AdjAssocProf Clare Stirzaker

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E-mail

c.stirzaker@garvan.org.au

Location

384 Victoria Street Darlinghurst NSW 2010

Book Chapters | 2022

Warton K; Stirzaker C; Samimi G; Clark S, 2022, 'DNA Methylation Analysis of Circulating DNA Biomarkers', in Cell-Free Circulating DNA: Purification and Analysis Techniques, WORLD SCIENTIFIC, pp. 247 - 277, http://dx.doi.org/10.1142/9789811244681_0009

Book Chapters | 2021

Stirzaker C; Armstrong NJ, 2021, 'Evaluation and measurement of epigenetic modifications in population-based studies', in Twin and Family Studies of Epigenetics, Elsevier, pp. 17 - 39, http://dx.doi.org/10.1016/B978-0-12-820951-6.00014-4

Book Chapters | 2019

Pidsley R; Stirzaker C, 2019, 'Cancer Methylation Biomarkers in Circulating Cell-Free DNA', in Clinical Epigenetics, Springer Singapore, pp. 217 - 245, http://dx.doi.org/10.1007/978-981-13-8958-0_10

Book Chapters | 2018

Valdés-Mora F; Stirzaker C, 2018, 'Epigenetic Alterations in Primary Prostate Cancer', in Molecular Pathology Library, Springer International Publishing, pp. 193 - 211, http://dx.doi.org/10.1007/978-3-319-64096-9_13
Journal articles | 2023

Graeser M; Harbeck N; Gluz O; Nitz UA; Christgen M; Kuemmel S; Grischke E-M; Forstbauer H; Braun M; Warm M; Hackmann JC; Uleer C; Aktas B; Würstlein R; Pelz E; Eulenburg CZ; Kreipe H; Trau M; Stirzaker C; Korbie D, 2023, '18P A translational project of the WSG-ADAPT-TN trial demonstrates immunomodulatory and anti-viral defense gene networks predicting pathological complete response (pCR) and survival after de-escalated neoadjuvant chemotherapy (NACT) in early triple-negative breast cancer (eTNBC)', ESMO Open, 8, pp. 101242 - 101242, http://dx.doi.org/10.1016/j.esmoop.2023.101242

Journal articles | 2023

Hastings JF; Latham SL; Kamili A; Wheatley MS; Han JZR; Wong-Erasmus M; Phimmachanh M; Nobis M; Pantarelli C; Cadell AL; O’Donnell YEI; Leong KH; Lynn S; Geng FS; Cui L; Yan S; Achinger-Kawecka J; Stirzaker C; Norris MD; Haber M; Trahair TN; Speleman F; De Preter K; Cowley MJ; Bogdanovic O; Timpson P; Cox TR; Kolch W; Fletcher JI; Fey D; Croucher DR, 2023, 'Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma', Science Advances, 9, pp. eabp8314, http://dx.doi.org/10.1126/sciadv.abp8314

Journal articles | 2022

Brown LJ; Achinger-Kawecka J; Portman N; Clark S; Stirzaker C; Lim E, 2022, 'Epigenetic Therapies and Biomarkers in Breast Cancer', Cancers, 14, pp. 474 - 474, http://dx.doi.org/10.3390/cancers14030474

Journal articles | 2022

Pidsley R; Lam D; Qu W; Peters TJ; Phuc-Loi L; Korbie D; Stirzaker C; Daly RJ; Stricker P; Kench JG; Horvath LG; Clark SJ, 2022, 'Comprehensive methylome sequencing reveals prognostic epigenetic biomarkers for prostate cancer mortality', CLINICAL AND TRANSLATIONAL MEDICINE, 12, http://dx.doi.org/10.1002/ctm2.1030

Journal articles | 2021

Achinger-Kawecka J; Stirzaker C; Portman N; Campbell E; Chia K-M; Du Q; Laven-Law G; Nair S; Yong A; Wilkinson A; Clifton S; Milioli H; Alexandrou S; Caldon E; Song J; Khoury A; Meyer B; Gee JMW; Schmitt A; Wong E; Hickey T; Lim E; Clark S, 2021, 'Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer', , http://dx.doi.org/10.1101/2021.06.21.449340

Journal articles | 2021

Cole AJ; Dickson KA; Liddle C; Stirzaker C; Shah JS; Clifton-Bligh R; Marsh DJ, 2021, 'Ubiquitin chromatin remodelling after DNA damage is associated with the expression of key cancer genes and pathways', Cellular and Molecular Life Sciences, 78, pp. 1011 - 1027, http://dx.doi.org/10.1007/s00018-020-03552-5

Journal articles | 2021

Du Q; Smith GC; Luu PL; Ferguson JM; Armstrong NJ; Caldon CE; Campbell EM; Nair SS; Zotenko E; Gould CM; Buckley M; Chia KM; Portman N; Lim E; Kaczorowski D; Chan CL; Barton K; Deveson IW; Smith MA; Powell JE; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark SJ, 2021, 'DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity', Cell Reports, 36, http://dx.doi.org/10.1016/j.celrep.2021.109722

Journal articles | 2021

Luu PL; Ong PT; Loc TTH; Lam D; Pidsley R; Stirzaker C; Clark SJ, 2021, 'MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection', Bioinformatics, 37, pp. 2198 - 2200, http://dx.doi.org/10.1093/bioinformatics/btaa1060

Journal articles | 2021

Meyer B; Clifton S; Locke W; Luu PL; Du Q; Lam D; Armstrong NJ; Kumar B; Deng N; Harvey K; Swarbrick A; Ganju V; Clark SJ; Pidsley R; Stirzaker C, 2021, 'Identification of DNA methylation biomarkers with potential to predict response to neoadjuvant chemotherapy in triple-negative breast cancer', Clinical Epigenetics, 13, http://dx.doi.org/10.1186/s13148-021-01210-6

Journal articles | 2021

Stirzaker C; Skvortsova K; Clark SJ, 2021, 'Epigenetic changes during tumour development – functional epigenetics study', Pathology, 53, pp. S10 - S11, http://dx.doi.org/10.1016/j.pathol.2021.05.040

Journal articles | 2020

Achinger-Kawecka J; Valdes-Mora F; Luu PL; Giles KA; Caldon CE; Qu W; Nair S; Soto S; Locke WJ; Yeo-Teh NS; Gould CM; Du Q; Smith GC; Ramos IR; Fernandez KF; Hoon DS; Gee JMW; Stirzaker C; Clark SJ, 2020, 'Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-019-14098-x

Journal articles | 2020

Du Q; Smith G; Luu PL; Ferguson J; Armstrong N; Caldon E; Campbell E; Nair S; Zotenko E; Gould C; Buckley M; Kaczorowski D; Barton K; Deveson I; Smith M; Powell J; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark S, 2020, 'DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity', , http://dx.doi.org/10.1101/2020.10.15.338855

Journal articles | 2020

Khoury A; Achinger-Kawecka J; Bert SA; Smith GC; French HJ; Luu PL; Peters TJ; Du Q; Parry AJ; Valdes-Mora F; Taberlay PC; Stirzaker C; Statham AL; Clark SJ, 2020, 'Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-019-13753-7

Journal articles | 2020

Lam D; Clark S; Stirzaker C; Pidsley R, 2020, 'Advances in Prognostic Methylation Biomarkers for Prostate Cancer', , http://dx.doi.org/10.20944/preprints202010.0154.v1

Journal articles | 2020

Lam D; Clark S; Stirzaker C; Pidsley R, 2020, 'Advances in prognostic methylation biomarkers for prostate cancer', Cancers, 12, pp. 1 - 39, http://dx.doi.org/10.3390/cancers12102993

Journal articles | 2020

Lam D; Luu PL; Song JZ; Qu W; Risbridger GP; Lawrence MG; Lu J; Trau M; Korbie D; Clark SJ; Pidsley R; Stirzaker C, 2020, 'Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels', Clinical Epigenetics, 12, pp. 90, http://dx.doi.org/10.1186/s13148-020-00880-y

Journal articles | 2020

Lawrence MG; Pidsley R; Niranjan B; Papargiris M; Pereira BA; Richards M; Teng L; Norden S; Ryan A; Frydenberg M; Stirzaker C; Taylor RA; Risbridger GP; Clark SJ, 2020, 'Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer', Clinical Epigenetics, 12, pp. 48, http://dx.doi.org/10.1186/s13148-020-00836-2

Journal articles | 2020

Stirzaker C; Skvortsova K; Masle-Farquhar E; Goodnow C; Clark SJ, 2020, 'Epigenetic changes during tumour development – Functional epigenetics study', Pathology, 52, pp. S29 - S29, http://dx.doi.org/10.1016/j.pathol.2020.01.121

Journal articles | 2019

Bradford ST; Nair SS; Statham AL; van Dijk SJ; Peters TJ; Anwar F; French HJ; von Martels JZH; Sutcliffe B; Maddugoda MP; Peranec M; Varinli H; Arnoldy R; Buckley M; Ross JP; Zotenko E; Song JZ; Stirzaker C; Bauer DC; Qu W; Swarbrick MM; Lutgers HL; Lord RV; Samaras K; Molloy PL; Clark SJ, 2019, 'Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes', Scientific Reports, 9, pp. 9511, http://dx.doi.org/10.1038/s41598-019-45777-w

Journal articles | 2019

Du Q; Bert SA; Armstrong NJ; Caldon CE; Song JZ; Nair SS; Gould CM; Luu PL; Peters T; Khoury A; Qu W; Zotenko E; Stirzaker C; Clark SJ, 2019, 'Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer', Nature Communications, 10, pp. 416, http://dx.doi.org/10.1038/s41467-019-08302-1

Journal articles | 2019

Giles KA; Gould CM; Du Q; Skvortsova K; Song JZ; Maddugoda MP; Achinger-Kawecka J; Stirzaker C; Clark SJ; Taberlay PC, 2019, 'Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups', Epigenetics and Chromatin, 12, pp. 12, http://dx.doi.org/10.1186/s13072-019-0258-9

Journal articles | 2019

Peters TJ; French HJ; Bradford ST; Pidsley R; Stirzaker C; Varinli H; Nair S; Qu W; Song J; Giles KA; Statham AL; Speirs H; Speed TP; Clark SJ, 2019, 'Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements', Bioinformatics, 35, pp. 560 - 570, http://dx.doi.org/10.1093/bioinformatics/bty675

Journal articles | 2019

Skvortsova K; Masle-Farquhar E; Luu PL; Song JZ; Qu W; Zotenko E; Gould CM; Du Q; Peters TJ; Colino-Sanguino Y; Pidsley R; Nair SS; Khoury A; Smith GC; Miosge LA; Reed JH; Kench JG; Rubin MA; Horvath L; Bogdanovic O; Lim SM; Polo JM; Goodnow CC; Stirzaker C; Clark SJ, 2019, 'DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns', Cancer Cell, 35, pp. 297 - 314.e8, http://dx.doi.org/10.1016/j.ccell.2019.01.004

Journal articles | 2019

Skvortsova K; Stirzaker C; Taberlay P, 2019, 'The DNA methylation landscape in cancer', Essays in Biochemistry, 63, pp. 797 - 811, http://dx.doi.org/10.1042/EBC20190037

Journal articles | 2018

O'Toole SA; Pidsley R; Harvey K; Karim R; Lee CS; Chan B; Stirzaker C, 2018, 'Using the epigenome to understand and better classify phyllodes tumours', Pathology, 50, pp. S7 - S8, http://dx.doi.org/10.1016/j.pathol.2017.12.015

Journal articles | 2018

Pidsley R; Lawrence MG; Zotenko E; Niranjan B; Statham A; Song J; Chabanon RM; Qu W; Wang H; Richards M; Nair SS; Armstrong NJ; Nim HT; Papargiris M; Balanathan P; French H; Peters T; Norden S; Ryan A; Pedersen J; Kench J; Daly RJ; Horvath LG; Stricker P; Frydenberg M; Taylor RA; Stirzaker C; Risbridger GP; Clark SJ, 2018, 'Enduring epigenetic landmarks define the cancer microenvironment', Genome Research, 28, pp. 625 - 638, http://dx.doi.org/10.1101/gr.229070.117

Journal articles | 2018

Stirzaker C; Song JZ; Statham AL; Clark SJ, 2018, 'Bisulphite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq)', Methods in Molecular Biology, 1708, pp. 285 - 302, http://dx.doi.org/10.1007/978-1-4939-7481-8_15

Journal articles | 2017

Cybulski C; Kluźniak W; Huzarski T; Wokołorczyk D; Kashyap A; Jakubowska A; Szwiec M; Byrski T; Dębniak T; Górski B; Sopik V; Akbari MR; Sun P; Gronwald J; Narod SA; Lubiński J; Dębniak T; Dymerska D; Kurzawski G; Lubiński J; Dymerska D; Tutlewska K; Kuswik M; Rudnicka H; Scott RJ; Billings R; Pławski A; Lubinski J; Kurzawski G; Gromowski T; Kąklewski K; Marciniak W; Durda K; Lener M; Sukiennicki G; Kaczmarek K; Jaworska-Bieniek K; Paszkowska-Szczur K; Waloszczyk P; Lubiński J; Dębniak T; Gronwald J; Hemminki K; Försti A; Huzarski T; Gronwald J; Cybulski C; Oszurek O; Szwiec M; Gugała K; Stawicka M; Morawiec Z; Mierzwa T; Falco M; Janiszewska H; Kilar E; Marczyk E; Kozak-Klonowska B; Siołek M; Surdyka D; Wiśniowski R; Posmyk M; Domagała P; Byrski T; Sun P; Lubiński J; Narod SA; Imyanitov EN; Kaczmarek K; Muszyńska M; Marciniak W; Sukiennicki G; Lener M; Durda K; Jaworska-Bieniek K; Gromowski T; Prajzendanc K; Peruga N; Huzarski T; Byrski T; Gronwald J; Cybulski C; Dębniak T; Morawski A; Jakubowska A; Lubiński J; Lener MR; Scott RJ; Kluźniak W; Gronwald J; Baszuk P; Cybulski C; Wiechowska-Kozłowska A; Huzarski T; Kładny J; Pietrzak S; Soluch A; Jakubowska A; Lubiński J; Plawski A; Prajzendanc K; Jakubowska A; Lubiński J; Rashid UR; Naeemi H; Muhammad N; Lubiński J; Jakubowska A; Loya A; Yusuf MA; Savanevich A; Aszurek O; Gronwald J; Lubiński J; Mathe A; Wong-Brown M; Locke W; Stirzaker C; Braye SG; Forbes JF; Clark S; Avery-Kiejda K; Scott RJ; Tomiczek-Szwiec J; Huzarski T; Szwiec M; Gronwald J; Cybulski C; Marczyk E; Jakubowicz J; Kilar E; Sibilski R; Stawicka M; Morawiec Z; Mierzwa T; Falco M; Janiszewska H; Kozak-Klonowska B; Siołek M; Surdyka D; Wiśniowski R; Posmyk R; Domagała P; Lubiński J; Szwiec M; Tomiczek-Szwiec J; Huzarski T; Cybulski C; Lubiński J, 2017, 'Meeting abstracts from the Annual Conference on Hereditary Cancers 2016', Hereditary Cancer in Clinical Practice, 15, http://dx.doi.org/10.1186/s13053-017-0081-x

Journal articles | 2017

Lawrence M; Pidlsey R; Zotenko E; Niranjan B; Nair S; French H; Statham A; Song J; Chabanon R; Papargiris M; Ellem S; Frydenberg M; Pedersen J; Stirzaker C; Taylor R; Clark S; Risbridger G, 2017, 'Hypomethylation of estrogen receptor alpha: a landmark in the epigenome landscape of prostate cancer stroma', CLINICAL ENDOCRINOLOGY, 86, pp. 23 - 23, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000393453600061&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Journal articles | 2017

Skvortsova K; Zotenko E; Luu PL; Gould CM; Nair SS; Clark SJ; Stirzaker C, 2017, 'Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA', Epigenetics and Chromatin, 10, http://dx.doi.org/10.1186/s13072-017-0123-7

Journal articles | 2017

Stirzaker C; Song JZ; Ng W; Du Q; Armstrong NJ; Locke WJ; Statham AL; French H; Pidsley R; Valdes-Mora F; Zotenko E; Clark SJ, 2017, 'Methyl-CpG-binding protein MBD2 plays a key role in maintenance and spread of DNA methylation at CpG islands and shores in cancer', Oncogene, 36, pp. 1328 - 1338, http://dx.doi.org/10.1038/onc.2016.297

Journal articles | 2017

Valdés-Mora F; Gould CM; Colino-Sanguino Y; Qu W; Song JZ; Taylor KM; Buske FA; Statham AL; Nair SS; Armstrong NJ; Kench JG; Lee KML; Horvath LG; Qiu M; Ilinykh A; Yeo-Teh NS; Gallego-Ortega D; Stirzaker C; Clark SJ, 2017, 'Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer', Nature Communications, 8, http://dx.doi.org/10.1038/s41467-017-01393-8

Journal articles | 2016

Bock C; Halbritter F; Carmona FJ; Tierling S; Datlinger P; Assenov Y; Berdasco M; Bergmann AK; Booher K; Busato F; Campan M; Dahl C; Dahmcke CM; Diep D; Fernández AF; Gerhauser C; Haake A; Heilmann K; Holcomb T; Hussmann D; Ito M; Kläver R; Kreutz M; Kulis M; Lopez V; Nair SS; Paul DS; Plongthongkum N; Qu W; Queirós AC; Reinicke F; Sauter G; Schlomm T; Statham A; Stirzaker C; Strogantsev R; Urdinguio RG; Walter K; Weichenhan D; Weisenberger DJ; Beck S; Clark SJ; Esteller M; Ferguson-Smith AC; Fraga MF; Guldberg P; Hansen LL; Laird PW; Martín-Subero JI; Nygren AOH; Peist R; Plass C; Shames DS; Siebert R; Sun X; Tost J; Walter J; Zhang K, 2016, 'Quantitative comparison of DNA methylation assays for biomarker development and clinical applications', Nature Biotechnology, 34, pp. 726 - 737, http://dx.doi.org/10.1038/nbt.3605

Journal articles | 2016

Mathe A; Wong-Brown M; Locke WJ; Stirzaker C; Braye SG; Forbes JF; Clark SJ; Avery-Kiejda KA; Scott RJ, 2016, 'DNA methylation profile of triple negative breast cancer-specific genes comparing lymph node positive patients to lymph node negative patients', Scientific Reports, 6, http://dx.doi.org/10.1038/srep33435

Journal articles | 2016

Pidsley R; Zotenko E; Peters TJ; Lawrence MG; Risbridger GP; Molloy P; Van Djik S; Muhlhausler B; Stirzaker C; Clark SJ, 2016, 'Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling', GENOME BIOLOGY, 17, http://dx.doi.org/10.1186/s13059-016-1066-1

Journal articles | 2016

Pidsley R; Zotenko E; Peters TJ; Lawrence MG; Risbridger GP; Molloy P; Van Djik S; Muhlhausler B; Stirzaker C; Clark SJ, 2016, 'Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling', Genome Biology, 17, http://dx.doi.org/10.1186/s13059-016-1066-1

Journal articles | 2016

Stirzaker C; Zotenko E; Clark SJ, 2016, 'Genome-wide DNA methylation profiling in triple-negative breast cancer reveals epigenetic signatures with important clinical value', Molecular and Cellular Oncology, 3, http://dx.doi.org/10.1080/23723556.2015.1038424

Journal articles | 2016

Taberlay PC; Achinger-Kawecka J; Lun ATL; Buske FA; Sabir KS; Gould CM; Zotenko E; Bert SA; Giles KA; Bauer D; Smyth GK; Stirzaker C; O Donoghue SI; Clark SJ, 2016, 'Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations', Genome Research, 26, pp. 719 - 731, http://dx.doi.org/10.1101/gr.201517.115

Journal articles | 2015

Du Q; Luu PL; Stirzaker C; Clark SJ, 2015, 'Methyl-CpG-binding domain proteins: Readers of the epigenome', Epigenomics, 7, pp. 1051 - 1073, http://dx.doi.org/10.2217/epi.15.39

Journal articles | 2015

Korbie D; Lin E; Wall D; Nair SS; Stirzaker C; Clark SJ; Trau M, 2015, 'Multiplex bisulfite PCR resequencing of clinical FFPE DNA', Clinical Epigenetics, 7, http://dx.doi.org/10.1186/s13148-015-0067-3

Journal articles | 2015

Locke WJ; Zotenko E; Stirzaker C; Robinson MD; Hinshelwood RA; Stone A; Reddel RR; Huschtscha LI; Clark SJ, 2015, 'Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis', Clinical Epigenetics, 7, http://dx.doi.org/10.1186/s13148-015-0086-0

Journal articles | 2015

Stirzaker C; Zotenko E; Song JZ; Qu W; Nair SS; Locke WJ; Stone A; Armstong NJ; Robinson MD; Dobrovic A; Avery-Kiejda KA; Peters KM; French JD; Stein S; Korbie DJ; Trau M; Forbes JF; Scott RJ; Brown MA; Francis GD; Clark SJ, 2015, 'Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value', Nature Communications, 6, pp. 5899 - 5899, http://dx.doi.org/10.1038/ncomms6899

Journal articles | 2015

Stone A; Zotenko E; Locke WJ; Korbie D; Millar EKA; Pidsley R; Stirzaker C; Graham P; Trau M; Musgrove EA; Nicholson RI; Gee JMW; Clark SJ, 2015, 'DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer', Nature Communications, 6, http://dx.doi.org/10.1038/ncomms8758

Journal articles | 2014

Riebler A; Menigatti M; Song JZ; Statham AL; Stirzaker C; Mahmud N; Mein CA; Clark SJ; Robinson MD, 2014, 'BayMeth:Improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach', Genome Biology, 15, http://dx.doi.org/10.1186/gb-2014-15-2-r35

Journal articles | 2014

Stirzaker C; Taberlay PC; Statham AL; Clark SJ, 2014, 'Mining cancer methylomes: Prospects and challenges', Trends in Genetics, 30, pp. 75 - 84, http://dx.doi.org/10.1016/j.tig.2013.11.004

Journal articles | 2013

Bert SA; Robinson MD; Strbenac D; Statham AL; Song JZ; Hulf T; Sutherland RL; Coolen MW; Stirzaker C; Clark SJ, 2013, 'Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling', Cancer Cell, 23, pp. 9 - 22, http://dx.doi.org/10.1016/j.ccr.2012.11.006

Journal articles | 2013

Clark AK; Taubenberger AV; Taylor RA; Niranjan B; Chea ZY; Zotenko E; Sieh S; Pedersen JS; Norden S; Frydenberg M; Grummet JP; Pook DW; Stirzaker C; Clark SJ; Lawrence MG; Ellem SJ; Hutmacher DW; Risbridger GP, 2013, 'A bioengineered microenvironment to quantitatively measure the tumorigenic properties of cancer-associated fibroblasts in human prostate cancer', Biomaterials, 34, pp. 4777 - 4785, http://dx.doi.org/10.1016/j.biomaterials.2013.03.005

Journal articles | 2013

Hulf T; Sibbritt T; Wiklund ED; Patterson K; Song JZ; Stirzaker C; Qu W; Nair S; Horvath LG; Armstrong NJ; Kench JG; Sutherland RL; Clark SJ, 2013, 'Epigenetic-induced repression of microRNA-205 is associated with MED1 activation and a poorer prognosis in localized prostate cancer', Oncogene, 32, pp. 2891 - 2899, http://dx.doi.org/10.1038/onc.2012.300

Journal articles | 2012

Robinson MD; Strbenac D; Stirzaker C; Statham A; Song JZ; Speed TP; Clark SJ, 2012, 'Copy-number-aware differential analysis of quantitative DNA sequencing data', Genome Research, 22, pp. 2490 - 2496, http://dx.doi.org/10.1101/gr.139055.112

Journal articles | 2012

Statham AL; Robinson MD; Song JZ; Coolen MW; Stirzaker C; Clark SJ, 2012, 'Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA', Genome Research, 22, pp. 1120 - 1127, http://dx.doi.org/10.1101/gr.132076.111

Journal articles | 2012

Valdes-Mora F; Song JZ; Statham AL; Strbenac D; Robinson MD; Nair SS; Patterson K; Tremethick DJ; Stirzaker C; Clark SJ, 2012, 'Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer', Genome Research, 22, pp. 307 - 321, http://dx.doi.org/10.1101/gr.118919.110

Journal articles | 2011

Devaney J; Stirzaker C; Qu W; Song JZ; Statham AL; Patterson K; Horvath LG; Tabor B; Coolen MW; Hulf T; Kench JG; Henshall SM; Pe benito R; Haynes AM; Mayor R; Peinado M; Sutherland RL; Clark SJ, 2011, 'Epigenetic deregulation across chromosome 2q14.2 differentiates normal from prostate cancer and provides a regional panel of novel DNA methylation cancer biomarkers', Cancer Epidemiology Biomarkers and Prevention, 20, pp. 148 - 159, http://dx.doi.org/10.1158/1055-9965.EPI-10-0719

Journal articles | 2011

Kohonen-Corish MRJ; Selinger CI; Cooper WA; Al-Sohaily S; Mladenova DN; Pangon L; Kennedy CW; McCaughan BC; Stirzaker C, 2011, 'LOSS OF SATB 1 EXPRESSION IS A MARKER OF POOR SURVIVAL IN LUNG CANCER', JOURNAL OF THORACIC ONCOLOGY, 6, pp. S4 - S4, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000287990600013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Journal articles | 2011

Nair SS; Coolen MW; Stirzaker C; Song J; Statham AL; Strbenac D; Robinson MR; Clark SJ, 2011, 'Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias', Epigenetics, 6, pp. 34 - 44, http://dx.doi.org/10.4161/epi.6.1.13313

Journal articles | 2011

Patterson K; Molloy L; Qu W; Clark SJ, 2011, 'DNA methylation: Bisulphite modification and analysis', Journal of Visualized Experiments, pp. e3170, http://dx.doi.org/10.3791/3170

Journal articles | 2011

Robinson MD; Stirzaker C; Statham AL; Coolen MW; Song JZ; Nair SS; Strbenac D; Speed TP; Clark SJ, 2011, 'Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation (Genome Research (2010), 20 (1719-1729))', Genome Research, 21, pp. 146

Journal articles | 2011

Selinger CI; Cooper WA; Al-Sohaily IA; Mladenova DN; Pangon L; Kennedy C; McCaughan B; Stirzaker C; Stirzaker C; Kohonen-Corish M, 2011, 'Loss of special at-rich binding protein 1 expression is a marker of poor survival in lung cancer', Journal of Thoracic Oncology, 6, pp. 1179 - 1189, http://dx.doi.org/10.1097/JTO.0b013e31821b4ce0

Journal articles | 2010

Coolen M; Stirzaker C; Song JZ; Statham AL; Kassir Z; Moreno CS; Young AM; Varma V; Speed TP; Cowley MJ; Lacaze P; Kaplan W; Robinson M; Clark SJ, 2010, 'Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity', Nature Cell Biology, 12, pp. 235 - 246, http://dx.doi.org/10.1038/ncb2023

Journal articles | 2010

Robinson M; Stirzaker C; Statham AL; Coolen M; Song J; Nair S; Strbenac D; Speed TP; Clark SJ, 2010, 'Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation', Genome Research, 20, pp. 1719 - 1729, http://dx.doi.org/10.1101/gr.110601.110

Journal articles | 2010

Statham AL; Strbenac D; Coolen M; Stirzaker C; Robinson M; Clark SJ, 2010, 'Repitools: an R package for the analysis of enrichment-based epigenomic data', Bioinformatics, 26, pp. 1662 - 1663, http://dx.doi.org/10.1093/bioinformatics/btq247

Journal articles | 2009

Hinshelwood R; Melki J; Huschtscha L; Paul C; Song JZ; Stirzaker C; Reddel RR; Clark SJ, 2009, 'Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning', Human Molecular Genetics, 18, pp. 3098 - 3109, http://dx.doi.org/10.1093/hmg/ddp251

Journal articles | 2007

Hinshelwood R; Huschtscha L; Melki J; Stirzaker C; Abdipranoto A; Vissel B; Ravasi T; Wells C; Hume DP; Reddel R; Clark SJ, 2007, 'Concordant epigenetic silencing of transforming growth factor-beta signaling pathway genes occurs early in breast carcinogenesis', Cancer research, 67, pp. 11517 - 11527, http://dx.doi.org/10.1158/0008-5472.CAN-07-1284

Journal articles | 2007

Hitchins MP; Ap Lin V; Buckle AD; Cheong KF; Halani N; Ku S; Kwok C; Packham D; Suter CM; Meagher AP; Stirzaker C; Clark SJ; Hawkins NJ; Ward RL, 2007, 'Epigenetic inactivation of a cluster of genes flanking MLH1 in microsatellite-unstable colorectal cancer', Cancer research, 67, pp. 9107 - 9116, http://dx.doi.org/10.1158/0008-5472.CAN-07-0869

Journal articles | 2007

Stirzaker C; Dia H, 2007, 'Evaluation of transportation infrastructure management strategies using microscopic traffic simulation', Journal of Infrastructure Systems, 13, pp. 168 - 174, http://dx.doi.org/10.1061/(ASCE)1076-0342(2007)13:2(168)

Journal articles | 2006

Clark SJ; Statham A; Stirzaker C; Molloy PL; Frommer M, 2006, 'DNA methylation: Bisulphite modification and analysis', Nature Protocols, 1, pp. 2353 - 2364, http://dx.doi.org/10.1038/nprot.2006.324

Journal articles | 2006

Frigola J; Song J; Stirzaker C; Hinshelwood R; Peinado M; Clark SJ, 2006, 'Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band', Nature Genetics, 38, pp. 540 - 549, http://dx.doi.org/10.1038/ng1781

Journal articles | 2004

Stirzaker C; Song J; Davidson B; Clark SJ, 2004, 'Transcriptional Gene Silencing Promotes DNA Hypermethylation through a sequential Change in Chromatin Modifications in Cancer Cells', Cancer research, 64, pp. 3871 - 3877, http://dx.doi.org/10.1158/0008-5472.CAN-03-3690

Journal articles | 2002

Song JZ; Stirzaker C; Harrison J; Melki JR; Clark SJ, 2002, 'Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells', Oncogene, 21, pp. 1048 - 1061, http://dx.doi.org/10.1038/sj.onc.1205153

Journal articles | 2002

Warnecke PM; Stirzaker C; Song J; Grunau C; Melki JR; Clark SJ, 2002, 'Identification and resolution of artifacts in bisulfite sequencing', Methods, 27, pp. 101 - 107, http://dx.doi.org/10.1016/S1046-2023(02)00060-9

Journal articles | 1998

Harrison J; Stirzaker C; Clark SJ, 1998, 'Cytosines adjacent to methylated CpG sites can be partially resistant to conversion in genomic bisulfite sequencing leading to methylation artifacts', Anal Biochem, 264, pp. 129 - 132, http://dx.doi.org/10.1006/abio.1998.2833

Journal articles | 1997

Stirzaker C; Millar DS; Paul CL; Warnecke PM; Harrison J; Vincent PC; Frommer M; Clark SJ, 1997, 'Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors', Cancer Research, 57, pp. 2229 - 2237

Journal articles | 1997

Warnecke PM; Stirzaker C; Melki JR; Millar DS; Paul CL; Clark SJ, 1997, 'Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA', Nucleic Acids Res, 25, pp. 4422 - 4426, http://dx.doi.org/10.1093/nar/25.21.4422

Journal articles | 1990

Stirzaker SC; Poncet D; Both GW, 1990, 'Sequences in rotavirus glycoprotein VP7 that mediate delayed translocation and retention of the protein in the endoplasmic reticulum', Journal of Cell Biology, 111, pp. 1343 - 1350, http://dx.doi.org/10.1083/jcb.111.4.1343

Journal articles | 1989

Stirzaker SC; Both GW, 1989, 'The signal peptide of the rotavirus glycoprotein VP7 is essential for its retention in the ER as an integral membrane protein', Cell, 56, pp. 741 - 747, http://dx.doi.org/10.1016/0092-8674(89)90677-6

Journal articles | 1987

Stirzaker SC; Whitfield PL; Christie DL; Bellamy AR; Both GW, 1987, 'Processing of rotavirus glycoprotein VP7: Implications for the retention of the protein in the endoplasmic reticulum', Journal of Cell Biology, 105, pp. 2897 - 2903, http://dx.doi.org/10.1083/jcb.105.6.2897

Journal articles | 1987

Whitfeld PL; Tyndall C; Stirzaker SC; Bellamy AR; Both GW, 1987, 'Location of sequences within rotavirus SA11 glycoprotein VP7 which direct it to the endoplasmic reticulum.', Molecular and cellular biology, 7, pp. 2491 - 2497, http://dx.doi.org/10.1128/MCB.7.7.2491
Preprints | 2020

Luu P-L; Ong P-T; Loc TTH; Lam D; Pidsley R; Stirzaker C; Clark SJ, 2020, MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection, , http://dx.doi.org/10.1101/2020.02.09.941013

Conference Abstracts | 2019

Stirzaker C; Chia KM; Portman N; Milioli HH; Clifton S; Achinger-Kawecka J; Nair S; Lim E; Clark S, 2019, 'DNA demethylation agents as a therapeutic approach in endocrine-resistant breast cancer', in Oncolabs, presented at 7th PacRim Breast & Prostate Cancer Meeting, http://dx.doi.org/10.1530/oncolabs.1.P049

Conference Abstracts | 2018

Blazevski A; Pidsley R; Qu W; Korbie D; Luu L; Chang J; Yuen B; Scheltema MJ; Masand N; Haynes A-M; Quoc N; Stirzaker C; Song J; Stricker P; Clark S, 2018, 'When Focal Therapy Fails for Localised Prostate Cancer - Can Epigenetics Predict Which Patients Fail and Improve Patient Selection?', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, Vol. 14, pp. 33 - 33, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000437670700023&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Conference Papers | 2018

Cole AJ; Dickson K-A; Liddle C; Stirzaker C; Clifton-Bligh R; Marsh DJ, 2018, 'Abstract A06: Cisplatin-induced DNA damage modifies the chromatin landscape of histone H2B monoubiquitination in a p53-dependent manner', in Clinical Cancer Research, American Association for Cancer Research (AACR), pp. A06 - A06, presented at Abstracts: AACR Special Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; October 1-4, 2017; Pittsburgh, PA, http://dx.doi.org/10.1158/1557-3265.ovca17-a06

Preprints | 2018

Du Q; Bert SA; Armstrong NJ; Caldon CE; Song JZ; Nair SS; Gould CM; Luu PL; Khoury A; Qu W; Zotenko E; Stirzaker C; Clark SJ, 2018, Replication timing shapes the cancer epigenome and the nature of chromosomal rearrangements, , http://dx.doi.org/10.1101/251280

Conference Abstracts | 2018

Mathe A; Wong-Brown M; Morten BC; Braye SG; Locke WJ; Stirzaker C; Clark SJ; Scott R; Avery-Kiejda KA, 2018, 'Defining the Key Mediators of Breast Cancer Progression and Treatment Resistance in the triple Negative Subtype', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, Vol. 14, pp. 9 - 9, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000446654600003&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Conference Abstracts | 2017

Cole AJ; Dickson K-A; Liddle C; Stirzaker C; Clifton-Bligh R; Marsh DJ, 2017, 'Cisplatin-induced DNA damage modifies the chromatin landscape of histone H2B monoubiquitination in a p53-dependent manner.', in CLINICAL CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, PA, Pittsburgh, Vol. 24, pp. 40 - 41, presented at AACR Special Conference on Addressing Critical Questions in Ovarian Cancer Research and Treatment, PA, Pittsburgh, 01 October 2017 - 04 October 2017, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000440823600042&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Conference Papers | 2017

Lawrence MG; Pidsley R; Zotenko E; Niranjan B; Statham A; Song J; Armstrong N; Pedersen J; Frydenberg M; Taylor R; Stirzaker C; Risbridger G; Clark S, 2017, 'Abstract 1997: Charting the DNA methylation landscape of prostate cancer associated fibroblasts', in Cancer Research, American Association for Cancer Research (AACR), pp. 1997 - 1997, presented at Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC, http://dx.doi.org/10.1158/1538-7445.am2017-1997

Conference Abstracts | 2016

Mathe A; Wong-Brown M; Locke W; Stirzaker C; Braye S; Forbes J; Clark S; Avery-Kiejda K; Scott R, 2016, 'DNA METHYLATION PROFILE OF TRIPLE NEGATIVE BREAST CANCER-SPECIFIC GENES COMPARING LYMPH NODE POSITIVE PATIENTS TO LYMPH NODE NEGATIVE PATIENTS', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, Vol. 12, pp. 27 - 27, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000387772400056&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Preprints | 2013

Riebler A; Menigatti M; Song JZ; Statham AL; Stirzaker C; Mahmud N; Mein CA; Clark SJ; Robinson MD, 2013, BayMeth: Improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach, , http://dx.doi.org/10.48550/arxiv.1312.3115

Conference Papers | 2009

Stirzaker C; Song JZ; Statham AL; Robinson M; Lacaze P; Coolen M; Moreno CS; Warren K; Clark SJ, 2009, 'CONSOLIDATION OF THE CANCER EPIGENOME TO REGIONS OF UNIFORM CHROMATIN', in CELLULAR ONCOLOGY, IOS PRESS, SCOTLAND, Edinburgh, pp. 136 - 136, presented at 3rd Marie Curie-Genome Architecture in Relation to Disease Meeting (MC-GARD), SCOTLAND, Edinburgh, 01 April 2009 - 05 April 2009, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000265635300098&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Conference Papers | 2009

Stirzaker C; Song JZ; Statham AL; Robinson M; Lacaze P; Coolen M; Moreno CS; Warren K; Clark SJ, 2009, 'CONSOLIDATION OF THE CANCER EPIGENOME TO REGIONS OF UNIFORM CHROMATIN', in CELLULAR ONCOLOGY, SPRINGER, SCOTLAND, Edinburgh, pp. 101 - 101, presented at 3rd Marie Curie-Genome Architecture in Relation to Disease Meeting (MC-GARD), SCOTLAND, Edinburgh, 01 April 2009 - 05 April 2009, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000265635300028&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Conference Papers | 2008

Coolen M; Song J; Statham AL; Lacaze P; Moreno CS; Kaplan W; Stirzaker C; Clark SJ, 2008, 'Long range epigenetic silencing (LRES): A common phenomenon in prostate cancer', in CELLULAR ONCOLOGY, IOS PRESS, SPAIN, Madrid, pp. 225 - 225, presented at 2nd Marie Curie-Genome Architecture in Relation to Disease Meeting (MC-GARD), SPAIN, Madrid, 04 May 2008 - 07 May 2008, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000255341800005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Conference Papers | 2006

Frigola J; Song JZ; Stirzaker C; Peinado MA; Clark SJ, 2006, 'Epigenetic Silent Neighborhoods in Cancer Cells', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000454606204232&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

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AdjAssocProf Clare Stirzaker