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

Director, Centre for Comparative Genomics (CCG)

About me

My formal qualifications include a PhD from The University of Western Australia in 1994, completing a thesis in Computer Science and Specialising in Artificial Intelligence with applications. In 2005, I became the inaugural Director of the Western Australian State Government Centre of Excellence, the Centre for Comparative Genomics (CCG). The CCG undertakes unique biomedical and agricultural research and development by promoting a collaborative understanding within and across fields of study. Under my leadership, the Centre has attracted over $45m in research funding in the last 13 years and has some 40 staff, most of whom are externally funded. As a Murdoch University Centre, the Director has overall responsibility for the strategic and operational leadership and management of the Centre.

In addition to these responsibilities, I am also Director of iVEC@Murdoch that houses the 2nd largest supercomputer in Australia (ranked #87 in the world in June 2011) and Convenor of the Australian Bioinformatics Facility (ABF), which is one of four national platforms of the National Collaborative Research Infrastructure Scheme (NCRIS) 5.1 Evolving Biomolecular Platforms and Informatics Investment plan. I am co-leader of the Australian consortium in the FP7 EU €12 million RD Connect: an integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research.

Teaching area

2003 – Present: Murdoch University – Perth, WA: Professor and Foundation Chair in Bioinformatics

2000 – 2003: Murdoch University – Perth, WA:  Associate Professor in Computer Science

1998 – 1999:  Murdoch University – Perth, WA:  Senior Lecturer in Computer Science

1994 – 1997:  Murdoch University – Perth, WA:  Lecturer in Computer Science

Research areas

  • Comparative genomic analysis
  • Computational biology
  • Molecular evolution
  • Bioinformatics
  • Genomics
  • Integrated system development
  • Pattern recognition
  • Food security
  • Digital Agriculture
  • Personalised Medicine

Current projects

2013 – 2017:  NHMRC

Project Title: RD-CONNECT: An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research

Investigators: Dawkins H, Bellgard MI, Golblatt J, Wilton SD, Fletcher S, Baynam G, Weeramanthri T, Mallal S, Nolan D

2013 – 2016:  MDA USA

Project Title: Oligomer design & validation for DMD: quantum improvements in exon skipping

Investigators: Wilton SD, Fletcher S, Bellgard MI

2013 – 2016:  CRC Plant Biosecurity

Project Title: Delivery of an integrated Internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids

Investigators: Bellgard M, Barrero R, Bulman S

2013 – 2015:  NHMRC Grant ID: 1043758

Project Title: Optimization of splice switching therapies to treat Duchenne muscular dystrophy

Investigators: Bellgard MI, Wilton SD, Fletcher S

2012 – 2015:  CRC for National Plant Biosecurity

Project Title: Exemplar Project: New approaches for diagnosing bacterial pathovars

Investigators: Stack J, Smith G, Rodoni B, Chapman T, Bellgard MI

2013 – 2016:  Department of Agriculture and Food Western Australia

Grains Research and Development Corporation

Project Title: Sequencing the Barley Chromosome 7H

Investigators: Li C, Bellgard MI, Zhang X-Q,  Zhang Q, Fleury D, Langridge P

2012 – 2015:  University of Queensland – ARC Discovery Contribution

Project Title: Harnessing the genome of the Australian paralysis tick to develop effective control products

Investigators: Lew-Tabor A, Bellgard M,  Rodriguez VM, Atwell R, Vankan D, Broady K

2007 – Present:  iVEC@Murdoch

Project Title: Epic Supercomputer and NeCTAR Research Cloud

Investigators: Bellgard MI

2007 – Present:  Bioplatforms Australia Pty Ltd

Project Title: The Australian Bioinformatics Facility

Investigators: Bellgard MI, Forest S, Gorman J, Bacic T, Molloy M, Gilbert A

 

Awards and grants

AWARDS:

2014:  Senior Researcher Award:  An Outstanding Contribution to the Field of Ticks & Tick-borne Pathogens

2012:  OECD Co-operative Research Program Fellowship Award

2006:  Top 40 Business Leaders under 40 years of age (40 Under 40 WA Business News)

1995:  Western Australian State Government:   Young Australia of the Year, Science & Technology Category Winner (WA)

GRANTS:

2008 – 2010:  Australian Research Council

Project Title: An integrated genomics approach to improve our understanding of the biology of genital campylobacteriosis in beef cattle

Investigators: Lew-Tabor A, Bellgard MI

2007 – 2011Department of Education Science & Training

Project Title: National Collaborative Research Infrastructure Strategy

Investigators: Bellgard MI

2007 – 2011:  Bioplatforms Australia Ltd

Project Title: NCRIS: Super Science Project for the Education Investment Fund

Investigators: Bellgard MI

2005 – 2012:  Department of Industry, Innovation, Science, Research and Tertiary Education       

Project Title: CRC for Beef Genetic Technologies

Investigators: Lew-Tabor A, Bellgard MI, Guerrero F

2010 – 2015Grains Research & Development Corporation

Project Title: International Wheat Genome Sequencing Consortium assembly of chromosome 7A

Investigators: Appels R, Bellgard MI

2010 – 2012:  CRC for National Plant Biosecurity

Project Title: Targeting mechanisms of phosphine resistance in stored grain pests

Investigators: Schillpalius D, Bellgard MI

2010 – 2011:  Australian Research Collaboration Services

Project Title: NeAT Bioflows Project – Centre for Comparative Genomics

Investigator: Bellgard MI

2007 – 2008CRC for Beef Genetic Technologies

Project Title: Identification of Novel Tick Therapeutic Targets

Investigators: Lew-Tabor A, Bellgard MI

2006 – 2008:  ARC Linkage

Project Title: An Integrated Proteomic and Bioinformatic Approach for

Classifying Raw and Cooked Fish: Truth in labeling of foodstuffs

Investigators: Bellgard MI, Taplin R, Lipscombe R

2005 – 2008Government of Western Australia

Western Australia Centre of Excellence in Science and Innovation Program

Awarded: Western Australian Centre of Excellence for Comparative Genomics

Investigator: Bellgard MI

2005 – 2008Australian Research Council

Project Title: Understanding the molecular basis of virulence in Brachyspira hyodysenteriae to improve vaccine

Investigators: Hampson D, Bellgard MI

2005 – 2008Australian Research Council

Project Title: Devising sophisticated computational comparative genomic analysis strategies for animal and plant genomes

Investigators: Bellgard MI, Kulski J, Taplin R, Appels R

2005 – 2008Molecular Plant Breeding CRC

Project Title: An Investigation into decision support for molecular plant breeding with application to grain quality: PGrad s/ship: Dean Diepeveen ID# 30442549

Investigators: Appels R, Bellgard MI

2005ARC LIEF

Project Title: Western Australian Supercomputer program (co-CI total $2.65 million)

Investigator: Bellgard MI

2004 – 2010CRC Grain Foods

Project Title: Development of a Nutrient Database for Grains

Investigators: Bellgard MI

2004 – 2006Department of Agriculture, Western Australia

Project Title: Redevelopment of PB Genesis plant breeding software

Investigators: Bellgard MI

2003 – 2006Australian Research Council

Project Title: Genomic sequencing and comparative genomic analysis for animal bacterial vaccine discovery

Investigators: Hampson D, Bellgard MI

2003 – 2005:  WA Lotteries Commission

Project Title: State Medical Biotechnology Facility (co-CI total $4 million)

Investigators: Bellgard MI

2002 – 2009:  CRC Molecular Plant Breeding

Project Title: Bioinformatics and Biological Computing

Investigators: Bellgard MI

2001 – 2004:  WA Lotteries Commission                                                                               

Project Title: WA Microarray Facility Bioinformatics Support

Investigators: Swanson N, Bellgard MI

2001 – 2004:  Grains & Research Development Corporation Research Grant

Project Title: Development of a Legume-specific Bioinformatics Resource for Legume Researchers

Investigators: Bellgard MI, Jones M, Oliver R

2001 – 2005:  Tokai University of Medicine

Project Title: Collaboration Between Centre For Biological Computing And Bioinformatics (Murdoch)

And Department Of Genetic  Information  Tokai University (Japan)

Investigators: Bellgard MI

2001 – 2002:  Department of Industry Science & Resources

Project Title: Development of biotechnology and bioinformatics research alliances with key Japanese molecular genetic research, business and investment organisations

Investigators: Bellgard, MI

2000 – 2002:  Genetype

Project Title: Consulting For Bioinformatics

Investigators: Bellgard MI

2000 – 2002:  DEETYA Science Lectureship Initiative                                                               

Project Title: Food Science: From Farm to Plate.

2000:  ARC LIEF Grant                                                                                                     

Project Title: ANGIS Regional Nodes – bioinformatics service and training infrastructure for national biological research and education

1998-1999:  Japan Society for the Promotion of Science (JSPS)                                                 

Postdoctoral Research Fellowship – 17 months

Investigator: Bellgard MI

Events and speaking engagements

2014

  • Rare Diseases (RD) Connect Meeting, Marseille, 27 June – 4 July
  • International Congress on Neuromuscular Diseases (icnmd xiii) Nice, 5-10 July
  • PAG Asia 19-21 May Singapore (Key Note Speaker)
  • Rare Diseases (RD) Connect, Germany, 26 February

2013

  • Australasian Plant Pathology Conference, New Zealand, November
  • Wold Association for the Advancement of Veterinary Parasitology, Perth, 25-29 Aug
  • Australian Research Council, Canberra, 19-21 Aug
  • International Rare Diseases Research Consortium Ireland April
  • Plant & Animal Genome, Singapore March (PAG Asia)
  • RD Connect, Barcelona Spain, Jan
  • Plant and Animal Genomic Conference XXII, San Diego, Jan 12-16

2012

  • NeCTAR Platforms, Sydney, 1 Nov
  • Muscular Dystrophy 2012 Congress, Perth, 8 Oct
  • Australian Weeds Conference, Melbourne, 8-11 Oct
  • Wheat Pathogeonomics Consortium, Adelaide, 27 Sept
  • Yabi workshop, CSIRO Plant Industry, Perth, Aug
  • Plant Biosecurity (PBCRC), Canberra, 29 Aug
  • Smart Phone Conference, Brisbane, 23-25 June
  • Bioplatforms & Melanoma, Sydney, 11-13 June
  • Science Exchange Plant Biosecurity (PBCRC), Perth May

2011

  • Society for Molecular Biology and Evolution (SMBE) Workshop, Kyoto, Japan 26-30 July
  • 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology ISMB/ECCB, Vienna, 15-19 July
  • Yabi: A sophisticated Internet-based cross -omnics analytic environment workshop, EBI, Cambridge, UK, 9-13 May
  • 2 Invited Seminars:  Yabi:  A sophisticated Internet-based cross -omnics analytic environment workshop:  The Genome Analysis Centre, John Innes Centre, Norwich & EBI, Cambridge, UK
  • Awakening Australia to Rare Diseases: Global perspectives on establishing a coordinated approach to a national plan, 18-20 April
  • 3rd Triticeae Genome Annual Meeting and IWGSC Coordinating Committee Workshop, Czech Republic, 4-8 April
  • Asian Conference on Plant Pathology (ACPP) and Australasian Plant Pathology Society Conference (APPS) 2011 Conference, 24-29 April, (Key Note Speaker)

2010

  • ICOPA XII 2010, Melbourne, Australia 15-16 August
  • Transformational Biology Capability Platform, ACT, Australia, 28-30 June

2009

  • Technical Data Workshop, Perth Dec 7
  • Genes for Health Symposium, Perth May 2-6

2008

  • ACPFG Seminar, Adelaide, July 10
  • GSA 2008 Conference, Adelaide, 7-10

2004

  • US/Australian APAC Workshop on GRID Computing, Sydney, June 7-9.
  • Invited speaker for seminar at the Department of Computer Science and Software Engineering, University of Melbourne, Melbourne, 6 July
  • Keynote speaker at the ARC Centre in Bioinformatics, 2004 Annual All Hands Meeting, Brisbane, 10-11 May
  • Invited speaker for seminar at the Department of Clinical Immunology, Royal Perth Hospital, Perth, 3 May
  • New Directions for Bioinformatics Research and Systems Delivery, Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China, 6 April

2003

  • Australian Winter Cereals Molecular Marker Program, Adelaide, March 17.
  • Plant and Animal Genomic Conference XI, San Diego, Jan 9-16.
  • First NZ Bioinformatics Conference, Wellington, Feb 11-16.
  • Australian Winter Cereals Molecular Marker Program, Adelaide, March 17.
  • Intelligent Systems in Molecular Biology, ISMB’03, Brisbane, Jun 28 – Jul 3.

2002

  • Invitation to present (closed meeting) at Waterfront Symposium of Human Genome Science (WASH), March 2002, Japan.
  • Invitation to participate (closed meeting) in Preparatory Meeting for Human Genome Annotation Central (H-Central), March 2002, Japan.

2001

  • Evolution of the CBBC, Ninth Frank and Bobbie Fenner Conference in Medical Research (Bioinformation Science), Canberra, September 2001
  • Directions of Bioinformatics research in Western Australia, Japan Biological Information Research Centre, Tokyo, Japan.
  • A Spectrum of Bioinformatics research activities in Western Australia, National Institute of Genetics, Mishima, Japan.
  • The importance of hypothesis-driven (re)analysis and an appropriate Bioinformatics Infrastructure, Tokai University, Japan, Feb 2.
  • Ninth Frank and Bobbie Fenner Conference in Medical Research
    (Bioinformation Science), Canberra, September 2001
  • Neural Networks Applications, NNA’01, Canary Islands, Tenerife, Feb 12-14.

2000

  • Bioinformatics: Global Issue, Lotteries Commission Research Symp., Per. Nov 27.
  • Bioinformatics: Only Scope, No Limits Seminar to Psychology Colloquium, MU, Sept 6.
  • The importance of hypothesis-driven (re)analysis and an appropriate Bioinformatics Infrastructure, WAIMR, Rottnest Island, March.
  • Australian Biotechnology Association Conference (ABA 2000) Biotechnology: Our Passport to the Next Millennium, Brisbane, July 2-6
  • Microarray Forum (organised as part of the CSIRO Genome Project/ANGIS/e-Bioinformatics collaboration), Sydney, Feb 1.

1999

  • West Australian Workshop on Information Systems Research (WAWISR), Perth, Nov.
  • 6th International Conference on Neural Information Processing (ICONIP’99), Perth,
    Nov 16-20
  • Fourth Chromosome 6 Workshop, Sanger Centre, Hinxton, UK, June 11-12.
  • Human Genome Meeting, HGM’99, Brisbane, Australia, March 27-30.
  • International Symposium on Evolutionary Genomics, ISME’99, Puntarenas, Costa Rica,
    Jan 11-15.  Bioinformatics: What’s all the fuss?

1998

  • Bioinformatics research to SABC and DCI, Perth

1997

  • Bioinformatics in Information Biology to CIB, NIG, Mishima, Japan.
  • International Workshop on Objects in Bioinformatics, EBI, Hinxton, UK, June 18-19.
  • International Conference on Molecular Biology and Evolution, 5th SMBE, Garmisch-Partenkirchen, Bavaria, Germany, June 1-4.

1996

  • Australian Society for Biochemistry and Molecular Biology, Canberra, October.
  • Molecular Modelling Workshop, Canberra, October.
  • Intelligent Systems for Molecular Biology ‘96, Washington University, St Louis, Missouri, USA, June 12-15.
  • Bioinformatics & Genome Research, Baltimore, Maryland, USA, June 10-11.
  • Human Genome Meeting ’96, HUGO ’96, Heidelberg, Germany, March 22-24.

 

 

Professional and community service

2013 – Present:  International Rare Diseases Research Consortium (IRDiRC), Bioinformatics and Data Sharing Committee

2012 – Present:  Australian Research Council College of Experts

2007 – Present:  Convener of the Australian Bioinformatics Facility, Bioplatforms Australia

2007 – Present:  Director iVEC@Murdoch Supercomputing Facility

2000 – 2003:  Associate Professor of Bioinformatics, Full-time, continuing

2000 – 2003:  Director, Centre for Bioinformatics and Biological Computing

2000 – 2003:  Coordinator for the WA Bioinformatics Consortium

2000 – 2003:  Subprogram Leader for the Co-operative Research Centre (CRC) for Molecular Plant Breeding

2000 – 2003:  Expert Taskforce Committee member for National Bioinformatics Strategy

2000 – 2003:  Coordinator and Host of the WA ANGIS regional node (2000-present)

 

Doctoral and masters supervisions

PhD Students

2014 – Present:  Cong Tan

Barley Genomics

2012 – Present:  Daithi Murray

An Arid Zone Time Capsule: the potential of ancient DNA preserved in middens as a source of palaeoecological data – in progress

2011 – Present:  Brett Chapman

Developing a Framework for Comparative Proteogenomics – in progress

2010 – Present:  John McCooke

PKD mutation in Rats –in progress – Key Supervisor Prof. Jacqueline K. Phillips, Director, Medical Research Unit. The Australian School of Advanced Medicine, Macquarie University

2007 – 2012:  Paula Moolhuijzen

Expanding bioinformatics predictive capabilities in diverse informatics environmentscompleted

2005 – 2010:  Sebastian Kurscheid

Bioinformatics and vaccine research- completed

2005– 2011:  Dean Diepeveen

Data Integration for Decision Making in Wheat Breeding-completed

2003 – 2006:  Yair Motro

Bacterial Bioinformatics-completed

2001 – 2005:  David Dunn

MHC Evolution and Bioinformatics-completed

2000 – 2004:  Kim Carter

Bioinformatics-completed

Honours Students – Completed

2007:  Matthew Dell

2005:  James Breen

2004:  Richard Hall, Allie Speed, Yovina Sontani

2003:  Eve Strombeck, Adam Hunter (P/T), Bill Kenworthy (P/T)

2002:  Chris Ellis, Adam Hunter (P/T), Bill Kenworthy (P/T), Adam Zumbo

2001:  Lee Wilmore

1996:  Owen Lamont, Eileen Lim, Lois Balmer, Antony Monaco, Corey Moore, Shane Linley, Wendy Monks

1995:  Shane Petterson

ISC (Independent Study Contract)

2005:  Eric Lin, Bioinformatics

2001:  Rebecca Hawkes and Christina Hadad, Molecular Evolution

2000:  Geoff Murphy, Interactive Bioinformatics Software

 

Publications

Chapters

  • Chapman, B., Castellana, N., Apffel, A., Ghan, R., Cramer, G., Bellgard, M., Haynes, P., Van Sluyter, S., (2013),Plant proteogenomics: from protein extraction to improved gene predictions,In: Proteomics for Biomarker Discovery, Humana Press, pages 267 to 294.
  • Bellgard, M., (2005),Bioinformatics from comparative genomic analysis through to integrated systems,In: Mammalian Genomics, CABI, pages 393 to 409.
  • Bellgard, M., Gojobori, T., (2005),A Comparative Analysis of Mammalian Genomics: Prokaryote and Eukaryote Perspectives,In: Mammalian Genomics, CABI, pages 263 to 278.
  • Bellgard, M., Itoh, T., Watanabe, H., Imanishi, T., Gojobori, T., (1999),Dynamic evolution of Genomes and the Concept of Genomc Space,In: ANALS NEW YORK ACADEMY of SCIENCES, Not given, pages 293 to 300.

Journals

  • Guerrero, F., Kellogg, E., Ogrey, A., Heekin, A., Barrero, R., Bellgard, M., Dowd, S., Leung, M., (2016), Prediction of G protein-coupled receptor encoding sequences from the synganglion transcriptome of the cattle tick, Rhipicephalus microplus, Ticks and Tick-borne Diseases, 7, 5, pages 670 - 677.
  • Forster, L., McCooke, J., Bellgard, M., Joske, D., Finlayson, J., Ghassemifar, R., (2015), Differential gene expression analysis in early and late erythroid progenitor cells in beta-thalassaemia, British Journal of Haematology, 170, 2, pages 257 - 267.
  • Bladen, C., Salgado, D., Monges, S., Foncuberta, M., Kekou, K., Kosma, K., Dawkins, H., Lamont, L., Roy, A., Bellgard, M., (2015), The TREAT-NMD DMD global database: Analysis of more than 7,000 duchenne muscular dystrophy mutations, Human Mutation, 36, 4, pages 395 - 402.
  • Black, M., Moolhuijzen, P., Barrero, R., La, T., Phillips, N., Hampson, D., Herbst, W., Barth, S., Bellgard, M., (2015), Analysis of multiple Brachyspira hyodysenteriae genomes confirms that the species is relatively conserved but has potentially important strain variation., PLoS One, 10, 6, pages -.
  • Barrero, R., Guerrero, F., Moolhuijzen, P., Goolsby, J., Tidwell, J., Bellgard, S., Bellgard, M., (2015), Shoot transcriptome of the giant reed, Arundo donax, Data in Brief, 3, , pages 1 - 6.
  • Coghlan, M., Maker, G., Crighton, E., Haile, J., Murray, D., White, N., Byard, R., Bellgard, M., Mullaney, I., Trengove, R., Allcock, R., Nash, E., Hoban, C., Jarrett, K., Edwards, R., Musgrave, I., Bunce, M., (2015), Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM), Scientific Reports, 5, , pages 17475 -.
  • Bendele, K., Guerrero, F., Miller, R., Li, A., Barrero, R., Moolhuijzen, P., Black, M., McCooke, J., Meyer, J., Hill, C., Bellgard, M., (2015), Acetylcholinesterase 1 in populations of organophosphate-resistant North American strains of the cattle tick, Rhipicephalus microplus (Acari: Ixodidae), Parasitology Research, 114, 8, pages 3027 - 3040.
  • Barrero, R., Guerrero, F., Moolhuijzen, P., Goolsby, J., Tidwell, J., Bellgard, S., Bellgard, M., (2015), Shoot transcriptome of the giant reed, Arundo donax, Data in Brief, 3, , pages 1 - 6.
  • Baynam, G., Walters, M., Claes, P., Kung, S., LeSouef, P., Dawkins, H., Bellgard, M., Girdea, M., Brudno, M., Robinson, P., Zankl, A., Groza, T., Gillett, D., Goldblatt, J., (2015), Phenotyping: targeting genotype's rich cousin for diagnosis, Journal of Paediatrics and Child Health, 51, 4, pages 381 - 386.
  • McCooke, J., Guerrero, F., Barrero, R., Black, M., Hunter, A., Bell, C., Schilkey, F., Miller, R., Bellgard, M., (2015), The mitochondrial genome of a Texas outbreak strain of the cattle tick, Rhipicephalus (Boophilus) microplus, derived from whole genome sequencing Pacific Biosciences and Illumina reads, Gene, 571, 1, pages 135 - 141.
  • Bellgard, M., Napier, K., Render, L., Radochonski, M., Lamont, L., Graham, C., Wilton, S., Fletcher, S., Goldblatt, J., Hunter, A., Weeramanthri, T., (2015), A Registry Framework Enabling Patient-Centred Care, Studies in Health Technology and Informatics, 214, , pages 8 - 14.
  • Barrett, L., Fletcher, S., Barrero, R., Bellgard, M., Flanigan, K., Wong, B., Wilton, S., (2014), Targeted Suppression of a Dystrophin Pseudo-exon using Antisense Oligonucleotides, Journal of Genetic Syndromes & Gene Therapy, 5, 4, pages -.
  • Bellgard, M., Render, L., Radochonski, M., Hunter, A., (2014), Second generation registry framework, Source Code for Biology and Medicine, 9, 1, pages 14 -.
  • Graham, C., Molster, C., Baynam, G., Bushby, K., Hansson, M., Kole, A., Mora, M., Monaco, L., Bellgard, M., Carpentieri, D., Posada, M., Riess, O., Rubinstein, Y., Schaefer, F., Taruscio, D., Terry, S., Zatloukal, K., Knoppers, B., Lochmüller, H., Dawkins, H., (2014), Current trends in biobanking for rare diseases, Journal of Biorepository Science for Applied Medicine, 2, , pages 49 - 61.
  • Yang, Y., Zhao, H., Barrero, R., Zhang, B., Sun, G., Wilton, I., Xie, F., Walker, K., Parks, J., Bruce, R., Guo, G., Chen, L., Zhang, Y., Huang, X., Tang, Q., Liu, H., Bellgard, M., Qiu, D., Lai, J., Hoffman, A., (2014), Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431, BMC Genomics, 15, 69, pages 1 - 14.
  • Lukaszewski, A., Alberti, A., Sharpe, A., Kilian, A., Stanca, A., Keller, B., Clavijo, B., Friebe, B., Gill, B., Chapman, B., Bellgard, M., Appels, R., (2014), A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome, Science, 345, 6194, pages 1251788-1 - 1251788-11.
  • Bellgard, M., Sleeman, M., Guerrero, F., Fletcher, S., Baynam, G., Goldblatt, J., Rubinstein, Y., Bell, C., Groft, S., Barrero, R., Bittles, A., Wilton, S., Mason, C., Weeramanthri, T., (2014), Rare Disease Research Roadmap: Navigating the bioinformatics and translational challenges for improved patient health outcomes, Health Policy and Technology, 3, 4, pages 325 - 335.
  • Barrero, R., Moolhuijzen, P., Indjein, L., Venus, B., Keeble-Gagnere, G., Power, J., Bellgard, M., Lew-Tabor, A., (2014), Draft Genome Sequences of Campylobacter fetus subsp. venerealis bv. venerealis Strain B6 and bv. intermedius Strain 642-21, Genome Announcements, 2, 5, pages e00943 - e00944.
  • Chapman, B., Bellgard, M., (2014), High-throughput parallel proteogenomics: A bacterial case study, Proteomics, 14, 23, pages 2780 - 2789.
  • Coghlan, M., White, N., Murray, D., Houston, J., Rutherford, W., Bellgard, M., Haile, J., Bunce, M., (2013), Metabarcoding avian diets at airports: implications for birdstrike hazard management planning, Investigative Genetics, 4, 1, pages 27 -.
  • Appels, R., Barrero, R., 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, pages 1 - 9.
  • Rodriguez-Valle, M., Moolhuijzen, P., Piper, E., Weiss, O., Vance, M., Bellgard, M., 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, pages 739 - 752.
  • Murray, D., Haile, J., Dortch, J., White, N., Haouchar, D., Bellgard, M., Allcock, R., Prideaux, G., Bunce, M., (2013), Scrapheap challenge: a novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages, Scientific Reports, 3, 28, pages 3371 -.
  • Moolhuijzen, P., Manners, J., Wilcox, S., Bellgard, M., Gardiner, D., (2013), Genome sequences of six wheat-infecting fusarium species isolates, Genome Announcements, 1, 5, pages e00670 -.
  • Bellgard, M., Taplin, R., Chapman, B., Livk, A., Wellington, C., Hunter, A., Lipscombe, R., (2013), Classification of fish samples via an integrated proteomics and bioinformatics approach, Proteomics, 13, 21, pages 3124 - 3130.
  • Baynam, G., Walters, M., Dawkins, H., Bellgard, M., Halbert, A., Claes, P., (2013), Objective monitoring of mTOR inhibitor therapy by three-dimensional facial analysis, Twin Research and Human Genetics, 16, 4, pages 840 - 844.
  • Bellgard, M., Bellgard, S., (2012), A Bioinformatics Framework for plant pathologists to deliver global food security outcomes, Australasian Plant Pathology, 41, 2, pages 113 - 124.
  • Black, M., Moolhuijzen, P., Chapman, B., Barrero, R., Howieson, J., Hungria, M., Bellgard, M., (2012), The genetics of symbiotic nitrogen fixation: Comparative genomics of 14 rhizobia strains by resolution of protein clusters, Genes, 3, 1, pages 138 - 166.
  • Webster, H., Keeble-Gagnere, G., Dell, B., Fosu-Nyarko, J., Mukai, Y., Moolhuijzen, P., Bellgard, M., Jia, J., Kong, X., Feuillet, C., Choulet, F., Appels, R., (2012), Genome-level identification of cell wall invertase genes in wheat for the study of drought tolerance, Functional Plant Biology: an international journal of plant function, 39, 7, pages 569 - 579.
  • Murray, D., Pearson, S., Fullagar, R., Chase, B., Houston, J., Atchison, J., White, N., Bellgard, M., Clarke, E., Macphail, M., Gilbert, T., Haile, J., Bunce, M., (2012), High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens, Quaternary Science Reviews, 58, , pages 135 - 145.
  • Hunter, A., Macgregor, A., Szabo, T., Wellington, C., Bellgard, M., (2012), Yabi: An online research environment for grid, high performance and cloud computing, Source Code for Biology and Medicine, 7, 1, pages -.
  • Mappley, L., Black, M., AbuOun, M., Darby, A., Woodward, M., Parkhill, J., Turner, A., Bellgard, M., La, T., Phillips, N., La Ragione, R., Hampson, D., (2012), Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity, BMC Genomics, 13, 1, pages 454 -.
  • McCooke, J., Appels, R., Barrero, R., Ding, A., Ozimek-Kulik, J., Bellgard, M., Morahan, G., Philips, A., (2012), A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8., BMC Genomics, 13, 1, pages 1 - 16.
  • Bellgard, M., Macgregor, A., Janon, F., Harvey, A., O'Leary, P., Hunter, A., Dawkins, H., (2012), A modular approach to disease registry design: Successful adoption of an internet-based rare disease registry, Human Mutation, 33, 10, pages E2356 - E2366.
  • Edwards, D., Wilcox, S., Barrero, R., Fleury, D., Cavanagh, C., Forrest, K., Hayden, M., Moolhuijzen, P., Keeble-Gagnere, G., Bellgard, M., Lorenc, M., Shang, C., Baumann, U., Taylor, J., Morell, M., Lang-ridge, P., Appels, R., Fitzgerald, A., (2012), Bread matters: A national initiative to profile the genetic diversity of Australian wheat, Plant Biotechnology Journal, 10, 6, pages 703 - 708.
  • Appels, R., Barrero, R., 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, pages 1 - 9.
  • Coghlan, M., Haile, J., Houston, J., Murray, D., White, N., Moolhuijzen, P., Bellgard, M., Bunce, M., (2012), Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns, PLoS Genetics (Print), 8, 4, pages 1 - 11.
  • Bellgard, M., Moolhuijzen, P., Guerrero, F., Schibeci, D., Rodriguez-Valle, M., Peterson, D., Dowd, S., Barrero, R., Hunter, A., Miller, R., Lew-Tabor, A., (2012), CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus, International Journal for Parasitology, 42, 2, pages 161 - 169.
  • Moolhuijzen, P., Lew-Tabor, A., Morgan, J., Valle, M., Peterson, D., Dowd, S., Guerrero, F., Bellgard, M., Appels, R., (2011), The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones, BMC Research Notes, 4, 254, pages 1 - 16.
  • Sinha, S., Black, M., Agarwal, S., Das, R., Bittles, A., Bellgard, M., (2011), ThalInd, a -thalassemia and hemoglobinopathies database for India: Defining a model country-specific and disease-centric bioinformatics resource, Human Mutation, 32, 8, pages 887 - 893.
  • Wang, K., Gao, L., Wang, S., Zhang, Y., Li, X., Zhang, M., Xie, Z., Yan, Y., Bellgard, M., Ma, W., (2011), Phylogenetic relationship of a new class of LMW-GS genes in the M genome of aegilops comosa, Theoretical and Applied Genetics: international journal of plant breeding research, 122, 7, pages 1411 - 1425.
  • Appels, R., Adelson, D., Moolhuijzen, P., Webster, H., Barrero, R., Bellgard, M., (2011), Genome studies at the PAG 2011 conference, Functional & Integrative Genomics, 11, 1, pages 1 - 11.
  • Barrero, R., Chapman, B., Yang, Y., Moolhuijzen, P., Keeble-Gagnere, G., Zhang, N., Tang, Q., Bellgard, M., Qiu, D., (2011), De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes, BMC Genomics, 12, 600, pages 1 - 14.
  • La, T., Phillips, N., Wanchanthuek, P., Bellgard, M., O'Hara, A., Hampson, D., (2011), Evidence that the 36kb plasmid of Brachyspira hyodysenteriae contributes to virulence, Veterinary Microbiology, 153, 1-2, pages 150 - 155.
  • Lew-Tabor, A., Kurscheid, S., Barrero, R., Gondro, C., Moolhuijzen, P., Rodriguez Valle, M., Morgan, J., Covacin, C., Bellgard, M., (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, pages 1001 - 1014.
  • Barrero, R., Bellgard, M., Zhang, X., (2011), Diverse approaches to achieving grain yield in wheat, Functional & Integrative Genomics, 11, 1, pages 37 - 48.
  • Murray, D., Bunce, M., Cannell, B., Oliver, R., Houston, J., White, N., Barrero, R., Bellgard, M., Haile, J., (2011), DNA-based faecal dietary analysis: A comparison of qPCR and high throughput sequencing approaches, PLoS One, 6, 10, pages 1 - 10.
  • She, M., Ye, X., Yan, Y., Howit, C., Bellgard, M., Ma, W., (2011), Gene networks in the synthesis and deposition of protein polymers during grain development of wheat, Functional & Integrative Genomics, 11, 1, pages 23 - 35.
  • Barrero, R., Keeble-Gagnere, G., Zhang, B., Moolhuijzen, P., Ikeo, K., Tateno, Y., Gojobori, T., Guerrero, F., Lew-Tabor, A., Bellgard, M., (2011), Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus, BMC Genomics, 12, , pages -.
  • Lew, A., Moolhuijzen, P., Vance, M., Guerrero, F., Bellgard, M., 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, 437, pages -.
  • Guerrero, F., Moolhuijzen, P., Peterson, D., Bidwell, S., Caler, E., Bellgard, M., Nene, V., Djikeng, A., (2010), Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus, BMC Genomics, 11, 374, pages -.
  • Sinha, S., Black, M., Agarwal, S., Colah, R., Das, R., Ryan, K., Bellgard, M., Bittles, A., (2010), Profiling -thalassaemia mutations in India at state and regional levels: Implications for genetic education, screening and counselling programmes, The H U G O Journal, 3, 1, pages 51 - 62.
  • Nelson, M., Moolhuijzen, P., Boersma, J., Chudy, M., Lesniewska, K., Bellgard, M., Oliver, R., Swiecicki, W., Wolko, B., Cowling, W., Ellwood, S., (2010), Aligning a new reference genetic map of lupinus angustifolius with the genome sequence of the model legume, lotus japonicus, DNA Research, 17, 2, pages 73 - 83.
  • Moolhuijzen, P., Kulski, J., Dunn, D., Schibeci, D., Barrero, R., Gojobori, T., Bellgard, M., (2010), The transcript repeat element: The human Alu sequence as a component of gene networks influencing cancer, Functional & Integrative Genomics, 10, 3, pages 307 - 319.
  • Breen, J., Wicker, T., Xiuying, K., Zhang, J., Ma, W., Paux, E., Feuillet, C., Appels, R., 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, 98, pages -.
  • Wanchanthuek, P., Bellgard, M., La, T., Ryan, K., Moolhuijzen, P., Chapman, B., Black, M., Schibeci, D., Hunter, A., Barrero, R., Phillips, N., Hampson, D., (2010), The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes, PLoS One, 5, 7, pages -.
  • Black, M., Sinha, S., Agarwal, S., Colah, R., Das, R., Bellgard, M., Bittles, A., (2010), A descriptive profile of -thalassaemia mutations in India, Pakistan and Sri Lanka, Journal of Community Genetics, 1, 3, pages 149 - 157.
  • Breen, J., Li, D., Dunn, D., Bekes, F., Kong, X., Zhang, J., Jia, J., Wicker, T., Mago, R., Ma, W., Bellgard, M., 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, 99, pages -.
  • Bellgard, M., Breen, J., (2010), Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence, Functional & Integrative Genomics, 10, 4, pages 463 - 476.
  • Appels, R., Barrero, R., Keeble-Gagnere, G., Bellgard, M., (2010), Advances in genome studies: The PAG 2010 conference, Functional & Integrative Genomics, 10, 1, pages 1 - 9.
  • Lew, A., Moolhuijzen, P., Vance, M., Kurscheid, S., Jackson, L., Jonsson, N., Bellgard, M., Guerrero, F., (2010), Suppressive subtractive hybridization analysis of Rhipicephalus (Boophilus) microplus larval and adult transcript expression during attachment and feeding, Veterinary Parasitology, 167, 2-4, pages 304 - 320.
  • Bellgard, M., Wanchanthuek, P., La, T., Ryan, K., Moolhuijzen, P., Albertyn, Z., Shaban, B., Motro, Y., Dunn, D., Schibeci, D., Hunter, A., Barrero, R., Phillips, N., Hampson, D., (2009), Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine, PLoS One, 4, 3, pages -.
  • Song, Y., La, T., Phillips, N., Bellgard, M., Hampson, D., (2009), A reverse vaccinology approach to swine dysentery vaccine development, Veterinary Microbiology, 137, , pages 111 - 119.
  • Kurscheid, S., Lew, A., Doogan, V., Munderloh, U., Guerrero, F., Barrero, R., Bellgard, M., (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, , pages 26 -.
  • Jia, Q., Zhang, J., Westcott, S., Zhang, X., Bellgard, M., Lance, R., Li, C., (2009), GA-20 oxidase as a candidate for the semidwarf gene sdw1/denso in barley, Functional & Integrative Genomics, 9, , pages 255 - 262.
  • La, T., Phillips, N., Harland, B., Wanchanthuek, P., Bellgard, M., Hampson, D., (2009), Multilocus sequence typing as a tool for studying the molecular epidemiology and population structure of Brachyspira hyodysenteriae, Veterinary Microbiology, 138, , pages 330 - 338.
  • Motro, Y., La, T., Bellgard, M., Dunn, D., Phillips, N., Hampson, D., (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, , pages 340 - 345.
  • Moolhuijzen, P., Lew, A., Wlodek, B., Comerci, D., Ugalde, R., Sanchez, D., Appels, R., Bellgard, M., (2009), Genomic analysis of campylobacter fetus subspecies: identification of candidate virulence determinants and diagnostic assay targets, BMC Molecular Biology, 9, , pages -.
  • Yamasaki, C., Murakami, K., Fujii, Y., Sato, Y., Harada, E., Takeda, J., Taniya, T., Sakate, R., Kikugawa, S., Shimada, M., Bellgard, M., Shionyu, M., Jia, L., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Zhang, Q., Go, M., Minoshima, S., Ohtsubo, M., Tanino, M., Hanada, K., Tonellato, P., Isogai, T., Zhang, J., Lenhard, B., Kim, S., Chen, Z., Hinz, U., Estreicher, A., Nakai, K., Koyanagi, K., Makalowska, I., Hide, W., Tiffin, N., Wilming, L., Chakraborty, R., Soares, M., Chiusano, M., Suzuki, Y., Auffray, C., Yamaguchi-Kabata, Y., Barrero, R., Itoh, T., Hishiki, T., Fukuchi, S., Nishikawa, K., Sugano, S., Nomura, N., Tateno, Y., Imanishi, T., Gojobori, T., Gough, C., Chun, H., Habara, T., Hanaoka, H., Hayakawa, Y., Hilton, P., Kaneko, Y., Kanno, M., Kawahara, Y., Kawamura, T., Matsuya, A., Nagata, N., Nishikata, K., Noda, A., 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., Lin, Y., 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., Hirakawa, M., Makalowski, W., Nakao, M., Kim, N., Yoo, H., De Souza, S., Bonaldo, M., Niimura, Y., Kuryshev, V., Schupp, I., Wiemann, S., (2008), The H-Invitational Database (H-InvDB), a Comprehensive Annotation Resource for Human Genes and Transcripts., Nucleic Acids Research, 36, SUPPL. 1, pages D793 - D799.
  • Motro, Y., Dunn, D., La, T., Phillips, N., Hampson, D., Bellgard, M., (2008), Intestinal Spirochaetes of the Genus Brachyspira Share a Partially Conserved 26 Kilobase Genomic Region with Enterococcus faecalis and Escherichia coli, Microbiology Insights, 1, , pages 3 - 11.
  • Kongsuwan, K., Piper, E., Bagnall, N., Ryan, K., Moolhuijzen, P., Bellgard, M., Lew, A., Jackson, L., Jonsson, N., (2008), Identification of genes involved with tick infestation in Bos taurus and Bos indicus, Developmental Biology, 132, , pages 77 - 88.
  • McNeil, M., Paux, E., Dunn, D., McLean, R., Feuillet, C., Li, D., Kong, X., Lagudah, E., Spielmeyer, W., Bellgard, M., Appels, R., (2008), BAC-derived markers for assaying the stem rust resistance gene, Sr2, in wheat breeding programs., Molecular Breeding: new strategies in plant improvement, 22, 1, pages 15 - 24.
  • Greene, W., Sontani, Y., Sharp, M., Dunn, D., Kees, U., Bellgard, M., (2007), A promoter with bidirectional activity is located between TLX1/HOX11 and a divergently transcribed novel human gene, Gene, 391, 1-Feb, pages 223 - 232.
  • Moolhuijzen, P., Dunn, D., Bellgard, M., Carter, M., Jia, J., Kong, X., Gill, B., Feuillet, C., Breen, J., Appels, R., (2007), Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium, Australian Journal of Agricultural Research, 58, , pages 470 - 475.
  • Dunn, D., Hampson, D., Bellgard, M., La, T., Binnewies, T., Motro, Y., Hallin, P., Lund, O., Wassenaer, T., Ussery, D., (2006), Ten years of bacterial genome sequencing: comparative genomics based discoveries, Functional & Integrative Genomics, 6, 3, pages 165 - 185.
  • O'Lone, C., Fosu-Nyarko, J., Scobie, M., Cakir, M., Jones, M., Bellgard, M., Wolko, B., Barker, S., Nelson, M., Oliver, R., Cowling, W., (2006), The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula, Theoretical and Applied Genetics: international journal of plant breeding research, 113, , pages 225 - 238.
  • Moolhuijzen, P., Cakir, M., Hunter, A., Schibeci, D., Macgregor, A., Smith, C., Francki, M., Jones, M., Appels, R., Bellgard, M., (2006), LegumeDB bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species, Genome, 49, 6, pages 689 - 699.
  • Moolhuijzen, P., Cakir, M., Hunter, A., Schibeci, D., Macgregor, A., Smith, C., Francki, M., Jones, M., Appels, R., 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, pages 1206 - 1207.
  • Appels, R., Bellgard, M., (2005), Looking through genomics - from the editors, Functional & Integrative Genomics, 5, 1, pages 1 - 3.
  • Dunn, D., Romphruk, A., Leelayuwat, C., Bellgard, M., Kulski, J., (2005), Polymorphic Alu insertions and their associations with MHC class I alleles and haplotypes in the northeastern Thais, Annals of Human Genetics, 69, , pages 364 - 372.
  • Nozaki, Y., 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 (Print Edition), 21, 8, pages 1421 - 1428.
  • Lew, A., Jackson, L., Bellgard, M., (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, 7 & 8, pages 995 - 1010.
  • Kulski, J., Kenworthy, W., Bellgard, M., Taplin, R., Okomoto, K., Oka, A., Mabuchi, T., Ozawa, A., Tamiya, G., Inoko, H., (2005), Gene expression profiling of Japanese psoriatic skin reveals an increase activity in molecular stress and immune response signals, Journal of molecular medicine (Berlin, Germany), 83, 12, pages 964 - 975.
  • Bellgard, M., (2004), Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones, PLoS Biology (Print), 2, 6, pages 856 - 875.
  • 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., Appels, R., (2004), Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison, Functional & Integrative Genomics, 4, 2, pages 84 - 93.
  • Francki, M., Carter, M., Ryan, K., Hunter, A., Bellgard, M., Appels, R., (2004), Comparative organization of wheat homoeologour 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, pages 118 - 130.
  • Bellgard, M., Ye, J., Gojobori, T., Appels, R., (2004), The bioinformatics challenges in comparative analysis of cereal genomes - an overview, Functional & Integrative Genomics, 4, 1, pages 1 - 11.
  • Bellgard, M., Gamble, T., Reynolds, M., Hunter, A., Trifonov, E., Taplin, R., Taplin, R., (2003), Gap mapping: a paradigm for aligning two sequences, Applied Bioinformatics, 2, , pages 1 - 5.
  • Carter, K., Bellgard, M., (2003), MASV - Multiple (BLAST) Annotation System Viewer, Bioinformatics (Print Edition), 19, 17, pages 2313 - 2315.
  • Bellgard, M., Hunter, A., Kenworthy, W., (2003), Microarry analaysis using bioinformatics analysis audit trails (BAATs), Biologies, 326, 10-Nov, pages 1083 - 1087.
  • Bellgard, M., Kenworthy, W., (2003), FBSA: feature-based sequence alignment technique for very large sequences, Applied Bioinformatics, 2, 3, pages 145 - 150.
  • Kulski, J., Lim, C., Dunn, D., 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, pages 397 - 406.
  • Bellgard, M., Schibeci, D., Trifonov, E., 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-May, pages 465 - 468.
  • Tsunoyama, K., Bellgard, M., Gojobori, T., (2001), Intragenic variation of synonymous substitution rates is caused by nonrandom mutations of methylated CpG, Journal of Molecular Evolution, 53, 4-May, pages 456 - 464.
  • Bellgard, M., Hiew, H., Hunter, A., Wiebrands, M., (1999), ORBIT: an integrated environment for user-customized bioinformatics tools, Bioinformatics (Print Edition), 15, , pages 847 - 851.
  • Bellgard, M., Gojobori, T., (1999), Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G + C content, Gene, 238, , pages 33 - 37.
  • Herbison, C., Sayer, D., Bellgard, M., Allcock, R., Christiansen, F., Price, P., (1999), Structure and polymorphism of two stress-activated protein kinase genes centromeric of the MHC:SAPK2a and SAPK4, DNA Seq, 10, , pages 229 - 243.
  • Bellgard, M., Gojobori, T., (1999), Inferring the direction of evolutionary changes of genomic base composition, Trends in Genetics, 15, 7, pages 254 - 256.
  • Bellgard, M., 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, , pages 6 - 8.
  • Bellgard, M., Tay, G., Hiew, H., Witt, C., Ketheesan, N., Christiansen, F., Dawkins, R., (1998), MHC Haplotype Analysis by Artificial Neural Networks., Human Immunology, Vol 59, , pages 56 - 62.
  • Kulski, J., Gaudieri, S., Bellgard, M., Balmer, L., Giles, K., Inoko, H., Dawkins, R., (1997), The Evolution of MHC Diversity by Segmental Duplication and Transposition of Retroelements, Journal of Molecular Evolution, 7, 45, pages 599 - 609.

Conference

  • Keeble-Gagnere, G., Nyström-Persson, J., Bellgard, M., Mizuguchi, K., (2012),An open framework for extensible multi-stage bioinformatics software,In: 7th International Association for Pattern Recognition (IAPR) International Conference on Pattern Recognition in Bioinformatics (2012).
  • Wang, Z., King, E., Smith, G., Bellgard, M., Broomhall, M., Chedzey, H., Fearns, P., Garcia, R., Hunter, A., Lynch, M., Shibeci, D., (2011),RS-YABI: A workflow system for Remote Sensing Processing in AusCover,In: 19th International Congress on Modelling and Simulation (MODSIM) (2011).
  • Diepeveen, D., Armstrong, L., Clarke, P., Abrecht, D., Appels, R., Bellgard, M., (2008),Applying data mining tools to improve grain quality for growers,In: Agribusiness Crop Updates (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., (2008),A dense reference map of the Lupinus Angustifolius L. Genome: A foundation for building lupin genome research,In: 12th International Lupin Conference (2008).
  • Diepeveen, D., Clarke, G., Bellgard, M., Appels, R., Crosbie, G., (2007),Physical Grain Screenings of Plant Breeding Germplasm,In: 1st Latin American ICC Conference (2007).
  • Hiew, H., Bellgard, M., (2007),A bioinformatics reference model: towards a framework for developing and organising bioinformatics resources,In: International Symposium on Computational Models of Life Sciences (CMLS) (2007).
  • Hiew, H., Schibeci, D., Fraser, R., Rohl, A., Hunter, A., Bellgard, M., (2007),The APAC Genome Annotation System: Enabling Life Science Research Through the Grid,In: 4th International Conference on Asian and Pacific Coasts (APAC) (2007).
  • Lew, A., Guo, S., Venus, B., Moolhuijzen, P., Sanchez, D., Trott, D., Burrell, P., Wlodek, B., 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 (CHRO) (2007).
  • Nozaki, Y., Macgregor, A., Smith, C., Hunter, A., Bellgard, M., (2005),Multidotter: Dot-matrix Program for Multiple Sequences,In: Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS) International Conference (2005).
  • Bellgard, M., Williams, H., Smith, C., Macgregor, A., Hunter, A., Appels, R., Griffiths, T., (2005),Grains composition and nutrition online database,In: Grains composition and nutrition online database.
  • Anderson, J., Whitehand, S., Lichtenzveig, J., Moolhuijzen, P., Bellgard, M., Oliver, R., Singh, K., (2005),Genetic analysis of defence responses against necrotrophic pathogens in legumes,In: 2nd Australian Model Legume Workshop (2005).
  • Hunter, A., Schibeci, D., Hiew, H., 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).
  • Dwyer, G., Loo, H., Schibeci, D., Hunter, A., Siddique, K., Khan, T., Bellgard, M., Jones, M., (2002),Molecular and bioinformatics approaches for chickpea (Cicer arietinum L.) improvement.,In: 12th Australasian Plant Breeding Conference (2002).
  • Carter, K., Bellgard, M., Schibeci, D., (2001),WWW Issues for conducting sophisticated bioinformatic analysis,In: 7th Australian World Wide Web Conference (AusWeb) (2001).
  • Lamont, O., Liang, H., Bellgard, M., (2001),Data representation influences protein secondary structure predictio using artificial neural networks,In: 7th Australian and New Zealand Intelligent Information Systems (ANZIIS) Conference (2001).
  • Schibeci, D., Potter, R., Wathen-Dunn, K., Jones, M., Bellgard, M., (2001),Applying artificial neural networks to classification of wheat varieties processed by MALDI-TOF mass spectrometry,In: WSES International Conference: Advances in Neural Networks and Applications.
  • Bellgard, M., Taplin, R., (1999),Why a Window-based learning algorithm using an effective boltzmann machine is superior to the original BM learning algorithm,In: .
  • Hiew, H., Bellgard, M., Schibeci, D., (1999),Visualising the Evolutionary Dynamics of Molecular Data Using Self Organising Feature Maps,In: Proceedings of The Third Australia-Japan Joint Workshop on Intelligent and Evolutionary Systems.
  • Bellgard, M., Schibeci, D., Hiew, H., (1999),An Information System for Whole Genome Data,In: Proceedings of The Second Western Australian Workshop on Information Systems Research.