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Journal Article

Bellgard, M., Beroud, C., Parkinson, K., Harris, T., Ayme, S., Baynam, G., Weeramanthri, T., Dawkins, H. and Hunter, A. (2014) Correction: Dispelling myths about rare disease registry system development. Source Code for Biology and Medicine, 9 (1).

Yang, Y., Zhao, H., Barrero, R.A., Zhang, B., Sun, G., Wilson, I.W., Xie, F., Walker, K.D., Parks, J.W., Bruce, R., Guo, G., Chen, L., Zhang, Y., Huang, X., Tang, Qi, Liu, H., Bellgard, M.I., Qiu, D., Lai, J. and Hoffman, A. (2014) Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431. BMC Genomics, 15 (1).

Bellgard, M.I., Sleeman, M.W., Guerrero, F.D., Fletcher, S., Baynam, G., Goldblatt, J., Rubinstein, Y., Bell, C., Groft, S., Barrero, R., Bittles, A.H., Wilton, S.D., Mason, C.E. and Weeramanthri, T. (2014) Rare disease research roadmap: Navigating the bioinformatics and translational challenges for improved patient health outcomes. Health Policy and Technology . In Press.

Bellgard, M.I., Render, L., Radochonski, M. and Hunter, A. (2014) Second generation registry framework. Source Code for Biology and Medicine, 9 (1).

Mayer, K.F.X., Rogers, J., Dole el, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A.J., Sourdille, P., Endo, T.R., Kubalakova, M., Ihalikova, J., Dubska, Z., Vrana, J., Perkova, R., Imkova, H., Febrer, M., Clissold, L., McLay, K., Singh, K., Chuneja, P., Singh, N.K., Khurana, J., Akhunov, E., Choulet, F., Alberti, A., Barbe, V., Wincker, P., Kanamori, H., Kobayashi, F., Itoh, T., Matsumoto, T., Sakai, H., Tanaka, T., Wu, J., Ogihara, Y., Handa, H., Maclachlan, P.R., Sharpe, A., Klassen, D., Edwards, D., Batley, J., Olsen, O-A, Sandve, S.R., Lien, S., Steuernagel, B., Wulff, B., Caccamo, M., Ayling, S., Ramirez-Gonzalez, R.H., Clavijo, B.J., Wright, J., Pfeifer, M., Spannagl, M., Martis, M.M., Mascher, M., Chapman, J., Poland, J.A., Scholz, U., Barry, K., Waugh, R., Rokhsar, D.S., Muehlbauer, G.J., Stein, N., Gundlach, H., Zytnicki, M., Jamilloux, V., Quesneville, H., Wicker, T., Faccioli, P., Colaiacovo, M., Stanca, A.M., Budak, H., Cattivelli, L., Glover, N., Pingault, L., Paux, E., Sharma, S., Appels, R., Bellgard, M., Chapman, B., Nussbaumer, T., Bader, K.C., Rimbert, H., Wang, S., Knox, R., Kilian, A., Alaux, M., Alfama, F., Couderc, L., Guilhot, N., Viseux, C., Loaec, M., Keller, B. and Praud, S. (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, 345 (6194). p. 1251788.

Appels, R., Barrero, R. and Bellgard, M. (2013) Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals. Functional & Integrative Genomics, 13 (1). pp. 1-9.

Bellgard, M., Taplin, R., Chapman, B., Livk, A., Wellington, C., Hunter, A. and Lipscombe, R. (2013) Classification of fish samples via an integrated proteomics and bioinformatics approach. Proteomics, 13 (21). pp. 3124-3130.

Bellgard, M., Beroud, C., Parkinson, K., Harris, T., Ayme, S., Baynam, G., Weeramanthri, T., Dawkins, H. and Hunter, A. (2013) Dispelling myths about rare disease registry system development. Source Code for Biology and Medicine, 8 (1). p. 21.

Moolhuijzen, P.M., Manners, J.M., Wilcox, S.A., Bellgard, M.I. and Gardiner, D.M. (2013) Genome sequences of six Wheat-infecting fusarium species isolates. Genome Announcements, 1 (5). e00670-13.

Coghlan, M.L., White, N.E., Murray, D.C., Houston, J., Rutherford, W., Bellgard, M.I., Haile, J. and Bunce, M. (2013) Metabarcoding avian diets at airports: implications for birdstrike hazard management planning. Investigative Genetics, 4 (1).

Baynam, G.S., Walters, M., Dawkins, H., Bellgard, M., Halbert, A.R. and Claes, P. (2013) Objective monitoring of mTOR inhibitor therapy by Three-Dimensional facial analysis. Twin Research and Human Genetics, 16 (4). pp. 840-844.

Chapman, B., Castellana, N., Apffel, A., Ghan, R., Cramer, G.R., Bellgard, M., Haynes, P.A. and Sluyter, S.C. (2013) Plant proteogenomics: From protein extraction to improved gene predictions. Methods in Molecular Biology, 1002 . pp. 267-294.

Rodriguez-Valle, M., Moolhuijzen, P., Piper, E.K., Weiss, O., Vance, M., Bellgard, M. and Lew-Tabor, A. (2013) Rhipicephalus microplus lipocalins (LRMs): Genomic identification and analysis of the bovine immune response using in silico predicted B and T cell epitopes. International Journal for Parasitology, 43 (9). pp. 739-752.

Hammond, E., Watts, G.F., Rubinstein, Y., Farid, W., Livingston, M., Knowles, J.W., Lochmüller, H., Bellgard, M. and Dawkins, H.J.S. (2013) Role of international registries in enhancing the care of familial hypercholesterolaemia. International Journal of Evidence-Based Healthcare, 11 (2). pp. 134-139.

Murray, D.C., Haile, J., Dortch, J., White, N.E., Haouchar, D., Bellgard, M.I., Allcock, R.J., Prideaux, G.J. and Bunce, M. (2013) Scrapheap Challenge: A novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages. Scientific Reports, 3 .

Appels, R., Barrero, R. and Bellgard, M. (2012) Advances in biotechnology and linking outputs to variation in complex traits: Plant and Animal Genome meeting January 2012. Functional & Integrative Genomics, 12 (1). pp. 1-9.

Bellgard, M.I. and Bellgard, S.E. (2012) A Bioinformatics Framework for plant pathologists to deliver global food security outcomes. Australasian Plant Pathology, 41 (2). pp. 113-124.

Edwards, D., Wilcox, S., Barrero, R.A., Fleury, D., Cavanagh, C.R., Forrest, K.L., Hayden, M.J., Moolhuijzen, P., Keeble-Gagnère, G., Bellgard, M.I., Lorenc, M.T., Shang, C.A., Baumann, U., Taylor, J.M., Morell, M.K., Langridge, P., Appels, R. and Fitzgerald, A. (2012) Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnology Journal, 10 (6). pp. 703-708.

Mappley, L.J, Black, M.L., AbuOun, M., Darby, A.C., Woodward, M.J., Parkhill, J., Turner, A., Bellgard, M.I., La, T., Phillips, N.D., La Ragione, R.M. and Hampson, D.J. (2012) Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity. BMC Genomics, 13 (1). p. 454.

Coghlan, M.L., Haile, J., Houston, J., Murray, D.C., White, N.E., Moolhuijzen, P., Bellgard, M.I. and Bunce, M. (2012) Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns. PLoS Genetics, 8 (4). e1002657.

Webster, H., Keeble-Gagnère, G., Dell, B., Fosu-Nyarko, J., Mukai, Y., Moolhuijzen, P., Bellgard, M., Jia, J., Kong, X., Feuillet, C., Choulet, F., International Wheat Genome Sequencing Consortium, and Appels, R. (2012) Genome-level identification of cell wall invertase genes in wheat for the study of drought tolerance. Functional Plant Biology, 39 (7). pp. 569-579.

Murray, D.C., Pearson, S.G., Fullagar, R., Chase, B.M., Houston, J., Atchison, J., White, N.E., Bellgard, M.I., Clarke, E., Macphail, M., Gilbert, M.T.P., Haile, J. and Bunce, M. (2012) High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens. Quaternary Science Reviews, 58 . pp. 135-145.

Rodrigues, M., Hammond-Tooke, G., Kidd, A., Love, D., Patel, R., Dawkins, H., Bellgard, M. and Roxburgh, R. (2012) The New Zealand neuromuscular disease registry. Journal of Clinical Neuroscience, 19 (12). pp. 1749-1750.

Hunter, A.A., Macgregor, A.B., Szabo, T., Wellington, C. and Bellgard, M.I. (2012) Yabi: An online research environment for grid, high performance and cloud computing. Source Code for Biology and Medicine, 7 (1). p. 1.

Black, M., Moolhuijzen, P., Chapman, B., Barrero, R., Howieson, J., Hungria, M. and Bellgard, M. (2012) The genetics of symbiotic nitrogen fixation: Comparative genomics of 14 rhizobia strains by resolution of protein clusters. Genes, 3 (1). pp. 138-166.

Bellgard, M.I., Macgregor, A., Janon, F., Harvey, A., O'Leary, P., Hunter, A. and Dawkins, H. (2012) A modular approach to disease registry design: Successful adoption of an internet-based rare disease registry. Human Mutation, 33 (10). E2356-E2366.

McCooke, J.K., Appels, R., Barrero, R.A., Ding, A., Ozimek-Kulik, J.E., Bellgard, M.I., Morahan, G. and Phillips, J.K. (2012) A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8. BMC Genomics, 13 (1). p. 393.

Keeble-Gagnère, G., Nyström-Persson, J., Bellgard, M.I. and Mizuguchi, K. (2012) An open framework for extensible multi-stage bioinformatics software. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7632 (7632). pp. 106-117.

Bellgard, M.I., Moolhuijzen, P.M., Guerrero, F.D., Schibeci, D., Rodriguez-Valle, M., Peterson, D.G., Dowd, S.E., Barrero, R., Hunter, A., Miller, R.J. and Lew-Tabor, A.E. (2011) CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus. International Journal for Parasitology, 42 (2). pp. 161-169.

Murray, D.C., Bunce, M., Cannell, B.L., Oliver, R., Houston, J., White, N.E., Barrero, R.A., Bellgard, M.I. and Haile, J. (2011) DNA-based faecal dietary analysis: A comparison of qPCR and high throughput sequencing approaches. PloS one, 6 (10). e25776.

Barrero, R.A., Chapman, B., Yang, Y., Moolhuijzen, P., Keeble-Gagnère, G., Zhang, N., Tang, Q., Bellgard, M.I. and Qiu, D. (2011) De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes. BMC Genomics, 12 (1). p. 600.

Barrero, R.A., Bellgard, M. and Zhang, X. (2011) Diverse approaches to achieving grain yield in wheat. Functional & Integrative Genomics, 11 (1). pp. 37-48.

La, T., Phillips, N.D., Wanchanthuek, P., Bellgard, M.I., O'Hara, A.J. and Hampson, D.J. (2011) Evidence that the 36kb plasmid of Brachyspira hyodysenteriae contributes to virulence. Veterinary Microbiology, 153 (1-2). pp. 150-155.

Barrero, R.A., Keeble-Gagnère, G., Zhang, B., Moolhuijzen, P., Ikeo, K., Tateno, Y., Gojobori, T., Guerrero, F.D., Lew-Tabor, A. and Bellgard, M. (2011) Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus. BMC Genomics, 12 (1). Article No. 328.

Lew-Tabor, A.E., Kurscheid, S., Barrero, R., Gondro, C., Moolhuijzen, P.M., Rodriguez Valle, M., Morgan, J.A.T., Covacin, C. and Bellgard, M.I. (2011) Gene expression evidence for off-target effects caused by RNA interference-mediated gene silencing of Ubiquitin-63E in the cattle tick Rhipicephalus microplus. International Journal for Parasitology, 41 (9). pp. 1001-1014.

She, M., Ye, X., Yan, Y., Howit, C., Bellgard, M. and Ma, W. (2011) Gene networks in the synthesis and deposition of protein polymers during grain development of wheat. Functional & Integrative Genomics, 11 (1). pp. 23-35.

Appels, R., Adelson, D.L., Moolhuijzen, P., Webster, H., Barrero, R. and Bellgard, M. (2011) Genome studies at the PAG 2011 conference. Functional & Integrative Genomics, 11 (1). pp. 1-11.

Wang, K., Gao, L., Wang, S., Zhang, Y., Li, X., Zhang, M., Xie, Z., Yan, Y., Bellgard, M. and Ma, W. (2011) Phylogenetic relationship of a new class of LMW-GS genes in the M genome of Aegilops comosa. Theoretical and Applied Genetics, 122 (7). pp. 1411-1425.

Sinha, S., Black, M.L., Agarwal, S., Das, R., Bittles, A.H. and Bellgard, M. (2011) ThalInd, a β-thalassemia and hemoglobinopathies database for India: defining a model country-specific and disease-centric bioinformatics resource. Human Mutation, 32 (8). pp. 887-893.

Moolhuijzen, P.M., Lew-Tabor, A.E., Morgan, J.A.T., Valle, M.R., Peterson, D.G., Dowd, S.E, Guerrero, F.D., Bellgard, M.I. and Appels, R. (2011) The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones. BMC Research Notes, 4 (1). p. 254.

Appels, R., Barrero, R., Keeble, G. and Bellgard, M. (2010) Advances in genome studies: the PAG 2010 conference. Functional & Integrative Genomics, 10 (1). pp. 1-9.

Nelson, M.N., Moolhuijzen, P.M., Boersma, J.G., Chudy, M., Lesniewska, K., Bellgard, M., Oliver, R.P., Swiecicki, W., Wolko, B., Cowling, W.A. and Ellwood, S.R. (2010) Aligning a new reference genetic map of lupinus angustifolius with the genome sequence of the model legume, Lotus japonicus. DNA Research, 17 (2). pp. 73-83.

Rodriguez-Valle, M., Lew-Tabor, A., Gondro, C., Moolhuijzen, P., Vance, M., Guerrero, F.D., Bellgard, M. and Jorgensen, W. (2010) Comparative microarray analysis of Rhipicephalus (Boophilus) microplus expression profiles of larvae pre-attachment and feeding adult female stages on Bos indicus and Bos taurus cattle. BMC Genomics, 11 (1). p. 437.

Breen, J. and Bellgard, M. (2010) Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence. Functional & Integrative Genomics, 10 (4). pp. 463-476.

Guerrero, F.D., Moolhuijzen, P., Peterson, D.G., Bidwell, S., Caler, E., Bellgard, M., Nene, V.M. and Djikeng, A. (2010) Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus. BMC Genomics, 11 (1). p. 374.

Lew-Tabor, A.E., Moolhuijzen, P.M., Vance, M.E., Kurscheid, S., Valle, M.R., Jarrett, S., Minchin, C.M., Jackson, Louise A., Jonsson, N.N. and Bellgard, M.I. (2010) Suppressive subtractive hybridization analysis of Rhipicephalus (Boophilus) microplus larval and adult transcript expression during attachment and feeding. Veterinary Parasitology, 167 (2-4). pp. 304-320.

Breen, J., Li, D., Dunn, D.S., Bekes, F., Kong, X., Zhang, J., Jia, J., Wicker, T., Mago, R., Ma, W., Bellgard, M. and Appels, R. (2010) Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain. BMC Plant Biology, 10 (1). p. 99.

Wanchanthuek, P., Bellgard, M., La, T., Ryan, K., Moolhuijzen, P., Chapman, B., Black, M.L., Schibeci, D., Hunter, A., Barrero, R., Phillips, N.D. and Hampson, D.J. (2010) The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes. PLoS ONE, 5 (7). pp. 1-16.

Black, M.L., Sinha, S., Agarwal, S., Colah, R., Das, R., Bellgard, M. and Bittles, A.H. (2010) A descriptive profile of β-thalassaemia mutations in India, Pakistan and Sri Lanka. Journal of Community Genetics, 1 (3). pp. 149-157.

Breen, J., Wicker, T., Kong, X., Zhang, J., Ma, W., Paux, E., Feuillet, C., Appels, R. and Bellgard, M. (2010) A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block. BMC Plant Biology, 10 (1). p. 98.

Moolhuijzen, P., Kulski, J.K., Dunn, D.S., Schibeci, D., Barrero, R., Gojobori, T. and Bellgard, M. (2010) The transcript repeat element: the human Alu sequence as a component of gene networks influencing cancer. Functional & Integrative Genomics, 10 (3). pp. 307-319.

Sidhu, A.S., Bellgard, M. and Dillon, T.S. (2009) Current trends in biomedical data and applications. Studies in Computational Intelligence, 224 . pp. 1-9.

Kurscheid, S., Lew-Tabor, A.E., Rodriguez Valle, M., Bruyeres, A.G., Doogan, V.J, Munderloh, U.G., Guerrero, F.D., Barrero, R.A. and Bellgard, M.I. (2009) Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss-of-function phenotypes in Drosophila. BMC Molecular Biology, 10 (1). p. 26.

Jia, Q., Zhang, J., Westcott, S., Zhang, X-Q, Bellgard, M., Lance, R. and Li, C. (2009) GA-20 oxidase as a candidate for the semidwarf gene sdw1/denso in barley. Functional & Integrative Genomics, 9 (2). pp. 255-262.

Bellgard, M., Wanchanthuek, P., La, T., Ryan, K., Moolhuijzen, P., Albertyn, Z., Shaban, B., Motro, Y., Dunn, D.S., Schibeci, D., Hunter, A., Barrero, R., Phillips, N.D. and Hampson, D.J. (2009) Genome sequence of the pathogenic intestinal spirochete Brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine. PLoS ONE, 4 (3). e4641.

Moolhuijzen, P.M., Lew-Tabor, A.E., Wlodek, B.M., Agüero, F.G., Comerci, D.J., Ugalde, R.A., Sanchez, D.O., Appels, R. and Bellgard, M. (2009) Genomic analysis of Campylobacter fetus subspecies: identification of candidate virulence determinants and diagnostic assay targets. BMC Microbiology, 9 (1). p. 86.

Motro, Y., La, T., Bellgard, M., Dunn, D.S., Phillips, N.D. and Hampson, D.J. (2009) Identification of genes associated with prophage-like gene transfer agents in the pathogenic intestinal spirochaetes Brachyspira hyodysenteriae, Brachyspira pilosicoli and Brachyspira intermedia. Veterinary Microbiology, 134 (3-4). pp. 340-345.

La, T., Phillips, N.D., Harland, B.l., Wanchanthuek, P., Bellgard, M.I. and Hampson, D.J. (2009) Multilocus sequence typing as a tool for studying the molecular epidemiology and population structure of Brachyspira hyodysenteriae. Veterinary Microbiology, 138 (3-4). pp. 330-338.

Sinha, S., Black, M.L., Agarwal, S., Colah, R., Das, R., Ryan, K., Bellgard, M. and Bittles, A.H. (2009) Profiling β-thalassaemia mutations in India at state and regional levels: implications for genetic education, screening and counselling programmes. The HUGO Journal, 3 (1-4). pp. 51-62.

Sidhu, A.S. and Bellgard, M. (2009) Protein data integration problem. Studies in Computational Intelligence, 224 . pp. 55-69.

Song, Y., La, T., Phillips, N.D., Bellgard, M.I. and Hampson, D.J. (2009) A reverse vaccinology approach to swine dysentery vaccine development. Veterinary Microbiology, 137 (1-2). pp. 111-119.

McNeil, M.D., Kota, R., Paux, E., Dunn, D., McLean, R., Feuillet, C., Li, D., Kong, X., Lagudah, E., Zhang, J.C., Jia, J.Z., Spielmeyer, W., Bellgard, M. and Appels, R. (2008) BAC-derived markers for assaying the stem rust resistance gene, Sr2, in wheat breeding programs. Molecular Breeding, 22 (1). pp. 15-24.

Yamasaki, C., Murakami, K., Fujii, Y., Sato, Y., Harada, E., Takeda, J-I, Taniya, T., Sakate, R., Kikugawa, S., Shimada, M., Tanino, M., Koyanagi, K.O., Barrero, R.A., Gough, C., Chun, H-W, Habara, T., Hanaoka, H., Hayakawa, Y., Hilton, P.B., Kaneko, Y., Kanno, M., Kawahara, Y., Kawamura, T., Matsuya, A., Nagata, N., Nishikata, K., Noda, A.O., Nurimoto, S., Saichi, N., Sakai, H., Sanbonmatsu, R., Shiba, R., Suzuki, M., Takabayashi, K., Takahashi, A., Tamura, T., Tanaka, M., Tanaka, S., Todokoro, F., Yamaguchi, K., Yamamoto, N., Okido, T., Mashima, J., Hashizume, A., Jin, L., Lee, K-B, Lin, Y-C, Nozaki, A., Sakai, K., Tada, M., Miyazaki, S., Makino, T., Ohyanagi, H., Osato, N., Tanaka, N., Suzuki, Y., Ikeo, K., Saitou, N., Sugawara, H., O’Donovan, C., Kulikova, T., Whitfield, E., Halligan, B., Shimoyama, M., Twigger, S., Yura, K., Kimura, K., Yasuda, T., Nishikawa, T., Akiyama, Y., Motono, C., Mukai, Y., Nagasaki, H., Suwa, M., Horton, P., Kikuno, R., Ohara, O., Lancet, D., Eveno, E., Graudens, E., Imbeaud, S., Debily, M., Hayashizaki, Y., Amid, C., Han, M., Osanger, A., Endo, T., Thomas, M.A., Hirakawa, M., Makalowski, W., Nakao, M., Kim, N-S, Yoo, H-S, De Souza, S.J., Bonaldo, M., Niimura, Y., Kuryshev, V., Schupp, I., Wiemann, S., Bellgard, M., Shionyu, M., Jia, L., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Zhang, Q., Go, M., Minoshima, S., Ohtsubo, M., Hanada, K., Tonellato, P., Isogai, T., Zhang, J., Lenhard, B., Kim, S., Chen, Z., Hinz, U., Estreicher, A., Nakai, K., Makalowska, I., Hide, W., Tiffin, N., Wilming, L., Chakraborty, R., Soares, M.B., Chiusano, M.L., Suzuki, Y., Auffray, C., Yamaguchi-Kabata, Y., Itoh, T., Hishiki, T., Fukuchi, S., Nishikawa, K., Sugano, S., Nomura, N., Tateno, Y., Imanishi, T. and Gojobori, T. (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research, 36 (Supp 1). D793-D799.

Kongsuwan, K., Piper, E.K., Bagnall, N.H., Ryan, K., Moolhuijzen, P., Bellgard, M., Lew, A., Jackson, L. and Jonsson, N.N. (2008) Identification of genes involved with tick infestation in Bos taurus and Bos indicus. Developments in Biologicals, 132 . pp. 77-88.

Motro, Y., Dunn, D.S., La, T., Phillips, N.D., Hampson, D.J. and Bellgard, M.I. (2008) Intestinal spirochaetes of the genus Brachyspira share a partially conserved 26 kilobase genomic region with Enterococcus faecalis and Escherichia coli. Microbiology Insights, 1 . pp. 3-11.

Moolhuijzen, P., Dunn, D.S., Bellgard, M., Carter, M., Jia, J., Kong, X., Gill, B.S., Feuillet, C., Breen, J. and Appels, R. (2007) Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium. Australian Journal of Agricultural Research, 58 (6). pp. 470-475.

Greene, W.K., Sontani, Y., Sharp, M.A., Dunn, D.S., Kees, U.R. and Bellgard, M.I. (2007) A promoter with bidirectional activity is located between TLX1/HOX11 and a divergently transcribed novel human gene. Gene, 391 (1-2). pp. 223-232.

Moolhuijzen, P., Cakir, M., Hunter, A., Schibeci, D., Macgregor, A., Smith, C., Francki, M., Jones, M.G.K., Appels, R. and Bellgard, M. (2006) Erratum: LegumeDB bioinformatics resource: comparative genomic analysis and novel cross genera marker identification in lupin and pasture legume species. Genome, 49 (9). pp. 1206-1207.

Moolhuijzen, P., Cakir, M., Hunter, A., Schibeci, D., Macgregor, A., Smith, C., Francki, M., Jones, M.G.K., Appels, R. and Bellgard, M. (2006) LegumeDB1 bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species. Genome, 49 (6). pp. 689-699.

Binnewies, T.T., Motro, Y., Hallin, P.F., Lund, O., Dunn, D., La, T., Hampson, D.J., Bellgard, M., Wassenaar, T.M. and Ussery, D.W. (2006) Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Functional & Integrative Genomics, 6 (3). pp. 165-185.

Nelson, M.N., Phan, H.T.T., Ellwood, S.R., Moolhuijzen, P.M., Hane, J.K., Williams, A., O‘Lone, C.E., Fosu-Nyarko, J., Scobie, M., Cakir, M., Jones, M.G.K., Bellgard, M., Książkiewicz, M., Wolko, B., Barker, S., Oliver, R.P. and Cowling, W.A. (2006) 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). pp. 225-238.

Lew, A.E., Jackson, L.A. and Bellgard, M.I. (2005) Comparative genomic analysis of non-coding sequences and the application of RNA interference tools for bovine functional genomics. Australian Journal of Experimental Agriculture, 45 (8). pp. 995-1010.

Kulski, J.K., Kenworthy, W.D., Bellgard, M., Taplin, R., Okamoto, K., Oka, A., Mabuchi, T., Ozawa, A., Tamiya, G. and Inoko, H. (2005) Gene expression profiling of Japanese psoriatic skin reveals an increased activity in molecular stress and immune response signals. Journal of Molecular Medicine, 83 (12). pp. 964-975.

Bellgard, M., Williams, H., Smith, C., Macgregor, A., Hunter, A., Appels, R. and Griffiths, T. (2005) Grains composition and nutrition online database. Asia Pacific Journal of Clinical Nutrition, 14 (Supp. S110).

Appels, R. and Bellgard, M. (2005) Looking through genomics? From the editors. Functional & Integrative Genomics, 5 (1). pp. 1-3.

Dunn, D.S., Romphruk, A.V., Leelayuwat, C., Bellgard, M. and Kulski, J.K. (2005) Polymorphic Alu insertions and their associations with MHC class I alleles and haplotypes in the Northeastern Thais. Annals of Human Genetics, 69 (4). pp. 364-372.

Nozaki, Y. and Bellgard, M. (2005) Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties. Bioinformatics, 21 (8). pp. 1421-1428.

Francki, M., Carter, M., Ryan, K., Hunter, A., Bellgard, M. and Appels, R. (2004) Comparative organization of wheat homoeologous group 3S and 7L using wheat-rice synteny and identification of potential markers for genes controlling xanthophyll content in wheat. Functional & Integrative Genomics, 4 (2). pp. 118-130.

Li, C., Ni, P., Francki, M., Hunter, A., Zhang, Y., Schibeci, D., Li, H., Tarr, A., Wang, J., Cakir, M., Yu, J., Bellgard, M., Lance, R. and Appels, R. (2004) Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison. Functional & Integrative Genomics, 4 (2). pp. 84-93.

Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., Yura, K., Miyazaki, S., Ikeo, K., Homma, K., Kasprzyk, A., Nishikawa, T., Hirakawa, M., Thierry-Mieg, J., Thierry-Mieg, D., Ashurst, J., Jia, L., Nakao, M., Thomas, M.A., Mulder, N., Karavidopoulou, Y., Jin, L., Kim, S., Yasuda, T., Lenhard, B., Eveno, E., Suzuki, Y., Yamasaki, C., Takeda, J-I, Gough, C., Hilton, P., Fujii, Y., Sakai, H., Tanaka, S., Amid, Clara, Bellgard, M., Bonaldo, M., Bono, H., Bromberg, S.K., Brookes, A.J., Bruford, E., Carninci, P., Chelala, C., Couillault, C., Souza, S., Debily, M., Devignes, M., Dubchak, I., Endo, T., Estreicher, A., Eyras, E., Fukami-Kobayashi, K., R. Gopinath, G., Graudens, E., Hahn, Y., Han, M., Han, Z-G., Hanada, K., Hanaoka, H., Harada, E., Hashimoto, K., Hinz, U., Hirai, M., Hishiki, T., Hopkinson, I., Imbeaud, S., Inoko, H., Kanapin, A., Kaneko, Y., Kasukawa, T., Kelso, J., Kersey, P., Kikuno, R., Kimura, K., Korn, B., Kuryshev, V., Makalowska, I., Makino, T., Mano, S., Mariage-Samson, R., Mashima, J., Matsuda, H., Mewes, H-W, Minoshima, S., Nagai, K., Nagasaki, H., Nagata, N., Nigam, R., Ogasawara, O., Ohara, O., Ohtsubo, M., Okada, N., Okido, T., Oota, S., Ota, M., Ota, T., Otsuki, T., Piatier-Tonneau, D., Poustka, A., Ren, S-X, Saitou, N., Sakai, K., Sakamoto, S., Sakate, R., Schupp, I., Servant, F., Sherry, S., Shiba, R., Shimizu, N., Shimoyama, M., Simpson, A.J., Soares, B., Steward, C., Suwa, M., Suzuki, M., Takahashi, A., Tamiya, G., Tanaka, H., Taylor, T., Terwilliger, J.D., Unneberg, P., Veeramachaneni, V., Watanabe, S., Wilming, L., Yasuda, N., Yoo, H-S, Stodolsky, M., Makalowski, W., Go, M., Nakai, K., Takagi, T., Kanehisa, M., Sakaki, Y., Quackenbush, J., Okazaki, Y., Hayashizaki, Y., Hide, W., Chakraborty, R., Nishikawa, K., Sugawara, H., Tateno, Y., Chen, Z., Oishi, M., Tonellato, P., Apweiler, R., Okubo, K., Wagner, L., Wiemann, S., Strausberg, R.L., Isogai, T., Auffray, C., Nomura, N., Gojobori, T. and Sugano, S. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology, 2 (6). e162.

Cakir, M., Bellgard, M., Appels, R. and Francki, M. (2004) Looking through genomics: Concepts and technologies for plant and animal genomics. Functional & Integrative Genomics, 4 (2). pp. 71-73.

Bellgard, M., Ye, J., Gojobori, T. and Appels, R. (2004) The bioinformatics challenges in comparative analysis of cereal genomes: An overview. Functional & Integrative Genomics, 4 (1). pp. 1-11.

Bellgard, M. and Kenworthy, W.D. (2003) FBSA: feature-based sequence alignment technique for very large sequences. Applied Bioinformatics, 2 (3). pp. 145-150.

Bellgard, M., Gamble, T., Reynolds, M., Hunter, A., Trifonov, E. and Taplin, R. (2003) Gap mapping: A paradigm for aligning two sequences. Applied Bioinformatics, 2 (3 Suppl). S31-S35.

Kulski, J.K., Lim, C.P.K., Dunn, D.S. and Bellgard, M. (2003) Genomic and phylogenetic analysis of the S100A7 (Psoriasin) gene duplications within the region of the S100 gene cluster on human chromosome 1q21. Journal of Molecular Evolution, 56 (4). pp. 397-406.

Carter, K. and Bellgard, M. (2003) MASV - Multiple (BLAST) Annotation System Viewer. Bioinformatics, 19 (17). pp. 2313-2315.

Bellgard, M., Hunter, A. and Kenworthy, W.D. (2003) Microarray analysis using bioinformatics analysis audit trails (BAATs). Comptes Rendus Biologies, 326 (10-11). pp. 1083-1087.

Carter, K., Oka, A.I., Tamiya, G. and Bellgard, M.I. (2001) Bioinformatics issues for automating the annotation of genomic sequences. Genome informatics series : proceedings of the . Workshop on Genome Informatics. Workshop on Genome Informatics, 12 . pp. 204-211.

Bellgard, M., Schibeci, D., Trifonov, E. and Gojobori, T. (2001) 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 (4-5). pp. 465-468.

Tsunoyama, K., Bellgard, M.I. and Gojobori, T. (2001) Intragenic variation of synonymous substitution rates is caused by nonrandom mutations at methylated CpG. Journal of Molecular Evolution, 53 (4-5). pp. 456-464.

Bellgard, M.I., Itoh, T., Watanabe, H., Imanishi, T. and Gojobori, T. (1999) Dynamic evolution of genomes and the concept of genome space. Annals of the New York Academy of Sciences, 870 . pp. 293-300.

Bellgard, M.I. and Gojobori, T. (1999) 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 Letters, 445 (1). pp. 6-8.

Bellgard, M.I. and Gojobori, T. (1999) Inferring the direction of evolutionary changes of genomic base composition. Trends in Genetics, 15 (7). pp. 254-256.

Bellgard, M.I., Hiew, H.L., Hunter, A. and Wiebrands, M. (1999) ORBIT: An integrated environment for user-customized bioinformatics tools. Bioinformatics, 15 (10). pp. 847-851.

Bellgard, M.I. and Gojobori, T. (1999) Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content. Gene, 238 (1). pp. 33-37.

Herbison, C.E., Sayer, D.C., Bellgard, M., Allcock, R.J, Christiansen, F.T. and Price, P. (1999) Structure and polymorphism of two stress-activated protein kinase genes centromeric of the MHC: SAPK2a and SAPK4. DNA sequence : the journal of DNA sequencing and mapping, 10 (4-5). pp. 229-243.

Bellgard, M.I., Tay, G.K., Hiew, H.L., Witt, C.S., Ketheesan, N., Christiansen, F.T. and Dawkins, R.L. (1998) MHC haplotype analysis by artificial neural networks. Human Immunology, 59 (1). pp. 56-62.

Kulski, J.K., Gaudieri, S., Bellgard, M., Balmer, L., Giles, K., Inoko, H. and Dawkins, R.L. (1997) The evolution of MHC diversity by segmental duplication and transposition of retroelements. Journal of Molecular Evolution, 45 (6). pp. 599-609.

Bellgard, M.I. and Tsang, C.P. (1994) Harmonizing music the Boltzmann way. Connection Science, 6 (2-3). pp. 281-297.

Conference Paper

Guerrero, F.D., Andreotti, R., Perez de Leon, A., Moolhuijzen, P., Rodriguez-Valle, M. and Bellgard, M. (2011) Genome based selection of anti-cattle tick vaccine candidate antigens. In: Ticks and Tick-borne Pathogens International Conference (TTP-7) 2011, 28 August - 2 September 2011, Zaragoza, Spain

Lew-Tabor, A., Rodriguez-Valle, M., Kurscheid, S., Barrero, R., Gondro, C., Moolhuijzen, P.M., Morgan, J.A.T., Bruyeres, A.B., Zhang, B. and Bellgard, M.I. (2011) Microarray evidence for off target effects in tick RNA interference experiments, and the lack of strong correlation between DSRNA and antibody phenotypes in tick In vitro treatments for vaccine candidate screening. In: Ticks and Tick-borne Pathogens International Conference (TTP-7) 2011, 28 August - 2 September 2011, Zaragoza, Spain

Wang, Z., King, E., Smith, G., Bellgard, M., Broomhall, M., Chedzey, H., Fearns, P., Garcia, R., Hunter, A., Lynch, M. and Schibeci, D. (2011) RS-YABI: A workflow system for Remote Sensing Processing in AusCover. In: MODSIM 2011 - 19th International Congress on Modelling and Simulation - Sustaining Our Future: Understanding and Living with Uncertainty, 12 - 16 December, Perth, Western Australia pp. 1167-1173.

Guerrero, F.D., Dowd, S.E, Moolhuijzen, P., Bellgard, M., Andreotti, R. and Perez de Leon, A. (2011) Targeted studies of the genome, transcriptome and microbiome of the cattle tick, Rhipicephalus miroplus. In: 2011 Australian Society for Parasitology (ASP) Annual Conference, 10 - 13 July 2011, Cairns, Queensland

Fearns, P., Bellgard, M., Broomhall, M., Chedzey, H., Garcia, R., Hunter, A., King, E., Lynch, M., Schibeci, D. and Smith, G. (2011) Web-based processing of remote sensing data in a workflows environment. In: 34th International Symposium on Remote Sensing of Environment (ISRSE2011): The GEOSS Era: Towards Operational Environmental Monitoring , 10 - 15 April 2011, Sydney Convention & Exhibition Centre, N.S.W

Bellgard, M., Moolhuijzen, P., Guerrero, F.D., Appels, R., Schibeci, D., Rodriguez-Valle, M., Barrero, R., Hunter, A. and Lew-Tabor, A. (2011) A new web-based genomics resource for bioinformatics analysis of Rhipicephalus (Boophilus) microplus: CattleTickBase. In: Ticks and Tick-borne Pathogens International Conference (TTP-7) 2011, 28 August - 2 September 2011, Zaragoza, Spain

Guerrero, F.D., Moolhuijzen, P., Peterson, D.G., Bellgard, M.I., Schibeci, D., Hunter, A., Rodriguez-Valle, M., Barrero, R., Nene, V.M. and Lew-Tabor, A.E. (2010) Cot filtration approach for advancing genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus. In: Entomology 2010: ESA 58th Annual Meeting, 12 - 15 December 2010, San Diego, CA

Moolhuijzen, P., Lew-Tabor, A., Guerrero, F.D., Bellgard, M. and Appels, R. (2010) De-novo assembly of the complex Rhipicephalus (Boophilus) microplus available genome. In: XIIth International Conference for Parasitology (ICOPA), 15 - 20 August , Melbourne, Australia

Bellgard, M., Guerrero, F.D., Moolhuijzen, P., Schibeci, D., Hunter, A., Rodriguez-Valle, M., Barrero, R., Gondro, C. and Lew-Tabor, A.E. (2010) Toward a genome sequence for Rhipicephalus (Boophilus) microplus: Cattle tick base available resources for the research community. In: XIIth International Conference for Parasitology (ICOPA), 15 - 20 August , Melbourne, Australia

Diepeveen, D., Clarke, G.P.Y., Bellgard, M. and Appels, R. (2010) Understanding the genetic components of NIR spectra. In: ASC 2010 Australian Statistical Conference Statistics in the West: Understanding our World., 6 - 10 December, Fremantle, Western Australia

Diepeveen, D., Armstrong, L., Clarke, P., Abrecht, D., Appels, R. and Bellgard, M. (2008) Applying data mining tools to improve grain quality for growers. In: 2008 Agribusiness Crop Updates: Cereal Updates, 13 - 14 February 2008, Burswood Entertainment Complex, Perth, W.A

Piper, E.K., Jonsson, N., Constantinoiu, C., Jackson, L.A., Lew-Tabor, A.E., Jorgensen, W.K., Moolhuijzen, P., Bellgard, M.I. and Gondro, C. (2008) Gene expression in the skin of cattle following infestation with the cattle tick Rhipicephalus microplus. In: VIth International Conference on Ticks and Tick-Borne Pathogens, 21 - 26 September 2008, Buenos Aires, Argentina

Piper, E.K., Jackson, L.A., Constantinoiu, C.C., Gondro, C., Lew-Tabor, A.E., Moolhuijzen, P., Jorgensen, W.K., Bellgard, M. and Jonsson, N.N. (2008) Gene expression in the skin of tick-resistant and tick-susceptible cattle prior to and following infestation with Rhipicephalus microplus. In: VIth International Conference on Ticks and Tick-Borne Pathogens, 21 - 26 September 2008, Buenos Aires, Argentina

Lew-Tabor, A., Jackson, L., Rodriguez-Valle, M., Piper, E., Kurscheid, S., Moolhuijzen, P., Constantinoiu, C., Jones, M., Gondro, C., Bruyeres, A., Jarrett, S., Minchin, C., Venus, B., Zhang, B., Bellgard, M., Guerrero, F. and Jonsson, N. (2008) Reverse vaccinology approach for the identification of novel Rhipicephalus (boophilus) microplus vaccine candidates. In: VIth International Conference on Ticks and Tick-Borne Pathogens, 21 - 26 September 2008, Buenos Aires, Argentina

Lew-Tabor, A.E., Jackson, L.A., Rodriguez-Valle, M., Kurscheid, S., Moolhuijzen, P.M., Jones, M.E., Piper, E.K., Constantinoiu, C., Jorgensen, W.K., Jonsson, N.N., Bellgard, M.I. and Guerrero, F.D. (2008) Reverse vaccinology approach to identify Rhipicephalus (Boophilus) microplus tick vaccine candidates. In: ASP & ARC/NHMRC Research Network for Parasitology Annual Conference, 6 - 9 July 2008, Glenelg, S.A.

Rodriguez-Valle, M., Lew-Tabor, A., Gondro, C., Kurscheid, S., Jarrett, S., Minchin, C., Moolhuijzen, P., Bellgard, M. and Guerrero, F. (2008) Transcriptome analysis of Rhipicephalus (Boophilus) microplus. In: VIth International Conference on Ticks and Tick-Borne Pathogens, 21 - 26 September 2008, Buenos Aires, Argentina

Nelson, M., Boersma, J., Chudy, M., Lesniewska, K., Ellwood, S., Phan, H., Moolhuijzen, P., Bellgard, M., Oliver, R., Swiecicki, W., Wolko, B. and Cowling, W. (2008) A dense reference map of the Lupinus Angustifolius L. Genome: A foundation for building lupin genome research. In: 12th International Lupin Conference, 14 - 18 September, Perth, Western Australia pp. 255-258.

Hiew, H.L., Bellgard, M., Pham, T.D. and Zhou, X. (2007) A Bioinformatics Reference Model: Towards a Framework for Developing and Organising Bioinformatic Resources. In: 2007 International Symposium on Computational Models for Life Sciences, CMLS '07, 17-19 December 2007, Gold Coast, QLD pp. 349-359.

Lew-Tabor, A.E., Guo, S.Y., Venus, B., Moolhuijzen, P., Sanchez, D., Trott, D., Burrell, P., Wlodek, B. and Bellgard, M. (2007) Comparative genome analysis applied to develop novel PCR assays to characterise and identify Campylobacter fetus subsp venerealis isolates. In: 14th International Workshop on Campylobacter, Helicobacter and Related Organisms, 2 - 5 September 2007, Rotterdam, Netherlands

Cakir, M., McLean, R., Wilson, R., Barclay, I., Moore, C., Loughman, R., Haley, S., Kidwell, K., Anderson, J., Sorrells, M., Manes, Y., Hayden, M., Feuillet, C., William, M., Hunter, A. and Bellgard, M. (2007) Genome level targeted breeding in wheat. In: Plant & Animal Genomes XV Conference, 13 - 17 January 2007, San Diego, CA

Diepeveen, D., Clarke, G., Bellgard, M., Appels, R. and Crosbie, G. (2007) Physical grain screenings of plant breeding germplasm. In: 1st Latin American Conference on Cereal and Cereal Products (ICC) 2007, 23 - 26 September 2007, Rosario, Argentina

Bellgard, M. (2007) Trends impacting Bioinformatics on the grid. In: APAC07 Conference, 8 - 12 October 2007, Perth, Western Australia

Anderson, J., Whitehand, S., Lichtenzveig, J., Moolhuijzen, P., Bellgard, M., Oliver, R. and Singh, K. (2005) Genetic analysis of defence responses against necrotrophic pathogens in legumes. In: 2nd Australian Model Legume Workshop, 5 - 8 April 2005, Rottnest Island, Western Australia

Nelson, M., Phan, H., Ellwood, S., Moolhuijzen, P., Lone, C., Williams, A., Hane, J., Buirchell, B., Bellgard, M. and Cowling, W. (2005) Genetic mapping of domestication traits in narrow leafed lupin (lupinus angustifolius): Using synteny to search for candidate genes in Medicago truncatula. In: 2nd Australian Model Legume Workshop, 5-8 April 2005, Perth, Western Australia

Phan, H., Elwood, S., Moolhuijzen, P., Williams, A., Hane, J., Ford, R., Bellgard, M. and Oliver, R. (2005) Genomic synteny in legumes: Application to crop breeding. In: 2nd Australian Model Legume Workshop, 5 - 8 April 2005, Rottnest Island, Western Australia

Hunter, A., Schibeci, D., Hiew, H.L. and Bellgard, M. (2005) Grendel: A bioinformatics web service-based architecture for accessing HPC resources. In: 3rd Australasian Workshop on Grid Computing and e-Research, AusGrid 2005 and 3rd Australasian Information Security Workshop, AISW 2005, 31 January - 1 February, Newcastle, Australia

Nozaki, Y., Macgregor, A., Smith, C., Hunter, A. and Bellgard, M. (2005) Multidotter: Dot-matrix program for multiple sequences. In: Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'05, 20 - 23 June, Las Vegas, USA

Moolhuijzen, P., Cakir, M., Madsen, L., Li, D., Hunter, A., Schibeci, D., Francki, M., Appels, R., Sandal, N. and Bellgard, M. (2004) Detailed comparative genomics and novel cross-species marker identification in Lupin and pasture legume species: Application of the legumeDB bioinformatics resources. In: Plant Genomics European Meeting , 22 - 25 September 2004, Lyon, France

Hunter, A., Schibeci, D., Hiew, H.L. and Bellgard, M. (2004) GRID-enabled bioinformatics applications for comparative genomic analysis at the CBBC. In: 2004 IEEE International Conference on Cluster Computing, ICCC 2004, 20 - 23 September, San Diego, CA, USA p. 486.

Anderson, J., Whitehand, S., Lichtenzveig, J., Moolhuijzen, P., Bellgard, M., Oliver, R. and Singh, K. (2004) Genetic analysis of defence responses against necrotrophic pathogens in legumes. In: ComBio 2004, 26 - 30 September 2004, Burswood Convention Centre, Perth

Cakir, M., Appels, R., Hunter, A., Schibeci, D., Li, C. and Bellgard, M. (2004) A consensus molecular genetic map of barley. In: 9th International Barley Genetics Symposium, 20 - 26 June, Brno, Czech Republic pp. 144-148.

Dwyer, G., Loo, H.P., Schibeci, D., Hunter, A., Siddique, K., Khan, T., Bellgard, M. and Jones, M. (2002) Molecular and bioinformatics approaches for chickpea (Cicer arietinum L.) improvement. In: 12th Australasian Plant Breeding Conference: Plant breeding for the 11th millenium, 15 - 20 September 2002, Perth, W.A

Dwyer, G., Loo, H., Khan, T., Siddique, K., Bellgard, M. and Jones, M. (2002) Molecular studies of ascochyta blight disease in chickpea. In: Crop Updates 2002: Pulse Research and Industry Development in Western Australia, 20 - 21 February 2002, Sheraton Hotel, Perth

Lamont, O., Hiew, H.L. and Bellgard, M. (2001) Data representation influences protein secondary structure prediction using artificial neural networks. In: Seventh Australian and New Zealand Intelligent Information Systems Conference, 18 - 21 November 2001, Perth, Western Australia

Carter, K., Schibeci, D. and Bellgard, M. (2001) WWW issues for conducting sophisticated Bioinformatics analysis. In: AusWeb 01: The Seventh Australian World Wide Web Conference, 21 - 25 April 2001, Coffs Harbour, NSW

Sayer, D., Herbison, C., Bellgard, M.I., Price, P. and Christiansen, F.T. (1999) Genomic structure, localisation, and polymorphism studies of SAP2a and SAPK4. In: Human Genome Meeting '99, 27 - 30 March 1999, Brisbane, QLD

Hiew, H.L., Bellgard, M. and Schibeci, D. (1999) Visualising the evolutionary dynamics of molecular data using self organising feature maps. In: Third Australia-Japan Joint Workshop on Intelligent and Evolutionary Systems, 23 - 25 November 1999, Canberra, Australia

Bellgard, M.I. and Taplin, R.H. (1999) Why a window-based learning algorithm using an effective Boltzmann machine is superior to the original BM learning algorithm. In: ICONIP'99: 6th International Conference on Neural Information Processing, 16 - 20 November 1999, Perth, Western Australia pp. 896-902.

Bellgard, M., Schibeci, D. and Hiew, H.L. (1999) An information system for whole genome data. In: 2nd Western Australian Workshop on Information Systems Research (WAWISR), 27th November 1999, Perth, W.A

Bellgard, M.I. and Tsang, C.P. (1996) On the use of an effective Boltzmann machine for music style recognition and harmonisation. In: 1996 International Computer Music Conference (ICMC '96), 19 - 24 August 1996, Hong Kong

Bellgard, M.I. and Tsang, C.P. (1995) Using an effective Boltzmann machine to learn context dependencies of a sequence. In: 1995 IEEE International Conference on Neural Networks (ICNN '95), 27 November - 1 December 1995, Perth, W.A pp. 2841-2846.

Dixon, M.W., Cole, G.R. and Bellgard, M.I. (1995) Using the Hopfield model with mean field annealing to solve the routing problem in packet-switched communication networks. In: 1995 IEEE International Conference on Systems, Man and Cybernetics, 22 - 25 October 1995, Vancouver, Canada pp. 2966-2970.

Dixon, M.W., Cole, G.R. and Bellgard, M.I. (1995) Using the Hopfield neural network with mean field annealing to solve the shortest path problem in a communication network. In: 1995 IEEE International Conference on Neural Networks (ICNN '95), 27 November - 1 December 1995, Perth, W.A pp. 2652-2657.

Dixon, M.W., Bellgard, M.I. and Cole, G.R. (1995) A neural network algorithm to solve the routing problem in communication networks. In: International Workshop on Applications of Neural Networks to Telecommunications (IWANNT '95), 22 - 24 May 1995, Stockholm, Sweden

Dixon, M.W., Cole, G.R. and Bellgard, M.I. (1995) A neural network shortest path algorithm for routing in packet-switched communication networks. In: 1995 International Conference on Communications (ICC '95): Gateway to Globalization, 18 - 22 June 1995, Seattle, Washington, USA pp. 1602-1606.

Bellgard, M.I. and Tsang, C.P. (1992) Harmonising music using a network of Boltzmann machines. In: Fifth International Conference Neural Networks and their Applications, 2 - 6 November 1992, Nimes, France

Bellgard, M.I. and Tsang, C.P. (1991) Some experiments on the use of genetic algorithms in a Boltzmann machine. In: IEEE International Joint Conference of Artificial Neural Networks 1991 (IJCNN '91), 18 - 21 November 1991, Singapore pp. 2645-2652.

Tsang, C.P. and Bellgard, M.I. (1990) Sequence generation using a network of Boltzmann machines. In: 4th Joint Conference on Artificial Intelligence (AI '90), 21 - 23 November 1990, Hyatt Regency, Perth, WA

Conference Item

Appels, R., Keeble-Gagnère, G., Chapman, B., Fleury, D., Bellgard, M., Diepeveen, D., Zhang, J., Webster, H., Islam, S. and Ma, W. (2013) Sequencing chromosome 7A and the Australia-China centre for wheat improvement. In: Wheat Breeding Assembly 2013, 17 - 19 July, Brisbane, Australia.

Bellgard, M., Reeve, W., Yang, H., Zhang, J., Barrero, R. and Howieson, J. (2011) Interpreting sub-optimal nitrogen fixation in Lupinus angustifolius utilising the genome sequence of both symbiotic partners. In: 17th International Congress on Nitrogen Fixation, 27 November - 1 December 2011, Fremantle, WA.

Keeble, G., Black, M., Moolhuijzen, P., Barrero, R., Bellgard, M. and Appels, R. (2011) Structure–function studies in the wheat genome. In: XVIII International Botanical Congress IBC2011, 23 - 30 July, Melbourne, Australia.

Webster, H., Fosu-Nyarko, J., Keeble, G., Moolhuijzen, P., Bellgard, M. and Appels, R. (2011) The cell wall invertase (IVR1) gene from wheat. In: XVIII International Botanical Congress IBC2011, 23 - 30 July, Melbourne, Australia.

Moolhuijzen, P., Ryan, K., Lew-Tabor, A., Hunter, A., Schibeci, D. and Bellgard, M. (2009) Bioinformatics resource to capture, integrate and analyse diverse data types. In: Bioinformatics Australia (BA2009) 2009, 29 - 30 October 2009, Melbourne, VIC.

Moolhuijzen, P., Appels, R., Lew-Tabor, A., Rodriguez-Valle, M., Morgan, J., Guerrero, F.D., Hunter, A., Schibeci, D. and Bellgard, M. (2009) De-novo sequence assembly and characterization of the complex genome of five BACS from Rhipicephalus microplus. In: Bioinformatics Australia (BA2009) 2009, 29 - 30 October 2009, Melbourne, VIC.

Moolhuijzen, P., Lew-Tabor, A., Rodriguez-Valle, M., Guerrero, F.D., Hunter, A., Schibeci, D. and Bellgard, M. (2009) Transcriptome wide high throughput bioninformatics pipeline for vaccine candidate identification. In: Bioinformatics Australia (BA2009) 2009, 29 - 30 October 2009, Melbourne, VIC.

Black, M.L., Moolhuijzen, P., Bellgard, M. and Bittles, A.H. (2009) A bioinformatics approach to the study of autosomal recessive non syndromic intellectual disability. In: Genes for Health, 2 - 6 May 2009, Fremantle, Australia.

Barrero, R.A., Albertyn, Z., Hercus, C., Hunter, A., Dennis, L., Shannon, M.F. and Bellgard, M. (2008) Benchmarking tools for aligning millions of short reads and implementation of a web-based data processing interface. In: 19th International Conference on Genome Informatics (GIW2008), 1 - 3 December 2008, Gold Coast, QLD.

Black, M.L., Dunn, D., Tangtulyangkul, P., Hunter, A., Bellgard, M. and Bittles, A.H. (2008) Combining bioinformatics and population genetics in the study of Thalassaemia. In: International Conference on Medical and Community Genetics, 15 - 17 February, Chandigarh, India.

Wanchanthuek, P., Hampson, D. and Bellgard, M. (2008) Comparison of Brachyspira central metabolism pathways. In: 19th International Conference on Genome Informatics (GIW2008), 1 - 3 December 2008, Gold Coast, QLD.

Black, M.L., Tangtulyangkul, P., Hunter, A., Bellgard, M. and Bittles, A.H. (2008) The Consang-Mashup Database System for the study of consanguinity. In: International Conference on Medical and Community Genetics, 15 - 17 February, Chandigarh, India.

Wanchanthuek, P., Hampson, D. and Bellgard, M. (2008) Conservation and metabolic functional significance of overlapping gene in the bacterial genomes. In: The 20th Annual Meeting and International Conference of the Thai Society for Biotechnology, 14 - 17 October 2008, Maha Sarakham, Thailand.

Kurscheid, S., Rodriguez-Valle, M., Moolhuijzen, P.M., Barrero, R., Guerrero, F.D., Lew-Tabor, A.E. and Bellgard, M.I. (2008) In silico prediction of tick vaccine candidates. In: ASP & ARC/NHMRC Research Network for Parasitology Annual Conference, 6 - 9 July 2008, Glenelg, S.A..

Kurscheid, S., Rodriguez-Valle, M., Zhang, B., Bruyeres, A., Minchin, C., Barrero, R., Guerrero, F., Bellgard, M. and Lew, A. (2008) Putative RNA interference pathway in ticks. In: VI International Conference on Ticks and Tick-borne Pathogens, 21 - 26 September 2008, Buenos Aires, Argentina.

Dayalan, S., Hunter, A., Macgregor, A., Takayama, N., Bellgard, M., Bacic, T. and Likic, V. (2008) Scientific data management and workflow system for geographically distributed virtual organization. In: eResearch Australasia Conference 2008, 28 September - 3 October 2008, Melbourne, Australia.

Kurscheid, S., Rodriguez-Valle, M., Guerrero, F., Lew, A. and Bellgard, M. (2008) Serine proteinase inhibitor families in Rhipicephalus microplus. In: VIth International Conference on Ticks and Tick-Borne Pathogens, 21 - 26 September 2008, Buenos Aires, Argentina.

Jones, M.E., Piper, E.K., Minchin, C.M., Zhang, B., Moolhuijzen, P.M., Gondro, C., Jonsson, N.N., Bellgard, M.I., Lew-Tabor, A.E. and Jackson, L.A. (2008) Up-regulated expression of Interleukin-2 Receptor alpha in tick resistant cattle. In: ComBio 2008, 21 - 25 September 2008, Canberra, A.C.T.

Hunter, A., Macgregor, A., Takayama, N., Smith, C., Wellington, C., Hammond, B., Albertyn, Z., Schibeci, D. and Bellgard, M. (2008) YABI: A rich internet application for simplifying -omics workflow creation, customisation and data analysis. In: Cambridge Healthtech Institute 2nd Annual Next Generation Sequencing: Platforms Applications and Case Studies, 23 - 24 April 2008, San Diego, CA.

Nelson, M., Phan, H., Ellwood, S., Moolhuijzen, P., Bellgard, M., Hane, J., Williams, A., Fosu-Nyarko, J., Wolko, B., Ksiarkiewicz, M., Cakir, M., Jones, M., Scobie, M., O'Lone, C., Barker, S., Oliver, R. and Cowling, W. (2006) The first gene-based map of narrow-leafed lupin - location of domestication genes and conserved synteny with Medicago truncatula. In: Crop Updates 2006: Lupins and Pulses, 15 - 16 February 2006, The Burswood International Resort, Perth.

Zhang, J., Yang, X., Moolhuijzen, P., Li, C., Bellgard, M., Lance, R. and Appels, R. (2005) Towards isolation of the Barley Green Revolution gene. In: 12th Australian Barley Technical Symposium, 11 - 14 September 2005, Hobart, Tasmania.

Bellgard, M.I. and Gojobori, T. (1999) Evolutionary change of the GC content after speciation. In: International Symposiumon Evolutionary Genomics (ISME'99), 11 - 15 January 1999, Puntarenas, Costa Rica.

Tsunoyama, K., Bellgard, M.I. and Gojobori, T. (1999) Intragenic variation of synonymous substitution rates and its evolutionary implication. In: International Symposium on Evolutionary Genomics (ISME'99), 11 - 15 January 1999, Puntarenas, Costa Rica.

Tsunoyama, K., Bellgard, M.I. and Gojobori, T. (1998) Evolutionary pattern of genes revealed by intragenic variation of synonymous substitution rates. In: 70th Annual Meeting of the Genetics Society of Japan, 23 - 25 September 1998, Sapporo, Japan.

Kulski, J.K., Gaudieri, S., Bellgard, M.I., Balmer, L. and Dawkins, R.L. (1997) Segmental duplication and transposition of retroelements in the evolution of MHC class I genes. In: International Conference on Molecular Biology and Evolution (5th SMBE), 1 - 4 June 1997, Bavaria, Germany.

Bellgard, M.I., Tay, G.K., Purnomo, F. and Dawkins, R.L. (1996) Identifying features from MHC block matching profiles. In: '96 Bioinformatics & Genome Research, 10 - 11 June 1996, Baltimore, Maryland, USA.

Bellgard, M.I., Tay, G.K., Purnomo, F. and Dawkins, R.L. (1996) Identifying features from MHC block matching scans using artificial intelligence. In: Human Genome Meeting '96, 22 - 24 March 1996, Heidelberg, Germany.

Bellgard, M.I., Tay, G.K. and Dawkins, R.L. (1996) Using a machine learning technique to prospectively match Donor and Recipient pairs for bone marrow transplantation. In: Intelligent Systems for Microbiology '96, 12 - 15 June 1996, Missouri, USA.

Book Chapter

Roessner, U., Nahid, A., Chapman, B., Hunter, A. and Bellgard, M. (2011) Metabolomics – The combination of analytical biochemistry, biology, and informatics. In: Murray, M-Y, (ed.) Comprehensive Biotechnology (Second Edition). Academic Press, pp. 447-459.

Sidhu, A.S., Bellgard, M.I. and Dillon, T.S. (2009) Classification of information about proteins. In: Edwards, D., Stajich, J. and Hansen, D., (eds.) Bioinformatics: Tools and Applications. Springer New York, pp. 243-258.

Bellgard, M.I. (2005) Bioinformatics: From computational analysis through to integrated systems. In: Ruvinsky, A. and Marshall-Graves, J.A., (eds.) Mammalian Genomics. CABI Publishing, Wallingford, Oxfordshire, pp. 393-410.

Bellgard, M.I. and Gojobori, T. (2005) A comparative analysis of mammalian genomics: Prokaryote and eukaroyte perspectives. In: Ruvinsky, A. and Marshall-Graves, J.A., (eds.) Mammalian Genomics. CABI Publishing, Wallingford, Oxfordshire, pp. 263-274.

Schibeci, D., Potter, R., Wathen-Dunn, K., Jones, M. and Bellgard, M. (2001) Applying artificial neural networks to the classification of wheat varieties processed via MALDI-TOF mass spectrometry. In: Mastorakis, N.E., (ed.) Advances in Neural Networks and Applications. World Scientific and Engineering Society Press, pp. 262-267.

Bellgard, M.I. and Tsang, C.P. (1999) Harmonizing music the Boltzmann way. In: Griffith, N. and Todd, P.M., (eds.) Musical Networks: Parallel Distributed Perception and Performance. MIT Press, United States of America, pp. 261-277.

Working Paper

Bellgard, M., Schibeci, D. and Trifonov, E. (2001) Gap mapping : A new paradigm for aligning two sequences. Murdoch University. Division of Business, Information Technology and Law, Perth, Western Australia.

Schibeci, D. and Bellgard, M. (2001) cBLAST : a distributed version of BLAST using PVM. Murdoch University. School of Information Technology, Perth, Western Australia.

Report

Power, W. and Bellgard, M.I. (1995) UPREP for Windows manual. CSIRO

Others

Hampson, D.J., La, T., Bellgard, M.I. and Phillips, N.D. (2011) Vaccine strains of brachyspira hyodysenteriae. Patent, WO2010054437 .

Hampson, D.J., La, T., Bellgard, M.I. and Phillips, N.D. (2009) Novel sequences of Brachyspira, immunogenic compositions, methods for preparation and use thereof. Patent, WO/2009/105833 .

Bellgard, M., Hampson, D.J. and La, T. (2008) Genes and proteins of Brachyspira hyodysenteriae and uses thereof. Patent, WO/2008/017636 .

Bellgard, M., Hampson, D.J. and La, T. (2008) Genes and proteins of brachyspira hyodysenteriae and use of same for diagnosis and therapy. Patent: AU2006245965 .

Bellgard, M., Hampson, D.J. and La, T. (2008) Novel sequences of Brachyspira, immunogenic compositions, methods for preparation and use thereof. Patent, EP20080152093 .

Bellgard, M., Hampson, D.J. and La, T. (2007) Novel Brachyspira pilosicoli genes and proteins and uses thereof. Patent, WO/2007/113001 .

Hampson, D.J., Bellgard, M. and La, T. (2007) Novel genes and proteins of Brachyspira hyodysenteriae and use of same for diagnosis and therapy. Patent, WO/2007/107323 .

Bellgard, M., Hampson, D.J. and La, T. (2006) Novel genes and proteins of Brachyspira Pilosicoli and use of same for diagnosis and therapy. Patent, WO/2006/136392 .

Bellgard, M., Hampson, D.J. and La, T. (2006) Novel genes and proteins of Brachyspira hyodysenteriae and use of same for diagnosis and therapy. Patent, WO/2006/119983 .

Bellgard, M., Hampson, D.J. and La, T. (2005) Genes and proteins of brachyspira hyodysenteriae and use of same for diagnosis and therapy. Patent: EP2224008 A2 .

This list was generated on Sun Nov 23 12:58:49 2014 GMT.