Publications

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:



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.


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.


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.

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.

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

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.

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.


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.


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.




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.



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.

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;

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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