Overview

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

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

TEASDALE, R.D. and HAMILTON, N. Imaging the future: managing the exponential growth in cell image data. Australian Biochemist, in press.

BURRAGE, K., HOOD, L. and RAGAN, M.A. Advanced computing for systems biology. Briefings in Bioinformatics, Advance Access, published 25 Sept. 2006

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

T RICHTER, M FLOETENMEYER, C FERGUSON, J GALEA, J GOH, MR LINDSAY, GP MORGAN, BJ MARSH and RG PARTON. (2008) High-resolution 3D quantitative analysis of caveolar ultrastructure and caveola- cytoskeleton interactions. Traffic. doi: 10.1111/j.1600-0854.2008.00733.x

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 7:613-25.

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

AN, J., YU, J.X., RATANAMAHATANA, C.A. & CHEN, Y-P.P. (2006) A dimensionality reduction algorithm and its application for interactive visualization. Journal of Visual Languages and Computing, Elsevier (in press, accepted March 2006).

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 (in press)

HAMILTON, N., KERR, M.C., BURRAGE, K. & TEASDALE, R.D. (2006) 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. (in press)

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(1):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. J Struct Biol. 2006 Sep;155(3):395-408.