|
Young MD, Wakefield MJ, Smyth GK & Oshlack A (2010)
Gene ontology analysis for RNA-seq: accounting for selection bias
Genome Biology 11:R14
doi:10.1186/gb-2010-11-2-r14
html
pdf
GOseq software download page
Oshlack A & Wakefield MJ (2009) 
Transcript length bias in RNA-seq data confounds systems biology
Biology Direct 4:14
doi:10.1186/1745-6150-4-14
html
pdf
Cheng Y, Wakefield MJ, Siddle H, Coggill PC, Herbert C, Beck S, Belov K and Eldridge MDB. (2009)
Isolation and characterization of 10 MHC Class I-linked microsatellite loci in tammar wallaby (Macropus eugenii)
Molecular Ecology Resources 9:346–349
Deakin JE, Koina E, Waters PD, Doherty R, Patel VS, Delbridge ML, Dobson B, Fong J, Hu Y, van den Hurk C, Pask AJ, Shaw G, Smith C, Thompson K, Wakefield MJ, Yu H, Renfree MB, Graves JAM. (2008)
Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals
Chromosome Research 16:1159–1175
Hart E, Yang J, Kelly M, Tauschek M, Wakefield MJ, Frankel G, Hartland EL, Robins-Browne RM. (2008)
RegA, an AraC-like protein, is a global transcriptional regulator that controls virulence gene expression in Citrobacter rodentium.
Infection and Immunity 76:5247-5256
Warren WC, Hillier LW, Graves JAM, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang S, Heger A, Locke D, Miethke P, Waters PD, Veyrunes F, Fulton L, Graves T, Puente XS, Lopez-Otin C, Ordonez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Aslop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Renfree M, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell N, Buschiazzo E, Jentzsch IV, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison E, Sachidanandam R, Smith C, Stark A, Kheradpour P, Hannon G, Rens W, Ferguson-Smith M, Lefevre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhard R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux J, Niwa H, Sekita Y, Flicek P, Webber C, Hardison R, Washington University Genome Sequencing Center,
Mardis ER & Wilson RK. (2008)
Genome analysis of the platypus reveals unique signatures of evolution
Nature 453(7192):175-183
Wakefield MJ, Anderson M, Chang E, Wei K-J, Kaul R, Graves JAM, Grutzner F and Deeb SS (2008)
Cone Visual Pigments of Monotremes: Filling the Phylogenetic Gap
Visual Neuroscience 25:257-64
Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG,
Easton BC, Hamady M, Liu Z, Lozupone C, Sammut R,
Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S,
and Huttley GA (2007)
PyCogent: a toolkit for making sense from sequence
Genome Biology 8:R171
Online Resources: PyCogent SourceForge Repository
Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SMJ, Sharpe T, Baker M, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Graves JAM, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K (2007)
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Nature 447:167-177.
Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, and Jurka J (2007)
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
Genome Research 17:992-1004.
Huttley GA, Wakefield MJ, and Easteal S (2007)
Rates of genome evolution and branching order from whole genome analysis.
Molecular Biology and Evolution 24:1722-1730
Open Access Article
Hore T, Koina E, Wakefield MJ, and Graves JAM (2007)
XIST is absent from the X chromosome, and its flanking region is disrupted in non-placental mammals
Chromosome Research 15:147-161
El-Mogharbel N, Wakefield M, Deakin JE, Tsend-Ayush E, Grutzner F, Alsop A, Ezaz T, Marshall Graves JA (2007)
DMRT gene cluster analysis in the platypus: New insights into genomic organization and regulatory regions.
Genomics 89:10-21
Wakefield M.J. (2006)
Genomics - from Neanderthals to high-throughput sequencing
Genome Biology 7:326.
MacDonald A.J., Sankovic N., Sarre S.D., FitzSimmons N.N., Wakefield M.J., Graves J.A.M. and Zenger K.R. (2006)
Y chromosome microsatellite markers identified from the tammar wallaby (Macropus eugenii) and their application in three other macropod species.
Molecular Ecology Notes 6:1202-4
K. Belov, J.E. Deakin, A.T. Papenfuss, M.L. Baker, S.D. Melman, H.V. Siddle, N. Gouin, D.L. Goode, T.J. Sargeant, M.D. Robinson, M.J. Wakefield, S. Mahony, J.G.R. Cross, P.V. Benos, P.B. Samollow, T.P. Speed, J.A.M. Graves and R.D. Miller(2006)
Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial MHC.
PLOS Biology 4:e46
M. J. Wakefield and A. Alsop(2006)
Assignment of Breast Cancer Associated 1 (BRCA1) to tammar wallaby (Macropus eugenii) chromosome 2q3 by in situ hybridization.
Cytogenet Genome Res 112:180C
E. Koina, M. J. Wakefield, C. Walcher, C. M. Disteche, S. Whitehead, M. Ross and J. A. M. Graves (2005)
Isolation, X location and activity of the marsupial homologue of SLC16A2, an XIST-flanking gene in eutherian mammals
Chromosome Res. 13:687-98
M. J. Wakefield, P. Maxwell and G. A. Huttley (2005)
Vestige: maximum likelihood phylogenetic footprinting
BMC Bioinformatics 6: 130
M. J. Wakefield and J. A. M. Graves(2005)
Marsupials and monotremes sort genome treasures from junk
Genome Biology 6: 218
H. S. Booth, C. J. Burden, J. H. Maindonald, L. Santoso, M. J. Wakefield and S. R. Wilson (2005)
Discussion of "A Bayesian Approach to DNA Sequence Segmentation"
Biometrics 61: 635-7
J. Strachan, L. E. Chang, M. J. Wakefield, J. A. M. Graves and S. S. Deeb (2004)
The Cone Visual Pigments of the Australian Marsupials, the Stripe-Faced (Sminthopsis macroura) and Fat-Tailed (Sminthopsis crassicaudata) Dunnarts: Sequence and Inferred Spectral Properties
Visual Neuroscience 21: 223-9
A. Butterfield, V. Vedagiri, E. Lang, C. Lawrence, M. J. Wakefield, A. Isaev and G. A. Huttley (2004)
PyEvolve: a toolkit for statistical modelling of molecular evolution
BMC Bioinformatics 5: 1
J.A.M. Graves, M.J. Wakefield, M.B. Renfree, D.W. Cooper,T. Speed, K. Lindblad-Toh, E.S. Lander, R.K. Wilson (2003)
Proposal To Sequence The Genome Of The Model Marsupial Macropus Eugenii (Tammar Wallaby)
http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/WallabySEQ.pdf
M. J. Wakefield and J. A. M. Graves (2003)
Kangaroo Genomics Leaps Ahead
Todays Life Science 15: 34-37
M. J. Wakefield and J. A. Graves (2003)
The kangaroo genome. Leaps and bounds in comparative genomics
EMBO Rep 4: 143-7
[IF 7.6 - ISI Cited 12] GoogleScholar
S. S. Deeb, M. J. Wakefield, T. Tada, L. Marotte, S. Yokoyama and J. A. Marshall Graves (2003)
The cone visual pigments of an Australian marsupial, the tammar wallaby (Macropus eugenii): sequence, spectral tuning, and evolution
Mol Biol Evol 20: 1642-9
[IF 6.23 - ISI Cited 11] GoogleScholar
I. K. Greaves, M. Svartman, M. Wakefield, D. Taggart, A. De Leo, M. A. Ferguson-Smith, W. Rens, P. C. O'Brien, L. Voullaire, M. Westerman and J. A. Graves (2001)
Chromosomal painting detects non-random chromosome arrangement in dasyurid marsupial sperm
Chromosome Res 9: 251-9
R. Toder, M. J. Wakefield and J. A. Graves (2000)
The minimal mammalian Y chromosome - the marsupial Y as a model system
Cytogenet Cell Genet 91: 285-92
[ISI Cited 19] GoogleScholar
S. J. O'Brien, J. F. Eisenberg, M. Miyamoto, S. B. Hedges, S. Kumar, D. E. Wilson, M. Menotti-Raymond, W. J. Murphy, W. G. Nash, L. A. Lyons, J. C. Menninger, R. Stanyon, J. Wienberg, N. G. Copeland, N. A. Jenkins, J. Gellin, M. Yerle, L. Andersson, J. Womack, T. Broad, J. Postlethwait, O. Serov, E. Bailey, M. R. James, T. K. Watanabe, M. J. Wakefield and J. A. M. Graves (1999)
Comparative Genomics Mammalian Radiations Genome Maps 10
Science 286(5439):463 (insert)
M. J. Wakefield (1998)
Internet Comparative Mapping Resources
Ilar J 39: 66-67
M. J. Wakefield and J. A. Graves (1998)
Comparative Genome Maps of Vertebrates (Enclosed poster)
Ilar J 39: INSERT
J. A. Graves, M. J. Wakefield and R. Toder (1998)
The origin and evolution of the pseudoautosomal regions of human sex chromosomes
Hum Mol Genet 7: 1991-6
[IF 7.76 - ISI Cited 51] GoogleScholar
R. Glas, M. J. Wakefield, R. Toder and J. A. Graves (1998)
Comparative Chromosome Painting (Enclosed poster)
Ilar J 39: INSERT
M. J. Wakefield, A. M. Keohane, B. M. Turner and J. A. Graves (1997)
Histone underacetylation is an ancient component of mammalian X chromosome inactivation
Proc Natl Acad Sci U S A 94: 9665-8
[IF 10.23 - ISI Cited 32] GoogleScholar
M. J. Wakefield and J. A. Graves (1996)
Comparative maps of vertebrates
Mamm Genome 7: 715-6
[IF 2.74 - ISI Cited 46] GoogleScholar
L. Andersson, A. Archibald, M. Ashburner, S. Audun, W. Barendse, J. Bitgood, C. Bottema, T. Broad, S. Brown, D. Burt, C. Charlier, N. Copeland, S. Davis, M. Davisson, J. Edwards, A. Eggen, G. Elgar, J. T. Eppig, I. Franklin, P. Grewe, T. Gill, 3rd, J. A. Graves, R. Hawken, J. Hetzel, A. Hilyard, H. Jacob, L. Jaswinska, N. Jenkins, H. Kunz, G. Levan, O. Lie, L. A. Lyons, P. Maccarone, C. Mellersh, G. Montgomery, S. Moore, C. Moran, D. Morizot, M. Neff, F. Nicholas, S. J. O'Brien, Y. Parsons, J. Peters, J. Postlethwait, M. Raymond, M. Rothschild, L. Schook, Y. Sugimoto, C. Szpirer, M. Tate, J. VandeBerg, M. Wakefield, J. Wienberg and J. Womack (1996)
Comparative genome organization of vertebrates. The First International Workshop on Comparative Genome Organization
Mamm Genome 7: 717-34
[IF 2.74 - ISI Cited 104] GoogleScholar
|
