Susan J Clark

Susan J Clark

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Susan J Clark

Susan J Clark

Publications by authors named "Susan J Clark"

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96Publications

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Epigenomics of mammary gland development.

Breast Cancer Res 2018 Sep 3;20(1):100. Epub 2018 Sep 3.

The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.

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September 2018

Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements.

Bioinformatics 2018 Aug 1. Epub 2018 Aug 1.

Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.

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August 2018

Bisulphite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq).

Methods Mol Biol 2018 ;1708:285-302

Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW, 2010, Australia.

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July 2018

Alterations in Three-Dimensional Organization of the Cancer Genome and Epigenome.

Cold Spring Harb Symp Quant Biol 2016 19;81:41-51. Epub 2017 Apr 19.

Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.

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February 2018

Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA.

Epigenetics Chromatin 2017 20;10:16. Epub 2017 Apr 20.

Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia.

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January 2018

Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming.

Cell Stem Cell 2017 Dec;21(6):834-845.e6

Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia. Electronic address:

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December 2017

Smoke-Induced Changes to the Epigenome Provide Fertile Ground for Oncogenic Mutation.

Cancer Cell 2017 09;32(3):278-280

CSIRO Health and Biosecurity, PO Box 52, North Ryde, NSW 1670, Australia.

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September 2017

Disruption of the 3D cancer genome blueprint.

Epigenomics 2017 01 12;9(1):47-55. Epub 2016 Dec 12.

Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.

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January 2017

Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas.

Clin Epigenetics 2016 18;8:74. Epub 2016 Jul 18.

Department of Medical Oncology, Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre Building, 305 Grattan St, Melbourne, Victoria 3000 Australia.

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December 2016

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling.

Genome Biol 2016 10 7;17(1):208. Epub 2016 Oct 7.

Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, 2010, NSW, Australia.

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October 2016

Methyl-CpG-binding domain proteins: readers of the epigenome.

Epigenomics 2015 30;7(6):1051-73. Epub 2015 Apr 30.

Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.

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September 2016

Nucleotide-Level Profiling of m⁵C RNA Methylation.

Methods Mol Biol 2016 ;1358:269-84

Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton, Canberra, ACT, Australia.

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July 2016

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.

Genome Res 2016 06 6;26(6):719-31. Epub 2016 Apr 6.

Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia;

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June 2016

H2A.Z acetylation and transcription: ready, steady, go!

Epigenomics 2016 05 18;8(5):583-6. Epub 2016 Apr 18.

Histone Variants Group, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia.

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May 2016

Obesity and Prader-Willi Syndrome Affect Heart Rate Recovery from Dynamic Resistance Exercise in Youth.

Diseases 2016 Jan 15;4(1). Epub 2016 Jan 15.

Department of Kinesiology, California State University, Fullerton, 800 North State College Boulevard, Fullerton, CA 92834, USA.

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January 2016

Genome-wide DNA methylation profiling in triple-negative breast cancer reveals epigenetic signatures with important clinical value.

Mol Cell Oncol 2016 Jan 26;3(1):e1038424. Epub 2015 May 26.

Epigenetics Research Group, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, University of NSW, Sydney, New South Wales, Australia.

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January 2016

Cytokine Responses to Acute Intermittent Aerobic Exercise in Children With Prader-Willi Syndrome and Nonsyndromic Obesity.

Pediatr Exerc Sci 2015 Nov 14;27(4):525-34. Epub 2015 Jul 14.

Dept. of Kinesiology, California State University Fullerton, Fullerton, CA.

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November 2015

Hand Therapy Modalities for Proximal Interphalangeal Joint Stiffness.

J Hand Surg Am 2015 Nov 10;40(11):2293-6; quiz 2296. Epub 2015 Aug 10.

Department of Orthopaedic Surgery, Robert A. Chase Hand and Upper Extremity Center, Stanford University School of Medicine, Redwood City, CA. Electronic address:

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November 2015

COBRA-Seq: Sensitive and Quantitative Methylome Profiling.

Genes (Basel) 2015 Oct 23;6(4):1140-63. Epub 2015 Oct 23.

CSIRO Food and Nutrition Flagship, North Ryde, New South Wales 1670, Australia.

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October 2015

DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer.

Nat Commun 2015 Jul 14;6:7758. Epub 2015 Jul 14.

1] Epigenetics Research Program, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia [2] Faculty of Medicine, St Vincent's Clinical School, UNSW, NSW 2052 &St Vincent's Hospital, Sydney, New South Wales 2010, Australia.

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July 2015

Chromatin remodeler mutations in human cancers: epigenetic implications.

Epigenomics 2014 ;6(4):397-414

Chromatin Dynamics Group, Cancer Division, Garvan Institute of Medical Research, 394 Victoria Rd, Darlinghurst 2010, New South Wales, Australia.

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June 2015

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis.

Clin Epigenetics 2015 1;7:52. Epub 2015 May 1.

Epigenetic Research Laboratory, Genomics and Epigenetic Division, The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010 Australia ; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Level 5 deLacy Building, St Vincent's Hospital, Victoria Street, Darlinghurst, NSW 2010 Australia.

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May 2015

De novo identification of differentially methylated regions in the human genome.

Epigenetics Chromatin 2015 27;8. Epub 2015 Jan 27.

CSIRO Food and Nutrition Flagship, Riverside Life Sciences Centre, 11 Julius Avenue, Sydney, Australia.

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May 2015

Hormonal and metabolic responses to endurance exercise in children with Prader-Willi syndrome and non-syndromic obesity.

Metabolism 2015 Mar 2;64(3):391-5. Epub 2014 Dec 2.

Department of Kinesiology, California State University, Fullerton, 800N. State College Blvd, CA, 92834 USA.

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March 2015

Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines.

Genom Data 2015 Mar 8;3:94-6. Epub 2014 Dec 8.

Epigenetics Research Program, Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia ; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Australia, Darlinghurst, NSW 2010, Australia.

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March 2015

Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value.

Nat Commun 2015 Feb 2;6:5899. Epub 2015 Feb 2.

1] Epigenetics Group, Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia [2] St Vincent's Clinical School, University of NSW, Sydney, New South Wales 2010, Australia.

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February 2015

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer.

Genome Res 2014 Sep 10;24(9):1421-32. Epub 2014 Jun 10.

Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; Van Andel Research Institute, Grand Rapids, Michigan 49503, USA

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September 2014

Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma.

BMC Genomics 2014 Jun 15;15:476. Epub 2014 Jun 15.

Garvan Institute and The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia.

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June 2014

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

Bioinformatics 2014 May 26;30(10):1471-2. Epub 2014 Jan 26.

Cancer Epigenetics Program, Cancer Research Division, Kinghorn Cancer Centre, Garvan Institute of Medical Research, RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, St Vincent's Clinical School, University of NSW, Sydney 2010, Australia and Division of Computational Informatics, CSIRO, Sydney 2113, Australia.

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May 2014

Mining cancer methylomes: prospects and challenges.

Trends Genet 2014 Feb 21;30(2):75-84. Epub 2013 Dec 21.

Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia; St Vincent's Clinical School, University of NSW, Sydney 2010, NSW, Australia. Electronic address:

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February 2014

ZNF300P1 encodes a lincRNA that regulates cell polarity and is epigenetically silenced in type II epithelial ovarian cancer.

Mol Cancer 2014 Jan 6;13. Epub 2014 Jan 6.

Kinghorn Cancer Centre and Cancer Research Program, Garvan Institute of Medical Research, 370 Victoria Street, 2010, Darlinghurst, NSW, Australia.

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January 2014

Exploring and exploiting the aberrant DNA methylation profile of endocrine-resistant breast cancer.

Epigenomics 2013 Dec;5(6):595-8

Cancer Epigenetics Program, Garvan Institute of Medical Research, Sydney, NSW, Australia.

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December 2013

BCL-2 hypermethylation is a potential biomarker of sensitivity to antimitotic chemotherapy in endocrine-resistant breast cancer.

Mol Cancer Ther 2013 Sep 16;12(9):1874-85. Epub 2013 Jul 16.

Corresponding Author: Andrew Stone, Garvan Institute of Medical Research, L9 TKCC, 370 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia.

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September 2013

Regional activation of the cancer genome by long-range epigenetic remodeling.

Cancer Cell 2013 Jan 13;23(1):9-22. Epub 2012 Dec 13.

Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.

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January 2013

Copy-number-aware differential analysis of quantitative DNA sequencing data.

Genome Res 2012 Dec 9;22(12):2489-96. Epub 2012 Aug 9.

Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland.

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December 2012

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

Genome Res 2012 Jun 30;22(6):1120-7. Epub 2012 Mar 30.

Cancer Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia;

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June 2012

Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers.

Cancer Lett 2012 May 9;318(1):76-85. Epub 2011 Dec 9.

Cancer Research Program, The Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, New South Wales 2010, Australia.

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May 2012

Androgen receptor expression predicts breast cancer survival: the role of genetic and epigenetic events.

BMC Cancer 2012 Apr 2;12:132. Epub 2012 Apr 2.

School of Chemistry and Molecular Biosciences, The University of Queensland, St, Lucia 4072 Queensland, Australia.

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April 2012

Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer.

Genome Res 2012 Feb 25;22(2):307-21. Epub 2011 Jul 25.

Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia.

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February 2012

Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins.

PLoS One 2011 3;6(10):e25590. Epub 2011 Oct 3.

Epigenetics Research Group, Cancer Program, Garvan Institute of Medical Research, Sydney, Australia.

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February 2012

Epigenetics in prostate cancer: biologic and clinical relevance.

Eur Urol 2011 Oct 22;60(4):753-66. Epub 2011 Jun 22.

Cancer Epigenetics Group-Research Center, Department of Genetics, Portuguese Oncology Institute-Porto, Portugal.

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October 2011

Lineage specific methylation of the Elf5 promoter in mammary epithelial cells.

Stem Cells 2011 Oct;29(10):1611-9

Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.

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October 2011

Dynamics of bivalent chromatin domains upon drug induced reactivation and resilencing in cancer cells.

Epigenetics 2011 Sep 1;6(9):1138-48. Epub 2011 Sep 1.

Institut de Medicina Predictiva i Personalitzada del Càncer, Badalona, Barcelona, Spain.

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September 2011

miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA.

EMBO J 2011 Sep 30;30(21):4414-22. Epub 2011 Sep 30.

Department of Molecular Biology, Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.

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September 2011

Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription.

BMC Genomics 2011 Jan 21;12:54. Epub 2011 Jan 21.

Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.

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January 2011

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation.

Genome Res 2010 Dec 2;20(12):1719-29. Epub 2010 Nov 2.

Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.

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December 2010

Epigenetic architecture and miRNA: reciprocal regulators.

Epigenomics 2010 Dec;2(6):823-40

Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark.

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December 2010

Protocol matters: which methylome are you actually studying?

Epigenomics 2010 Aug;2(4):587-98

Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.

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August 2010

Repitools: an R package for the analysis of enrichment-based epigenomic data.

Bioinformatics 2010 Jul 10;26(13):1662-3. Epub 2010 May 10.

Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.

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July 2010

Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning.

Hum Mol Genet 2009 Aug 28;18(16):3098-109. Epub 2009 May 28.

Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia.

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August 2009

Breast cancer epigenetics: normal human mammary epithelial cells as a model system.

J Mol Med (Berl) 2008 Dec 21;86(12):1315-28. Epub 2008 Aug 21.

The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia.

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December 2008

Epigenetic and phenotypic changes result from a continuous pre and post natal dietary exposure to phytoestrogens in an experimental population of mice.

BMC Physiol 2008 Sep 15;8:17. Epub 2008 Sep 15.

Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, WA, 99164-4231, USA.

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September 2008

Epigenetic markers of ovarian cancer.

Adv Exp Med Biol 2008 ;622:35-51

Ovarian Cancer Center, Garvan Institute, Sydney, NSW, Australia.

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July 2008

DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment.

Gynecol Oncol 2008 Apr 29;109(1):129-39. Epub 2008 Jan 29.

Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia.

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April 2008

Bisulphite differential denaturation PCR for analysis of DNA methylation.

Epigenetics 2006 Apr-Jun;1(2):94-100. Epub 2006 Mar 7.

Preventative Health Flagship, CSIRO Molecular and Health Technologies, North Ryde, Australia.

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January 2008

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

Nucleic Acids Res 2007 13;35(18):e119. Epub 2007 Sep 13.

Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney 2010, New South Wales, Australia.

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November 2007

DNA methylation: bisulphite modification and analysis.

Nat Protoc 2006 ;1(5):2353-64

Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia.

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October 2007

Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis.

Authors:
Susan J Clark

Hum Mol Genet 2007 Apr;16 Spec No 1:R88-95

Cancer Program, Garvan Institute of Medical Research, Darlinghurst Sydney, 2010 NSW, Australia.

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April 2007

Telomere-driven karyotypic complexity concurs with p16INK4a inactivation in TP53-competent immortal endothelial cells.

Cancer Res 2006 Nov;66(22):10691-700

Children's Cancer Institute Australia for Medical Research, Randwick, New South Wales, Australia.

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November 2006

Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band.

Nat Genet 2006 May 23;38(5):540-9. Epub 2006 Apr 23.

Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney 2010, New South Wales, Australia.

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May 2006

Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation.

PLoS Genet 2006 Feb 10;2(2):e17. Epub 2006 Feb 10.

Chromosome Research Laboratory, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.

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February 2006

Hypermethylation of the prostacyclin synthase (PTGIS) promoter is a frequent event in colorectal cancer and associated with aneuploidy.

Oncogene 2005 Nov;24(49):7320-6

Molecular Oncology, IDIBELL-Institut de Recerca Oncològica, Gran Via km 2.7, Hospital Duran i Reynals, L'Hospitalet, Barcelona 08907, Spain.

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November 2005

Headloop suppression PCR and its application to selective amplification of methylated DNA sequences.

Nucleic Acids Res 2005 Aug 9;33(14):e127. Epub 2005 Aug 9.

CSIRO Molecular and Health Technologies PO Box 184, North Ryde, NSW 1670, Australia.

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August 2005

Incidence of low free T4 values in premature infants as determined by direct equilibrium dialysis.

J Perinatol 2004 Oct;24(10):640-4

Department of Pediatrics, Coleman Pavilion Room 11121C, Loma Linda University School of Medicine, 11175 Campus Street, Coleman Pavilion, Suite 11121, Loma Linda, CA 92354, USA.

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October 2004

Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells.

Cancer Res 2004 Jun;64(11):3871-7

Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.

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June 2004

Alterations in the p16(INK4a) and p53 tumor suppressor genes of hTERT-immortalized human fibroblasts.

Oncogene 2004 Apr;23(17):3116-21

Children's Medical Research Institute, 214 Hawkesbury Rd, Westmead, Sydney NSW 2145, Australia.

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April 2004

Bisulfite methylation analysis of tumor suppressor genes in prostate cancer from fresh and archival tissue samples.

Methods Mol Med 2003 ;81:219-40

Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, Australia.

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June 2003

DNA methylation changes in leukaemia.

Semin Cancer Biol 2002 Oct;12(5):347-57

Kanematsu Laboratories, Sydney Cancer Centre, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia.

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October 2002

DNA methylation and gene silencing in cancer: which is the guilty party?

Oncogene 2002 Aug;21(35):5380-7

Sydney Cancer Centre, Kanematsu Laboratories, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia.

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August 2002

Identification and resolution of artifacts in bisulfite sequencing.

Methods 2002 Jun;27(2):101-7

Sydney Cancer Centre, Kanematsu Laboratories, Royal Prince Alfred Hospital, Missenden Road, Camperdown, New South Wales 2050, Australia.

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June 2002

Methylation sequencing from limiting DNA: embryonic, fixed, and microdissected cells.

Methods 2002 Jun;27(2):108-13

Kanematsu Laboratories, Sydney Cancer Centre, Royal Prince Alfred Hospital, Missenden Road, Camperdown, New South Wales 2050, Australia.

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June 2002

Conversion-specific detection of DNA methylation using real-time polymerase chain reaction (ConLight-MSP) to avoid false positives.

Methods 2002 Jun;27(2):114-20

Sydney Laboratory, CSIRO Division of Molecular Science, P.O. Box 184, North Ryde, New South Wales 1670, Australia.

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June 2002

Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells.

Oncogene 2002 Feb;21(7):1048-61

Kanematsu Laboratories, Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia.

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February 2002