By AdjAssocProf Clare Stirzaker

Journal articles

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

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

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

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 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

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

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

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

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

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

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

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

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)

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

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

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 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

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

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://www.ncbi.nlm.nih.gov/pubmed/12095266

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

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

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://www.ncbi.nlm.nih.gov/pubmed/9336479

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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