Publications by authors named "Matthew J Wakefield"

46Publications

FokI-dCas9 mediates high-fidelity genome editing in pigs.

Xenotransplantation 2020 01 12;27(1):e12551. Epub 2019 Aug 12.

Immunology Research Centre, St Vincent's Hospital Melbourne, Melbourne, Vic., Australia.

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http://dx.doi.org/10.1111/xen.12551DOI Listing
January 2020

DNA repair processes are critical mediators of p53-dependent tumor suppression.

Nat Med 2018 07 11;24(7):947-953. Epub 2018 Jun 11.

Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1038/s41591-018-0043-5DOI Listing
July 2018

Autofluorescence Signatures of Seven Pathogens: Preliminary in Vitro Investigations of a Potential Diagnostic for Acanthamoeba Keratitis.

Cornea 2015 Dec;34(12):1588-92

*Department of Physics and Astronomy, University of Leicester, Leicester, United Kingdom; †Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom; and ‡Department of Ophthalmology, Leicester Royal Infirmary, Leicester, United Kingdom.

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http://pdfs.journals.lww.com/corneajrnl/2015/12000/Autofluor
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http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:land
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http://dx.doi.org/10.1097/ICO.0000000000000645DOI Listing
December 2015

Influx mechanisms in the embryonic and adult rat choroid plexus: a transcriptome study.

Front Neurosci 2015 28;9:123. Epub 2015 Apr 28.

Department of Pharmacology and Therapeutics, University of Melbourne Parkville, VIC, Australia ; Department of Neurobiology, Stanford University Stanford, CA, USA.

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http://dx.doi.org/10.3389/fnins.2015.00123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412010PMC
May 2015

Molecular correlates of platinum response in human high-grade serous ovarian cancer patient-derived xenografts.

Mol Oncol 2014 May 24;8(3):656-68. Epub 2014 Jan 24.

The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Royal Women's Hospital, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.molonc.2014.01.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4400120PMC
May 2014

Control of bacterial virulence by the RalR regulator of the rabbit-specific enteropathogenic Escherichia coli strain E22.

Infect Immun 2013 Nov 3;81(11):4232-43. Epub 2013 Sep 3.

Department of Microbiology and Immunology, The University of Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1128/IAI.00710-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811808PMC
November 2013

Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium.

PLoS One 2012 30;7(11):e50682. Epub 2012 Nov 30.

Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050682PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511308PMC
May 2013

Involvement of PatE, a prophage-encoded AraC-like regulator, in the transcriptional activation of acid resistance pathways of enterohemorrhagic Escherichia coli strain EDL933.

Appl Environ Microbiol 2012 Aug 11;78(15):5083-92. Epub 2012 May 11.

Department of Microbiology and Immunology, The University of Melbourne, Melbourne, and Murdoch Childrens Research Institute, Royal Children’s Hospital, Australia.

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http://aem.asm.org/lookup/doi/10.1128/AEM.00617-12
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http://dx.doi.org/10.1128/AEM.00617-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416394PMC
August 2012

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

Authors:
Marilyn B Renfree Anthony T Papenfuss Janine E Deakin James Lindsay Thomas Heider Katherine Belov Willem Rens Paul D Waters Elizabeth A Pharo Geoff Shaw Emily S W Wong Christophe M Lefèvre Kevin R Nicholas Yoko Kuroki Matthew J Wakefield Kyall R Zenger Chenwei Wang Malcolm Ferguson-Smith Frank W Nicholas Danielle Hickford Hongshi Yu Kirsty R Short Hannah V Siddle Stephen R Frankenberg Keng Yih Chew Brandon R Menzies Jessica M Stringer Shunsuke Suzuki Timothy A Hore Margaret L Delbridge Hardip R Patel Amir Mohammadi Nanette Y Schneider Yanqiu Hu William O'Hara Shafagh Al Nadaf Chen Wu Zhi-Ping Feng Benjamin G Cocks Jianghui Wang Paul Flicek Stephen M J Searle Susan Fairley Kathryn Beal Javier Herrero Dawn M Carone Yutaka Suzuki Sumio Sugano Atsushi Toyoda Yoshiyuki Sakaki Shinji Kondo Yuichiro Nishida Shoji Tatsumoto Ion Mandiou Arthur Hsu Kaighin A McColl Benjamin Lansdell George Weinstock Elizabeth Kuczek Annette McGrath Peter Wilson Artem Men Mehlika Hazar-Rethinam Allison Hall John Davis David Wood Sarah Williams Yogi Sundaravadanam Donna M Muzny Shalini N Jhangiani Lora R Lewis Margaret B Morgan Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Lynne Nazareth Andrew Cree Gerald Fowler Christie L Kovar Huyen H Dinh Vandita Joshi Chyn Jing Fremiet Lara Rebecca Thornton Lei Chen Jixin Deng Yue Liu Joshua Y Shen Xing-Zhi Song Janette Edson Carmen Troon Daniel Thomas Amber Stephens Lankesha Yapa Tanya Levchenko Richard A Gibbs Desmond W Cooper Terence P Speed Asao Fujiyama Jennifer A M Graves Rachel J O'Neill Andrew J Pask Susan M Forrest Kim C Worley

Genome Biol 2011 Aug 29;12(8):R81. Epub 2011 Aug 29.

The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia.

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http://dx.doi.org/10.1186/gb-2011-12-8-r81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277949PMC
August 2011

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity.

Nucleic Acids Res 2011 Sep 7;39(17):7415-27. Epub 2011 Jun 7.

Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia.

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http://dx.doi.org/10.1093/nar/gkr416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177187PMC
September 2011

Gene ontology analysis for RNA-seq: accounting for selection bias.

Genome Biol 2010 4;11(2):R14. Epub 2010 Feb 4.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3052, Australia.

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http://dx.doi.org/10.1186/gb-2010-11-2-r14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872874PMC
August 2010

Transcript length bias in RNA-seq data confounds systems biology.

Biol Direct 2009 Apr 16;4:14. Epub 2009 Apr 16.

Walter and Eliza Hall Institute of Medical Research, Parkville, Vic, Australia.

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http://dx.doi.org/10.1186/1745-6150-4-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678084PMC
April 2009

Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals.

Chromosome Res 2008 8;16(8):1159-75. Epub 2008 Nov 8.

ARC Centre of Excellence for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia.

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http://dx.doi.org/10.1007/s10577-008-1266-yDOI Listing
March 2009

RegA, an AraC-like protein, is a global transcriptional regulator that controls virulence gene expression in Citrobacter rodentium.

Infect Immun 2008 Nov 2;76(11):5247-56. Epub 2008 Sep 2.

Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010, Australia.

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http://dx.doi.org/10.1128/IAI.00770-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2573378PMC
November 2008

Cone visual pigments of monotremes: filling the phylogenetic gap.

Vis Neurosci 2008 May-Jun;25(3):257-64

ARC, Centre for Kangaroo Genomics, Bioinformatics, The Walter and Eliza Hall Institute, Parkville, Australia.

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http://dx.doi.org/10.1017/S0952523808080255DOI Listing
November 2008

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica.

Genome Res 2007 Jul 10;17(7):992-1004. Epub 2007 May 10.

Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6070707
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http://dx.doi.org/10.1101/gr.6070707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899126PMC
July 2007

Rates of genome evolution and branching order from whole genome analysis.

Mol Biol Evol 2007 Aug 9;24(8):1722-30. Epub 2007 May 9.

John Curtin School of Medical Research, The Australian National University, Canberra, Australia.

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http://dx.doi.org/10.1093/molbev/msm094DOI Listing
August 2007

The region homologous to the X-chromosome inactivation centre has been disrupted in marsupial and monotreme mammals.

Chromosome Res 2007 5;15(2):147-61. Epub 2007 Mar 5.

ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia.

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http://dx.doi.org/10.1007/s10577-007-1119-0DOI Listing
June 2007

Isolation, X location and activity of the marsupial homologue of SLC16A2, an XIST-flanking gene in eutherian mammals.

Chromosome Res 2005 24;13(7):687-98. Epub 2005 Oct 24.

ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia.

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http://dx.doi.org/10.1007/s10577-005-1006-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819140PMC
January 2006

Discussion of "A Bayesian approach to DNA sequence segmentation".

Biometrics 2005 Jun;61(2):635-7; discussion 637-9

Centre for Bioinformation Science, Australian National University, Australia.

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http://doi.wiley.com/10.1111/j.0006-341X.2005.040701_1.x
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http://dx.doi.org/10.1111/j.0006-341X.2005.040701_1.xDOI Listing
June 2005

Vestige: maximum likelihood phylogenetic footprinting.

BMC Bioinformatics 2005 May 29;6:130. Epub 2005 May 29.

John Curtin School of Medical Research, The Australian National University, Canberra 0200 ACT, Australia.

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http://dx.doi.org/10.1186/1471-2105-6-130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1156870PMC
May 2005

Marsupials and monotremes sort genome treasures from junk.

Genome Biol 2005 28;6(5):218. Epub 2005 Apr 28.

Division of Immunology and Genetics, John Curtin School of Medical Research, The Australian National University, Canberra 0200, Australia.

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http://dx.doi.org/10.1186/gb-2005-6-5-218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1175948PMC
May 2006

PyEvolve: a toolkit for statistical modelling of molecular evolution.

BMC Bioinformatics 2004 Jan 5;5. Epub 2004 Jan 5.

Centre for Bioinformation Science, John Curtin School of Medical Research and Mathematical Sciences Institute, Australian National University, Canberra, ACT 0200, Australia.

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http://dx.doi.org/10.1186/1471-2105-5-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC317364PMC
January 2004

The kangaroo genome. Leaps and bounds in comparative genomics.

EMBO Rep 2003 Feb;4(2):143-7

Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia.

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http://dx.doi.org/10.1038/sj.embor.embor739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1315837PMC
February 2003

Comparative Genome Maps of Vertebrates (Enclosed poster).

ILAR J 1998 ;39(2-3):INSERT

School of Genetics and Human Variations, LaTrobe University, Melbourne, Australia.

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January 1998

Comparative Chromosome Painting (Enclosed poster).

ILAR J 1998 ;39(2-3):INSERT

School of Genetics and Human Variations, LaTrobe University, Melbourne, Australia.

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January 1998