By AdjAssocProf Clare Stirzaker

Journal articles

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

Valdés-Mora F; Song JZ; Statham AL; Strbenac D; Robinson MD; Nair SS; Patterson KI; 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 Res, 22, pp. 307 - 321, http://dx.doi.org/10.1101/gr.118919.110

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 Res, 22, pp. 1120 - 1127, http://dx.doi.org/10.1101/gr.132076.111

Robinson MD; Strbenac D; Stirzaker C; Statham AL; Song J; Speed TP; Clark SJ, 2012, 'Copy-number-aware differential analysis of quantitative DNA sequencing data.', Genome Res, 22, pp. 2489 - 2496, http://dx.doi.org/10.1101/gr.139055.112

Patterson K; Molloy L; Qu W; Clark S, 2011, 'DNA methylation: bisulphite modification and analysis.', J Vis Exp, http://dx.doi.org/10.3791/3170

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

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

Nair SS; Coolen MW; Stirzaker C; Song JZ; Statham AL; Strbenac D; Robinson MD; 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

Devaney J; Stirzaker C; Qu W; Song JZ; Statham AL; Patterson KI; Horvath LG; Tabor B; Coolen MW; Hulf T; Kench JG; Henshall SM; Pe Benito R; Haynes A-M; Mayor R; Peinado MA; 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 Epidemiol Biomarkers Prev, 20, pp. 148 - 159, http://dx.doi.org/10.1158/1055-9965.EPI-10-0719

Selinger CI; Cooper WA; Al-Sohaily S; Mladenova DN; Pangon L; Kennedy CW; McCaughan BC; Stirzaker C; Kohonen-Corish MRJ, 2011, 'Loss of special AT-rich binding protein 1 expression is a marker of poor survival in lung cancer.', J Thorac Oncol, 6, pp. 1179 - 1189, http://dx.doi.org/10.1097/JTO.0b013e31821b4ce0

Statham AL; Strbenac D; Coolen MW; Stirzaker C; Clark SJ; Robinson MD, 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

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

Robinson MD; Stirzaker C; Statham AL; Coolen MW; Song JZ; Nair SS; 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 Res, 20, pp. 1719 - 1729, http://dx.doi.org/10.1101/gr.110601.110

Hinshelwood RA; Melki JR; Huschtscha LI; 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.', Hum Mol Genet, 18, pp. 3098 - 3109, http://dx.doi.org/10.1093/hmg/ddp251

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

Hitchins MP; Lin VA; Buckle A; Cheong K; Halani N; Ku S; Kwok C-T; Packham D; Suter CM; Meagher A; Stirzaker C; Clark S; Hawkins NJ; Ward RL, 2007, 'Epigenetic inactivation of a cluster of genes flanking MLH1 in microsatellite-unstable colorectal cancer.', Cancer Res, 67, pp. 9107 - 9116, http://dx.doi.org/10.1158/0008-5472.CAN-07-0869

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)

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

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

Stirzaker C; Song JZ; Davidson B; Clark SJ, 2004, 'Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells.', Cancer Res, 64, pp. 3871 - 3877, http://dx.doi.org/10.1158/0008-5472.CAN-03-3690

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

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

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

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

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

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

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

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

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

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