M.S., HANSON, K.A., MIRANDA, K.C., FORREST, A.R.R., GRIMMOND, S.M., SUZUKI, H., KANAMORI, M., KAI,C., KAWAI, J., CARNINCI, P., YOSHIHIDE HAYASHIZAKI, Y. & TEASDALE, R.D. (2006). Subcellular localisation of mammalian type II membrane proteins. Traffic 7: 613-625.

GARCIA, A., RAGAN, M.A. & CHEN, Y-P.P. (2005). Information integration in molecular bioscience: a review. Applied Bioinformatics 4:157-173.

CHEN, Y-P. P., & COLOMB, B.M. (2003). Database technologies for L-system simulations in virtual plant applications on bioinformatics. International Journal of Knowledge and Information Systems 5: 288-314.

CHEN, Y-P. P. & HANAN, J. (2002). Partial automation of database processing of simulation outputs from L-systems models of plant morphogenesis, BioSystems. (Journal of Biological and Information Processing Sciences), 65(2-3): 187-197.

CHEN, Q., CHEN, Y-P. P. & ZHANG, C. (2006). Detecting inconsistency in biological molecular databases using ontology. Data Mining and Knowledge Discovery (Accepted November 2005).

STANLEY, S., BAILEY, T.C. & MATTICK, J.S. (2006). GONOME: measuring correlations between GO terms and genomic positions. BMC Bioinformatics 7: 94.

LIN, X., LIU, Q., YUAN, Y. & ZHOU, X. (2003). Multiscale histograms: summarizing topological relations in large spatial datasets. In: Proceedings of 29th International Conference on Very Large Data Bases, September 9-12, 2003, Berlin, Germany (VLDB 2003), Berlin, Sept 2003, pp. 814-825 (J.C. Freytag et al., Eds) Morgan Kaufmann. ISBN 0- 12-722442-4.

PRASHER, S. & ZHOU, X. (2003). Efficient update and retrieval of objects in a multiresolution geospatial database. In: Proceedings of the 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003), Cambridge, MA, USA, 9- 11 July 2003, pp.193-201,. IEEE Computer Society Press. ISBN 0-7695-1964-4.

ZHOU, X., TRUFFET, D. & HAN, J. (1999). Efficient polygon amalgamation methods for spatial OLAP and spatial data mining. In: Proceedings of the 6th International Symposium on Large Spatial Databases (SSD'99), Hong Kong, 22-23 July 1999, pp. 167-187. (R.H. Güting, D. Papadias and F.H. Lochovsky, Eds) Lecture Notes in Computer Science 1651:167-187. Springer-Verlag.

Modelling and Visualisation and Image Processing

HAMILTON, N.A. (2009). Quantification and its applications in fluorescent microscopy imaging. Traffic 10: 951-961.

HAMILTON, N.A., WANG, J.T., KERR, M.C., and TEASDALE, R.D. (2009). Statistical and visual differentiation of subcellular imaging. BMC Bioinformatics 10:94.

MCCOMB, T., CAIRNCROSS, O., NOSKE, A.B., WOOD, D.L., MARSH, B.J., AND RAGAN, M.A. (2009). Illoura: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. Bioinformatics. 25: 1208-1210.

WOODCROFT, B., HAMMOND, L., STOW, J., and HAMILTON, N.A. (2009). Automated organelle-based colocalisation in whole-cell imaging. Cytometry A 75: 941-950.

AN, J., YU, J.X., RATANAMAHATANA, C.A. & CHEN, Y-P.P. (2007). A dimensionality reduction algorithm and its application for interactive visualization. Journal of Visual Languages and Computing 18: 48-70.

KERR, M., LINDSAY, M., LUETTERFORST, R., HAMILTON, N., SIMPSON, F., PARTON, R., GLEESON, P.A. & TEASDALE, R.D. (2006). Visualisation of macropinosome maturation by the recruitment of sorting nexins. Journal of Cell Science 119: 3967-3980.

HAMILTON, N., KERR, M.C., BURRAGE, K. & TEASDALE, R.D. (2007). Analysing real-time video microscopy: the dynamics and geometry of vesicles and tubules in endocytosis. In: Current Protocols in Cell Biology (K. Morgan, Ed.) Wiley Interscience. June 2007.

NICOLAU, JR, D., BURRAGE, K., PARTON, R.G., & HANCOCK, J. (2006). Optimal microdomain characteristics for nano-scale protein-protein interactions. Molecular and Cellular Biology 26: 313-323.

BURRAGE, K., TIAN, T. & BURRAGE, P. (2004). A multi-scaled approach for chemical reaction systems modelling cellular and tissue function. Progress in Biophysics and Molecular Biology, (N.P. Smith and E.J. Crampin, Eds), 85:217-234.

BALDWIN, N.E., CHESLER, E.J., KIROV, S., LANGSTON, M.A., SNODDY, J.R., WILLIAMS, R.W. & ZHANG, B. (2005). Computational, integrative and comparative methods for the elucidation of genetic co-expression networks. Journal of Biomedicine and Biotechnology 2:172-180.

PANTELIC, R.S., ROTHNAGEL, R., HUANG, C.Y., MULLER, D., WOOLFORD, D., LANDSBERG, M.J., McDOWALL, A., PAILTHORPE, B., YOUNG, P.R., BANKS, J., HANKAMER, B. & ERICKSSON, G. The discriminative bilateral filter: An enhanced denoising filter for electron microscopy data. Journal of Structural Biology 155: 395-408.

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