Publications: Bellgard, Matthew

2012

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.

2011

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.

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.

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.

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, 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.

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.

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.

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.

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

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.

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.

2010

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.

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.

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.

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.

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.

2009

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.

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.

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.

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, Jingjuan, 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.

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.

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 .

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.

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.

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.

2008

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.

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.

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.

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.

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.

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

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.

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..

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.

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.

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.

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.

2007

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.

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 .

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.

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.

2006

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.

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 .

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.

2005

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.

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.

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.

2004

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.

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.

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.

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.

2003

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