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Matthew Bellgard

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Rudi Appels; R Barrero; Matthew Bellgard
Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals.
Brett Chapman; Grant R Cramer; Ryan Ghan; Paul A Haynes; Alex Apffel; Matthew Bellgard; Natalie Castellana; Steven C Van Sluyter
Plant proteogenomics: from protein extraction to improved gene predictions.
Miriam Rodrigues; Matthew Bellgard; Hugh Dawkins; Graeme Hammond-Tooke; Alexa Kidd; Donald Love; Rakesh Patel; Richard Roxburgh
The New Zealand Neuromuscular Disease Registry.

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All Publications

2013: Rudi Appels; R Barrero; Matthew Bellgard
Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals.
Functional & integrative genomics 2013;13(1):1-9.
2013: Brett Chapman; Grant R Cramer; Ryan Ghan; Paul A Haynes; Alex Apffel; Matthew Bellgard; Natalie Castellana; Steven C Van Sluyter
Plant proteogenomics: from protein extraction to improved gene predictions.
Methods in molecular biology (Clifton, N.J.) 2013;1002():267-94.
2012: Miriam Rodrigues; Matthew Bellgard; Hugh Dawkins; Graeme Hammond-Tooke; Alexa Kidd; Donald Love; Rakesh Patel; Richard Roxburgh
The New Zealand Neuromuscular Disease Registry.
Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia 2012;19(12):1749-50.
2012: Matthew Bellgard; Adam Harvey; Adam Hunter; Fred Janon; Andrew Macgregor; Peter O'Leary; Hugh Dawkins
A modular approach to disease registry design: successful adoption of an internet-based rare disease registry.
Human mutation 2012;33(10):E2356-66.
2012: Rudi Appels; R Barrero; Matthew Bellgard
Advances in biotechnology and linking outputs to variation in complex traits: Plant and Animal Genome meeting January 2012.
Functional & integrative genomics 2012;12(1):1-9.
2012: Matthew Bellgard; Scot E Dowd; Felix D Guerrero; Adam Hunter; Robert J Miller; Manuel Rodriguez Valle; Daniel G Peterson; Manuel Rodriguez-Valle; David Schibeci; Roberto Barrero; Ala Lew
CattleTickBase: an integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus.
International journal for parasitology 2012;42(2):161-9.
2012: Luke J Mappley; Julian Parkhill; Nyree D Phillips; A Keith Turner; Martin J Woodward; manal abu oun; Matthew Bellgard; Michael L Black; Alistair C Darby; Roberto M La Ragione; Tom La; David J Hampson
Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity.
BMC genomics 2012;13():454.
2012: John K McCooke; Grant Morahan; Justyna E Ozimek-Kulik; Rudi Appels; Roberto A Barrero; Matthew Bellgard; Alice Ding; Jacqueline K Phillips
A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8.
BMC genomics 2012;13():393.
2012: Megan L Coghlan; James Haile; Jayne Houston; Paula Moolhuijzen; Dáithí C Murray; Nicole E White; Matthew Bellgard; Michael Bunce
Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns.
PLoS genetics 2012;8(4):e1002657.
2011: Tom La; Amanda J O'Hara; Nyree D Phillips; Phatthanaphong Wanchanthuek; Matthew Bellgard; David J Hampson
Evidence that the 36 kb plasmid of Brachyspira hyodysenteriae contributes to virulence.
Veterinary microbiology 2011;153(1-2):150-5.
2011: Ala Lew; Paula M Moolhuijzen; J A T Morgan; Manuel Rodriguez Valle; R Barrero; C Covacin; C Gondro; S Kurscheid; Matthew Bellgard
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 2011;41(9):1001-14.
2011: Sujata Sinha; Sarita Agarwal; Alan H Bittles; Michael L Black; Reena Das; Matthew Bellgard
ThalInd, a β-thalassemia and hemoglobinopathies database for India: defining a model country-specific and disease-centric bioinformatics resource.
Human mutation 2011;32(8):887-93.
2011: Rudi Appels; D L Adelson; Paula M Moolhuijzen; H Webster; R Barrero; Matthew Bellgard
Genome studies at the PAG 2011 conference.
Functional & integrative genomics 2011;11(1):1-11.
2011: Roberto A Barrero; Matthew Bellgard; Xueyong Zhang
Diverse approaches to achieving grain yield in wheat.
Functional & integrative genomics 2011;11(1):37-48.
2011: Roberto A Barrero; Matthew Bellgard; Brett Chapman; Gabriel Keeble-Gagnère; Paula Moolhuijzen; Qi Tang; Yanfang Yang; Nan Zhang; Deyou Qiu
De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes.
BMC genomics 2011;12():600.
2011: Dáithí C Murray; Rebecca Oliver; Nicole E White; Jayne Houston; Roberto A Barrero; Matthew Bellgard; Michael Bunce; Belinda L Cannell; James Haile
DNA-based faecal dietary analysis: a comparison of qPCR and high throughput sequencing approaches.
PloS one 2011;6(10):e25776.
2011: Manuel Rodriguez Valle; Jess A T Morgan; Daniel G Peterson; Manuel Rodriguez Valle; Matthew Bellgard; Scot E Dowd; Felix D Guerrero; Ala Lew; Rudi Appels
The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones.
BMC research notes 2011;4():254.
2011: Roberto A Barrero; Takashi Gojobori; Felix D Guerrero; Kazuho Ikeo; Gabriel Keeble-Gagnère; Ala Lew-Tabor; Paula M Moolhuijzen; Yoshio Tateno; Bing Zhang; Matthew Bellgard
Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus.
BMC genomics 2011;12():328.
2010: James Breen; Matthew Bellgard
Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence.
Functional & integrative genomics 2010;10(4):463-76.
2010: Michael Black; R Colah; R Das; S Sinha; S Agarwal; Matthew Bellgard; Alan H Bittles
A descriptive profile of β-thalassaemia mutations in India, Pakistan and Sri Lanka.
Journal of community genetics 2010;1(3):149-57.
2010: Matthew Nicholas Nelson; Paula M Moolhuijzen; Jeffrey G Boersma; Magdalena Chudy; Karolina Lesniewska; Matthew Bellgard; Richard Oliver; Wojciech Swiecicki; Bogdan Wolko; Wallace A Cowling; Simon Ellwood
Aligning a new reference genetic map of Lupinus angustifolius with the genome sequence of the model legume, Lotus japonicus.
DNA research : an international journal for rapid publication of reports on genes and genomes 2010;17(2):73-83.
2010: Manuel Rodriguez Valle; Ala Lew-Tabor; Cedric Gondro; Paula M Moolhuijzen; Megan Vance; Felix D Guerrero; Matthew Bellgard; Wayne Jorgensen
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 2010;11():437.
2010: Phatthanaphong Wanchanthuek; Matthew Bellgard; Tom La; Karon Ryan; Paula Moolhuijzen; Brett Chapman; Michael Black; David Schibeci; Adam Hunter; Roberto Barrero; Nyree D Phillips; David J Hampson
The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes.
PloS one 2010;5(7):e11455.
2010: Felix D Guerrero; Paula Moolhuijzen; Daniel G Peterson; Shelby Bidwell; Elisabet Caler; Matthew Bellgard; Vishvanath Nene; Appolinaire Djikeng
Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus.
BMC genomics 2010;11():374.
2010: James Breen; Dora Li; David S Dunn; Ferenc Békés; Xiuying Kong; Juncheng Zhang; Jizeng Jia; Thomas Wicker; Rohit Mago; Wujun Ma; Matthew Bellgard; Rudi Appels
Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain.
BMC plant biology 2010;10():99.
2010: James Breen; Thomas Wicker; Xiuying Kong; Juncheng Zhang; Wujun Ma; Etienne Paux; Catherine Feuillet; Rudi Appels; Matthew Bellgard
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 2010;10():98.
2009: Tom La; Nyree D Phillips; Belinda L Harland; Phatthanaphong Wanchanthuek; Matthew Bellgard; David J Hampson
Multilocus sequence typing as a tool for studying the molecular epidemiology and population structure of Brachyspira hyodysenteriae.
Veterinary microbiology 2009;138(3-4):330-8.
2009: Yong Song; Tom La; Nyree D Phillips; Matthew Bellgard; David J Hampson
A reverse vaccinology approach to swine dysentery vaccine development.
Veterinary microbiology 2009;137(1-2):111-9.
2009: Yair Motro; Tom La; Matthew Bellgard; David S Dunn; Nyree D Phillips; David J Hampson
Identification of genes associated with prophage-like gene transfer agents in the pathogenic intestinal spirochaetes Brachyspira hyodysenteriae, Brachyspira pilosicoli and Brachyspira intermedia.
Veterinary microbiology 2009;134(3-4):340-5.
2009: Paula M Moolhuijzen; Ala Lew; Bartosz M Wlodek; Fernán G Agüero; Diego COMERCI; Rodolfo A Ugalde; Daniel O Sanchez; Rudi Appels; Matthew Bellgard
Genomic analysis of Campylobacter fetus subspecies: identification of candidate virulence determinants and diagnostic assay targets.
BMC microbiology 2009;9():86.
2009: Matthew Bellgard; Phatthanaphong Wanchanthuek; Tom La; Karon Ryan; Paula Moolhuijzen; Zayed Albertyn; Babak Shaban; Yair Motro; David S Dunn; David Schibeci; Adam Hunter; Roberto Barrero; Nyree D Phillips; David J Hampson
Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.
PloS one 2009;4(3):e4641.
2007: Wayne K Greene; Yovina Sontani; Margaret A Sharp; David S Dunn; Ursula R Kees; Matthew Bellgard
A promoter with bidirectional activity is located between TLX1/HOX11 and a divergently transcribed novel human gene.
Gene 2007;391(1-2):223-32.
2006: Matthew Nicholas Nelson; Huyen T T Phan; Simon Ellwood; Paula M Moolhuijzen; James K Hane; Angela Williams; Clare E O'Lone; John Fosu-Nyarko; Marie Scobie; Mehmet Cakir; Michael G K Jones; Matthew Bellgard; Michał Ksiazkiewicz; Bogdan Wolko; Susan J Barker; Richard Oliver; Wallace A Cowling
The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 2006;113(2):225-38.
2006: Tim T Binnewies; Yair Motro; Peter F Hallin; Ole Lund; David Dunn; Tom La; David J Hampson; Matthew Bellgard; Trudy M. Wassenaar; David W Ussery
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries.
Functional & integrative genomics 2006;6(3):165-85.
2006: Paula M Moolhuijzen; Mehmet Cakir; Adam Hunter; David Schibeci; A Macgregor; C Smith; Michael G Francki; Michael G K Jones; Rudi Appels; Matthew Bellgard
LegumeDB1 bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species.
Genome / National Research Council Canada = Génome / Conseil national de recherches Canada 2006;49(6):689-99.
2005: Jerzy K Kulski; William Kenworthy; Matthew Bellgard; Ross Taplin; Koichi Okamoto; Akira Oka; Tomotaka Mabuchi; Akira Ozawa; Gen Tamiya; Hidetoshi Inoko
Gene expression profiling of Japanese psoriatic skin reveals an increased activity in molecular stress and immune response signals.
Journal of molecular medicine (Berlin, Germany) 2005;83(12):964-75.
2005: David S Dunn; Amornrat Romphruk; Chanvit Leelayuwat; Matthew Bellgard; Jerzy K Kulski
Polymorphic Alu insertions and their associations with MHC class I alleles and haplotypes in the northeastern Thais.
Annals of human genetics 2005;69(Pt 4):364-72.
2005: Yasuyuki Nozaki; Matthew Bellgard
Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties.
Bioinformatics (Oxford, England) 2005;21(8):1421-8.
2005: Rudi Appels; Matthew Bellgard
Looking through genomics--from the editors.
Functional & integrative genomics 2005;5(1):1-3.
2004: Rudi Appels; Michael G Francki; Mehmet Cakir; Matthew Bellgard
Looking through genomics: concepts and technologies for plant and animal genomics.
Functional & integrative genomics 2004;4(2):71-3.
2004: Michael G Francki; Meredith Carter; Karon Ryan; Adam Hunter; Matthew Bellgard; Rudi Appels
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 2004;4(2):118-30.
2004: Chengdao Li; Peixiang Ni; Michael G Francki; Adam Hunter; Yong Zhang; David Schibeci; Heng Li; Allen Tarr; Jun Wang; Mehmet Cakir; Jun Yu; Matthew Bellgard; Reg Lance; Rudi Appels
Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison.
Functional & integrative genomics 2004;4(2):84-93.
2004: Matthew Bellgard; Jia Ye; Takashi Gojobori; Rudi Appels
The bioinformatics challenges in comparative analysis of cereal genomes-an overview.
Functional & integrative genomics 2004;4(1):1-11.
2003: Kim Carter; Matthew Bellgard
MASV--Multiple (BLAST) Annotation System Viewer.
Bioinformatics (Oxford, England) 2003;19(17):2313-5.
2003: Matthew Bellgard; Adam Hunter; William Kenworthy
Microarray analysis using bioinformatics analysis audit trails (BAATs).
Comptes rendus biologies 2003;326(10-11):1083-7.
2003: Jerzy K Kulski; Chew Ping Lim; David S Dunn; Matthew Bellgard
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 2003;56(4):397-406.
2003: Matthew Bellgard; Thomas Gamble; Mark Reynolds; Adam Hunter; Ed Trifonov; Ross Taplin
Gap mapping: a paradigm for aligning two sequences.
Applied bioinformatics 2003;2(3 Suppl):S31-5.
2003: Matthew Bellgard; William Kenworthy
FBSA: feature-based sequence alignment technique for very large sequences.
Applied bioinformatics 2003;2(3):145-50.
2001: Matthew Bellgard; David Schibeci; E Trifonov; Takashi Gojobori
Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains.
Journal of molecular evolution 2001;53(4-5):465-8.
2001: K Carter; Akira Oka; G Tamiya; Matthew Bellgard
Bioinformatics issues for automating the annotation of genomic sequences.
Genome informatics. International Conference on Genome Informatics 2001;12():204-11.
1999: Matthew Bellgard; H L Hiew; Adam Hunter; M Wiebrands
ORBIT: an integrated environment for user-customized bioinformatics tools.
Bioinformatics (Oxford, England) 1999;15(10):847-51.
1999: Matthew Bellgard; Takashi Gojobori
Inferring the direction of evolutionary changes of genomic base composition.
Trends in genetics : TIG 1999;15(7):254-6.
1999: Carly E Herbison; David C Sayer; Matthew Bellgard; Richard J N Allcock; Frank T Christiansen; Patricia Price
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 1999;10(4-5):229-43.
1998: Matthew Bellgard; Guan K Tay; H L Hiew; Campbell S Witt; N Ketheesan; Frank T Christiansen; Roger L Dawkins
MHC haplotype analysis by artificial neural networks.
Human immunology 1998;59(1):56-62.
1997: Jerzy K Kulski; Silvana Gaudieri; Matthew Bellgard; L Balmer; Keith Giles; Hidetoshi Inoko; Roger L Dawkins
The evolution of MHC diversity by segmental duplication and transposition of retroelements.
Journal of molecular evolution 1997;45(6):599-609.