Research Topics
| M J WakefieldSummaryAffiliation: Australian National University Country: Australia Publications
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Detail Information
Publications
PyEvolve: a toolkit for statistical modelling of molecular evolutionAndrew Butterfield
Centre for Bioinformation Science, John Curtin School of Medical Research and Mathematical Sciences Institute, Australian National University, Canberra, ACT 0200, Australia
BMC Bioinformatics 5:1. 2004..Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation...- The kangaroo genome. Leaps and bounds in comparative genomicsMatthew J Wakefield
Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia
EMBO Rep 4:143-7. 2003..Here we summarize the contributions from cytogenetic and genetic studies of marsupials, describe the genomic resources currently available and those being developed, and explore the benefits of a kangaroo genome project... - Assignment of BReast Cancer Associated 1 (BRCA1) to tammar wallaby (Macropus eugenii) chromosome 2q3 by in situ hybridizationM J Wakefield
Division of Immunology and Genetics, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
Cytogenet Genome Res 112:180C. 2006 - Vestige: maximum likelihood phylogenetic footprintingMatthew J Wakefield
John Curtin School of Medical Research, The Australian National University, Canberra 0200 ACT, Australia
BMC Bioinformatics 6:130. 2005..Examination of the spatial incidence of these effects across regions of the genome can identify DNA segments that differ in the nature of the evolutionary process... - PyCogent: a toolkit for making sense from sequenceRob Knight
Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
Genome Biol 8:R171. 2007..The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent... - Genome analysis of the platypus reveals unique signatures of evolutionWesley C Warren
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 453:175-83. 2008..Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation... - Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequencesTarjei S Mikkelsen
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 447:167-77. 2007..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation... - Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domesticaAndrew J Gentles
Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA
Genome Res 17:992-1004. 2007..Many of these conserved repeats are also present in human, and are highly over-represented in predicted cis-regulatory modules. Seventy-six of the 83 families are present in chicken in addition to mammals... - Cone visual pigments of monotremes: filling the phylogenetic gapMatthew J Wakefield
ARC, Centre for Kangaroo Genomics, Bioinformatics, The Walter and Eliza Hall Institute, Parkville, Australia
Vis Neurosci 25:257-64. 2008..So far, the echidna and platypus are the only mammals that share the gene structure of the LWS-SWS2 pigment gene complex with reptiles, birds and fishes... - Rates of genome evolution and branching order from whole genome analysisGavin A Huttley
John Curtin School of Medical Research, The Australian National University, Canberra, Australia
Mol Biol Evol 24:1722-30. 2007.... - The region homologous to the X-chromosome inactivation centre has been disrupted in marsupial and monotreme mammalsTimothy A Hore
ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia
Chromosome Res 15:147-61. 2007..In the eutherian lineage, inserted and existing sequences provided the starting material for the non-translated RNAs of the X-inactivation centre, including XIST... - Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complexKatherine Belov
Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, The University of Sydney, Camden, Australia
PLoS Biol 4:e46. 2006.... - Isolation, X location and activity of the marsupial homologue of SLC16A2, an XIST-flanking gene in eutherian mammalsEdda Koina
ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia
Chromosome Res 13:687-98. 2005..In male and female cells, only a single signal was found, indicating that the marsupial SLC16A2 gene is silenced on the inactivated X... - Discussion of "A Bayesian approach to DNA sequence segmentation"Hilary S Booth
Centre for Bioinformation Science, Australian National University, Australia
Biometrics 61:635-7; discussion 637-9. 2005..It would be interesting to see an analysis that uses the codon alphabet... - Marsupials and monotremes sort genome treasures from junkMatthew J Wakefield
Division of Immunology and Genetics, John Curtin School of Medical Research, The Australian National University, Canberra 0200, Australia
Genome Biol 6:218. 2005..A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals (including humans) and more distant vertebrate species... - The cone visual pigments of an Australian marsupial, the tammar wallaby (Macropus eugenii): sequence, spectral tuning, and evolutionSamir S Deeb
Department of Medicine, University of Washington, Seattle, USA
Mol Biol Evol 20:1642-9. 2003..Introns interrupt the coding sequences of the wallaby, mouse, and human MWS pigment sequences at the same corresponding nucleotide positions. However, the length of introns varies widely among these species... - Cone visual pigments of the Australian marsupials, the stripe-faced and fat-tailed dunnarts: sequence and inferred spectral propertiesJessica Strachan
Department of Medicine, University of Washington, Seattle, USA
Vis Neurosci 21:223-9. 2004..The MWS pigments of the two species differ by two, and UVS by three amino acid positions. No evidence was obtained for a third cone pigment in either species... - RegA, an AraC-like protein, is a global transcriptional regulator that controls virulence gene expression in Citrobacter rodentiumEmily Hart
Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010, Australia
Infect Immun 76:5247-56. 2008..Taken together, these results show that RegA is a global regulator of virulence in C. rodentium which activates factors that are required for intestinal colonization...