Director, Professor Matthew Bellgard


Contact Details

Office: Murdoch Campus, BITL Building, Room 3.06
Phone Number: +61 8 9360 6088
Fax Number: +61 8 9360 7238
Mailing Address: Centre for Comparative Genomics, Murdoch University, Perth WA 6150, Australia
E-Mail Address: mbellgard@ccg.murdoch.edu.au

Information

Qualifications

BSc (Computer Science/Information Technology, First Class Hons Computer Science) UWA, PhD UWA

Research Interests

Bioinformatics, Computational Molecular Biology, Molecular Evolution and DNA/Protein sequence analysis, Machine learning (Artificial Intelligence), Artificial Neural Networks, Genetics Algorithms and Fuzzy Logic, Reusable software components Computer Music, Data Mining, Education Psychology and Multimedia

Publications

Book Chapters/Articles in Books

  1. (2005) MI Bellgard. Bioinformatics from comparative genomic analysis through to integrated systems. A Ruvinsky and J Marshall-Graves (Eds). Mammalian Genomics, 393-409.
  2. (2005) MI Bellgard and T Gojobori. A Comparative Analysis of Mammalian Genomics: Prokaryote and Eukaryote Perspectives. A Ruvinsky and J Marshall-Graves (Eds). Mammalian Genomics, 263-278.
  3. (1999) MI Bellgard,T Itoh, H Watanabe, T Imanishi and T Gojobori. Dynamic Evolution of Genomes and the Concept of Genome Space, L.H. Caporale (Ed). Ann N Y Acad Sci 870, 293-300.
  4. (1999) MI Bellgard and CP Tsang. Harmonising Music the Boltzmann Way, N. Griffith & P.M. Todd (Eds.) In: Musical Networks: Parallel Distributed Perception & Performance, MIT Press, ISBN 0-262-07181-9, 261-277.

Fully Refereed Journal and Conference papers

  1. (2008) Nelson M, Boersma J, Chudy M, Lesniewska K, Ellwood S, Phan H, Moolhuijzen P, Bellgard M, Oliver R, Swiecicki W, Wolko B, Cowling W. A dense reference map of the Lupinus Angustifolius L. Genome: A foundation for building lupin genome research. 12th International Lupin Conference. Fremantle, Western Australia, 14-18 September 2008.
  2. (2008) Motro Y, Dunn D, La T, Phillips N, Hampson D, and Bellgard M. Intestinal Spirochaetes of the Genus Brachyspira Share a Partially Conserved 26 Kilobase Genomic Region with Enterococcus faecalis and Escherichia coli. Microbiology Insights. 2008 May 15; 1: 3-11.
  3. (2008) McNeil MD, Kota R, Lagudah E, Feuillet C, Dunn D, Bellgard M, Li D, McLean R, Kong X and Appels R. BAC-derived markers for assaying the stem rust resistance gene, Sr2, in wheat breeding programs. Molecular Breeding. 2008;22(1):15-24.
  4. (2008) Diepeveen, D., Armstrong, L., Clarke, P., Abrecht, D., Appels, R., Bellgard, M. Applying data mining tools to improve grain quality for growers. In Proc. 2008 Agribusiness Crop Updates: Cereal Updates". Perth, Western Australia. 2008:103-105.
  5. (2008) Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, ……. Bellgard M, ……. Tateno Y, Imanishi T, Gojobori T (full author list comprises 138 names). The H-Invitational Database (H-InvDB), a Comprehensive Annotation Resource for Human Genes and Transcripts. Nucleic Acid Research. (Database issue):D793-9.
  6. (2008) Kongsuwan K, Piper E, Bagnall N, Ryan K, Moolhuijzen P, Bellgard M, Lew A, Jackson L and Jonsson N (2008). Identification of genes involved with tick resistance in Bos taurus and Bos indicus. In Animal Genomics for Animal Health, Eds. Pinard M-H, Gay C, Pastoret P-P, Dodet B. Basel, Karger, 132 77-88.
  7. (2007) Hiew HL and Bellgard M. A bioinformatics reference model: towards a framework for developing and organising bioinformatics resources. In Proceedings of 2007 International Symposium on Computational Models for Life Sciences - CMLS'07, 10–12 December 2007, Gold Coast, Queensland, Australia.
  8. (2007) Hiew HL, Schibeci D, Fraser R, Rohl A, Hunter A and Bellgard M. The APAC Genome Annotation System: Enabling Life Science Research Through the Grid. In APAC07 Conference Proceedings, 8-12 October 2007, Perth, Western Australia.
  9. (2007) Diepeveen D, Clarke G, Bellgard M, Appels R and Crosbie G. Physical grain screenings of plant breeding germplasm. In Proceedings of the 1st Latin American Conference, ICC 2007, ICC International Conference on Cereal and Cereal Products. Quality and Safety. September 2007, Argentina.
  10. (2007) Lew AE, Guo S-Y, Venus B, Moolhuijzen P, Sanchez D, Trott D, Burrell P, Wlodek B and Bellgard M. Comparative genome analysis applied to develop novel PCR assays to characterise and identify Campylobacter fetus subsp. venerealis isolates. In Proceedings from the 14th International Workshop on Campylobacter, Helicobacter and Related Organsims, 2-5th September 2007. Zoonoses and Public Health 54 (Supplement 1), 154.
  11. (2007) Moolhuijzen P, Dunn DS, Bellgard M, Carter M, Jia J, Kong X, Gill BS, Feuillet C, Breen J, Appels R. Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium. Australian Journal of Agricultural Research. 2007; 58, 470-75.
  12. (2007) Greene WK, Sontani Y, Sharp MA, Dunn DS, Kees UR, Bellgard MI. A promoter with bidirectional activity is located between TLX1/HOX11 and a divergently transcribed novel human gene. Gene. 2007 Apr 15;391(1-2):223-32.
  13. (2006) Moolhuijzen P, Cakir M, Macgregor A, Smith C, Hunter A, Schibeci D, Francki M, Jones M, Appels R, Bellgard M. LegumeDB bioinformatics resource: Comparative genomic anlaysis and novel cross-genera marker identification in Lupin and pasture legume species. Genome 49(6), 689-699.
  14. (2006) Binnewies T, Motro Y, Hallin P, Lund O, Dunn D, La T, Hampson D, Bellgard M, Wassenaar T, Ussery D. Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Functional and Integrative Genomics 6(3), 165-185.
  15. (2006) Nelson M, Phan H, Ellwood S, Moolhuijzen P, Bellgard M, Hane J, Williams A, O'Lone C, Fosu-Nyarko J, Scobie M, Cakir M, Jones M, Ksiazkiewicz M, Wolko B, Barker S, Oliver R, Cowling W. The first gene-based map of Lupinus angustifolius L. - location of domestication genes and conserved synteny with Medicago truncatula. Theoretical and Applied Genetics 113(2), 225-238.
  16. (2006) Nelson,M., Phan,H.T., Ellwood,S., Moolhuijzen,P., Bellgard,M.I., Hane,J.K.,Williams,A.H., FosNyarko,J.*, Wolko,B., Ksiazkewicz,M., Cakir,M., Jones,M.G., Scobie,M.N., O'Lone,C.*, Barker,S.J.* & Cowling,W.A. The first genebased map of narrowleafed lupin location of domestication genes and conserved synteny with Medicago truncatula.Lupins and Pulses Updates, Perth, Australia, 2006:23-24.
  17. (2005) Lew A, Jackson L, Bellgard M. A Comparative genomic analysis of non-coding sequences and the application of RNA interference tools for bovine functional genomics. Australian Journal of Experimental Agriculture 45, 995-1010.
  18. (2005) Kulski J, Kenworthy W, Bellgard M, Taplin R, Okomoto K, Oka A. Gene expression profiling of Japanese psoriatic skin reveals an increase activity in molecular stress and immune response signals. J Mol Med. 11 November 2005.
  19. (2005) Dunn D, Romphruk A, Leelayuwat C, Bellgard M, Kulski J. Polymorphic Alu insertions and their associations with MHC class I alleles and haplotypes in the northeastern Thais. Ann Hum Genet. 2005 Jul;69(Pt4):364-72
  20. (2005) Nozaki Y, Macgregor A, Smith C, Hunter A, Bellgard M. Multidotter: Dot-Matrix Program for Multiple Sequences, The 2005 World Congress in Applied Computing, Las Vegas, Nevada, USA, June 20-23, 2005.
  21. (2005) Nozaki Y, Bellgard M. Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalities. Bioinformatics. 2005 April 15;21(8):1421-8. Epub 2004 December 10.
  22. (2005) Hunter A, Schibeci D, Hiew H L, Bellgard M. Grendel: A bioinformatics Web Service-based architecture for accessing HPC resources. Australasian Workshop on Grid Computing and e-Research. Newcastle, Australia, 2-3 February 2005.
  23. (2005) Bellgard M, Williams H, Smith C, Macgregor A, Hunter A, Appels R, Griffiths T. Grains composition and nutrition online database. Asia Pac J Clin Nutr. 2005;14 Suppl:S110.
  24. (2005) Appels R, Bellgard M. Looking through genomics-from the editors. Functional and Integrative Genomics, 2005 Jan;5(1):1-3.
  25. (2004) R Appels, M Francki, M Cakir and MI Bellgard. Looking through genomics: concepts and technologies for plant and animal genomics. Functional and Integrative Genomics, 4, 71-73.
  26. (2004) T Imanishi, T Itoh, Y Suzuki, ... MI Bellgard, ... N Nomura, T Gojobori, S Sugano (full author list comprises 152 names). Integrative Annotation of 21,037 Human Genes Validatd by Full-Length cDNA Clones. Public Library of Science (PLOS) - Biology, 2(6), 856-875.
  27. (2004) MI Bellgard, J Ye, T Gojobori and R Appels. The Bioinformatics challenges in comparative analysis of cereal genomes - an overview. Functional and Integrative Genomics, 4, 1-11.
  28. (2004) M Francki, M Carter, K Ryan, A Hunter, MI Bellgard and R Appels. Comparative organization of wheat homoeologous group 3S and 7L using wheat-rice synteny and identification of potential markers for genes controlling xanthophylls content in wheat. Functional and Integrative Genomics, 4, 118-130.
  29. (2004) C Li, P Ni, M Francki, A Hunter, Y Zhang, D Schibeci, H Li, A Tarr, J Wang, M Cakir, J Yu, MI Bellgard, R Lance and R Appels. Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison. Functional and Integrative Genomics, 4(2): 84-93.
  30. (2003) MI Bellgard, and W Kenworthy. FBSA: Feature-based pair-wise sequence alignment for very large sequences, Applied Bioinformatics, 2(3), 145-150.
  31. (2003) MI Bellgard, T Gamble, M Reynolds, A Hunter, E Trifonov and R Taplin, Gap Mapping: A paradigm for sequence alignment, Applied Bioinformatics,. 2(3 Suppl), S31-S35.
  32. (2003) MI Bellgard, A Hunter, B Kenworthy, Microarray Analysis Using Bioinformatics Analysis Audit Trails (BAATs), Special Issue:From Functional Genomics to Systems Biology, Proceedings of the French Academy of Sciences, CR Biologies, 326, 1083-1087.
  33. (2003) K Carter and MI Bellgard. MASV Multiple (BLAST) Annotation System Viewer, Bioinformatics, 19(17), 2313-2315.
  34. (2003) Y Kulski, E Lim, D Dunn and MI Bellgard. Genomic and phylogenetic analysis of the S100-A7 (psoriasin) gene duplications within the region of the S100 gene cluster on human chromosome 1q21. Journal of Molecular Evolution, J Mol Evol. Apr;56(4):397-406.
  35. (2001) MI Bellgard, D Schibeci, E Trifonov and T Gojobori. Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. Journal of Molecular Evolution, 53, 465-468.
  36. (2001) K Carter, A Oka, T Gen and MI Bellgard. Bioinformatics issues for automating the annotation of genomic sequences. Genome Informatics Workshop, Tokyo, Japan, Dec. 19-21, 2001.
  37. (2001) K Tsunoyama, MI Bellgard and T Gojobori. Intragenic variation of synonymous substitution rates is caused by nonrandom mutations at methylated CpG sites. Journal of Molecular Evolution, 53, 456-464.
  38. (2001) K Carter, D Schibeci and MI Bellgard. WWW issues for conducting sophisticated Bioinformatics analysis, Proceedings of the Seventh Australian WWW Conference, Sydney, 2001. [1].
  39. (2001) D Schibeci, R Potter, K Wathen-Dunn, M Jones and MI Bellgard. Applying Artificial Neural Networks to the Classification of Wheat Varieties Processed Via MALDI-TOF Mass Spectrometry. Proceedings of the Neural Networks Applications (NNA'01), Tenerife, Canary Islands.
  40. (2001) O Lamont, HH Liang and MI Bellgard. Data Representation Influences Protein Secondary Structure Prediction using Artificial Neural Networks. Australia and New Zealand Intelligent Information Systems Conference, ANZIIS, Perth, The University of Western Australia 411-415.
  41. (2000) MI Bellgard, D Schibeci, T Gojobori and HL Hiew. An Information System for Whole Genome Data. Proceedings of the Second Western Australian Workshop on Information Systems Research (WAWISR), Perth, Murdoch University, Perth, Australia, pp 151-155.
  42. (1999) MI Bellgard and R Taplin. Why A Window-based Learning Algorithm Using an Effective Boltzmann Machine is Superior to the Original BM Learning Algorithm. 6th International Conference on Neural Information Processing (ICONIP'99), Perth, 16-20 Nov, 896-902.
  43. (1999) MI Bellgard, HL Hiew, A Hunter & M Wiebrands. ORBIT: an integrated environment for user customised bioinformatics tools. Bioinformatics 15/10, 847-851.
  44. (1999) MI Bellgard and T Gojobori. Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content. Gene 238/1, 33-37.
  45. (1999) MI Bellgard and T Gojobori. Inferring the Direction of Evolutionary Changes of Genomic Base Composition. Trends Genet 15/7, 254-256.
  46. (1999) MI Bellgard and T Gojobori. Identification of a Ribonuclease H Gene in both Mycoplasma genitalium and Mycoplasma pneumoniae by a New Method for Exhaustive Identification of ORFs in the Complete Genome Sequences. FEBS Letts 445/1, 6-8.
  47. (1999) CE Herbison, DC Sayer, MI Bellgard, RJ Allcock, FT Christiansen, P Price. Structure and polymorphism of two stress-activated protein kinase genes centromeric of the MHC: SAPK2a and SAPK4. DNA Seq 10/4-5, 229-243.
  48. (1999) HL Hiew, D Schibeci and MI Bellgard. Visualising the Evolutionary Dynamics of Molecular Sequence Data Using Self Organizing Feature Maps. Proceedings of the Third Australia-Japan Joint Workshop on Intelligent and Evolutionary Systems, Canberra, 23-25 Nov, 246-250.
  49. (1998) MI Bellgard, GK Tay, HL Hiew, CS Witt, N Ketheesan, FT Christiansen, RL Dawkins. MHC Haplotype Analysis by Artificial Neural Networks. Human Immunology 59, 56-62. Abstract
  50. (1997) JY Kulski, S Gaudieri, MI Bellgard, L Balmer, K Giles, RL Dawkins. The Evolution of MHC Diversity by Segmental Duplication and Transposition of Retroelements. J. Mol. Evol. 45/7, 599-609. Abstract
  51. (1996) MI Bellgard and CP Tsang. On the Use of an Effective Boltzmann Machine for Musical Style Recognition and Harmonisation. Proceedings of the International Computer Music Conference, 1CMC'96, Hong Kong, Sep.
  52. (1995) MI Bellgard and CP Tsang. Using an Effective Boltzmann Machine to Learn Context Dependencies of a Sequence. Proceedings of the 1995 IEEE International Conference on Neural Networks (ICNN'95), Perth, Nov.
  53. (1995) MW Dixon, MI Bellgard and GR Cole. A Neural Network Algorithm to Solve the Routing Problem in Communication Networks. International Workshop on Applications of Neural Networks to Telecommunications (IWANNT'95), Stockholm, May 22-24.
  54. (1995) MW Dixon, GR Cole and MI Bellgard. A Neural Network Shortest Path Algorithm for Routing in Packet-switched Communication Networks. ICC'95 Communications - Gateway to Globalisation, Seattle, June 18-22.
  55. (1995) MW Dixon, GR Cole and MI Bellgard. Using the Hopfield Model with Mean-Field Annealing to Solve the Routing Problem in a Communication Network. Proceedings of the 1995 IEEE International Conference on Neural Networks (ICNN'95), Perth, Nov.
  56. (1995) MW Dixon, GR Cole and MI Bellgard. Using the Hopfield Model with Mean-Field Annealing to Solve the Routing Problem in Packet-Switched Communication Networks. Proceedings of the 1995 IEEE International Conference on Systems, Man and Cybernetics, Vancouver, Canada, Oct.
  57. (1994) MI Bellgard and CP Tsang. Harmonising Music the Boltzmann Way. Connection Science 6, 281-297.
  58. (1992) MI Bellgard and CP Tsang. Harmonising Music Using a Network of Boltzmann Machines. Proceedings of Fifth International Conference of Artificial Neural Networks and their Applications (Neuro-Nimes`92), EC2, Nimes, France, 321-332, Nov.
  59. (1991) MI Bellgard and CP Tsang. Some Experiments on the Use of Genetic Algorithms in a Boltzmann Machine. Proceedings of the International Joint Conference of Artificial Neural Networks (IJCNN`91), Singapore, 2645-2652.
  60. (1990) CP Tsang and MI Bellgard. Sequence Generation Using a Network of Boltzmann Machines. Proceedings of the 4th Australian Joint Conference on Artificial Intelligence (AI`90), World Scientific, Perth, 224-233.

Reports

  1. (1995) W Power and MI Bellgard. UPREP for Windows Manual. CSIRO Division of Exploration and Mining Report.

Abstracts in Conference Proceedings

  1. (1999) D Sayer, C Herbison, MI Bellgard, P Price, FT Christiansen. Genomic structure, localisation, and polymorphism studies of SAP2a and SAPK4. Abstracts of the Human Genome Meeting (HGM99), Brisbane, Mar 27-30.
  2. (1999) MI Bellgard and T Gojobori. Evolutionary change of the GC content after speciation. Abstracts of International Symposium on Evolutionary Genomics, ISME'99, Puntarenas, Costa Rica, Jan 11-15, p29.
  3. (1999) K Tsunoyama, MI Bellgard and T Gojobori. Intragenic variation of synonymous substitution rates and its evolutionary implication. Abstracts of International Symposium on Evolutionary Genomics, ISME'99, Puntarenas, Costa Rica, Jan 11-15, p38.
  4. (1998) K Tsunoyama, MI Bellgard and T Gojobori. Evolutionary pattern of genes revealed by intragenic variation of synonymous substitution rates. 70th Annual Meeting of the Genetics Society of Japan, Sapporo, Japan, Sept 23-25, p82.
  5. (1997) JY Kulski, S Gaudieri, MI Bellgard, L Balmer, and RL Dawkins. Segmental duplication and transposition of retroelements in the evolution of MHC class I genes. Abstracts of International Conference on Molecular Biology and Evolution, 5th SMBE, Garmisch-Partenkirchen, Bavaria, Germany, June 1-4, G17, p60.
  6. (1996) MI Bellgard, GK Tay, F Purnomo and RL Dawkins. Using a Machine Learning Technique to Prospectively Match Donor and Recipient Pairs for Bone Marrow Transplantation. Intelligent Systems for Molecular Biology '96, Washington University, St Louis, Missouri, USA, June 12-15.
  7. (1996) MI Bellgard, GK Tay, F Purnomo and RL Dawkins. Identifying Features from MHC Block Matching Profiles. '96 Bioinformatics & Genome Research, Baltimore, Maryland, USA, June 10-11.
  8. (1996) MI Bellgard, GK Tay, F Purnomo and RL Dawkins. Identifying Features from MHC Block Matching Scans Using Artificial Intelligence. Human Genome Meeting '96, HUGO '96,Heidelberg, Germany, March 22-24.
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