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Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma.
Published in:
Journal of Pathology, 2024, v. 262, n. 4, p. 480, doi. 10.1002/path.6250
By:
- Meyer, Braydon;
- Stirzaker, Clare;
- Ramkomuth, Sonny;
- Harvey, Kate;
- Chan, Belinda;
- Lee, Cheok Soon;
- Karim, Rooshdiya;
- Deng, Niantao;
- Avery‐Kiejda, Kelly A;
- Scott, Rodney J;
- Lakhani, Sunil;
- Fox, Stephen;
- Robbins, Elizabeth;
- Shin, Joo‐Shik;
- Beith, Jane;
- Gill, Anthony;
- Sioson, Loretta;
- Chan, Charles;
- Krishnaswamy, Mrudula;
- Cooper, Caroline
Publication type:
Article
Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band.
Published in:
Nature Genetics, 2006, v. 38, n. 5, p. 540, doi. 10.1038/ng1781
By:
- Frigola, Jordi;
- Song, Jenny;
- Stirzaker, Clare;
- Hinshelwood, Rebecca A.;
- Peinado, Miguel A.;
- Clark, Susan J.
Publication type:
Article
MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection.
Published in:
Bioinformatics, 2021, v. 37, n. 15, p. 2198, doi. 10.1093/bioinformatics/btaa1060
By:
- Luu, Phuc-Loi;
- Ong, Phuc-Thinh;
- Loc, Tran Thai Huu;
- Lam, Dilys;
- Pidsley, Ruth;
- Stirzaker, Clare;
- Clark, Susan J
Publication type:
Article
DNA methylation profile of triple negative breast cancer-specific genes comparing lymph node positive patients to lymph node negative patients.
Published in:
Scientific Reports, 2016, p. 33435, doi. 10.1038/srep33435
By:
- Mathe, Andrea;
- Wong-Brown, Michelle;
- Locke, Warwick J.;
- Stirzaker, Clare;
- Braye, Stephen G.;
- Forbes, John F.;
- Clark, Susan J.;
- Avery-Kiejda, Kelly A.;
- Scott, Rodney J.
Publication type:
Article
Identification of DNA methylation biomarkers with potential to predict response to neoadjuvant chemotherapy in triple-negative breast cancer.
Published in:
Clinical Epigenetics, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13148-021-01210-6
By:
- Meyer, Braydon;
- Clifton, Samuel;
- Locke, Warwick;
- Luu, Phuc-Loi;
- Du, Qian;
- Lam, Dilys;
- Armstrong, Nicola J.;
- Kumar, Beena;
- Deng, Niantao;
- Harvey, Kate;
- Swarbrick, Alex;
- Ganju, Vinod;
- Clark, Susan J.;
- Pidsley, Ruth;
- Stirzaker, Clare
Publication type:
Article
Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells.
Published in:
Oncogene, 2002, v. 21, n. 7, p. 1048, doi. 10.1038/sj.onc.1205153
By:
- Song, Jenny Z.;
- Stirzaker, Clare;
- Harrison, Janet;
- Melki, John R.;
- Clark, Susan J.
Publication type:
Article
Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-08302-1
By:
- Du, Qian;
- Bert, Saul A.;
- Armstrong, Nicola J.;
- Caldon, C. Elizabeth;
- Song, Jenny Z.;
- Nair, Shalima S.;
- Gould, Cathryn M.;
- Luu, Phuc-Loi;
- Peters, Timothy;
- Khoury, Amanda;
- Qu, Wenjia;
- Zotenko, Elena;
- Stirzaker, Clare;
- Clark, Susan J.
Publication type:
Article
Advances in Prognostic Methylation Biomarkers for Prostate Cancer.
Published in:
Cancers, 2020, v. 12, n. 10, p. 2993, doi. 10.3390/cancers12102993
By:
- Lam, Dilys;
- Clark, Susan;
- Stirzaker, Clare;
- Pidsley, Ruth
Publication type:
Article
Comprehensive methylome sequencing reveals prognostic epigenetic biomarkers for prostate cancer mortality.
Published in:
Clinical & Translational Medicine, 2022, v. 12, n. 10, p. 1, doi. 10.1002/ctm2.1030
By:
- Pidsley, Ruth;
- Lam, Dilys;
- Qu, Wenjia;
- Peters, Timothy J.;
- Luu, Phuc‐Loi;
- Korbie, Darren;
- Stirzaker, Clare;
- Daly, Roger J.;
- Stricker, Phillip;
- Kench, James G.;
- Horvath, Lisa G.;
- Clark, Susan J.
Publication type:
Article
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity.
Published in:
Nature Cell Biology, 2010, v. 12, n. 3, p. 235, doi. 10.1038/ncb2023
By:
- Coolen, Marcel W.;
- Stirzaker, Clare;
- Song, Jenny Z.;
- Statham, Aaron L.;
- Kassir, Zena;
- Moreno, Carlos S.;
- Young, Andrew N.;
- Varma, Vijay;
- Speed, Terence P.;
- Cowley, Mark;
- Lacaze, Paul;
- Kaplan, Warren;
- Robinson, Mark D.;
- Clark, Susan J.
Publication type:
Article
Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA.
Published in:
Nucleic Acids Research, 1997, v. 25, n. Supplement, p. 4422, doi. 10.1093/nar/25.21.4422
By:
- Warnecke, Peter M.;
- Stirzaker, Clare;
- Melki, John R.;
- Millar, Douglas S.;
- Paul, Cheryl L.;
- Clark, Susan J.
Publication type:
Article
Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA.
Published in:
Epigenetics & Chromatin, 2017, v. 10, p. 1, doi. 10.1186/s13072-017-0123-7
By:
- Skvortsova, Ksenia;
- Zotenko, Elena;
- Phuc-Loi Luu;
- Gould, Cathryn M.;
- Nair, Shalima S.;
- Clark, Susan J.;
- Stirzaker, Clare
Publication type:
Article
Ubiquitin chromatin remodelling after DNA damage is associated with the expression of key cancer genes and pathways.
Published in:
Cellular & Molecular Life Sciences, 2021, v. 78, n. 3, p. 1011, doi. 10.1007/s00018-020-03552-5
By:
- Cole, Alexander J.;
- Dickson, Kristie-Ann;
- Liddle, Christopher;
- Stirzaker, Clare;
- Shah, Jaynish S.;
- Clifton-Bligh, Roderick;
- Marsh, Deborah J.
Publication type:
Article
Characterisation and reproducibility of the Human Methylation EPIC v2.0 Bead Chip for DNA methylation profling.
Published in:
BMC Genomics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12864-024-10027-5
By:
- Peters, Timothy J.;
- Meyer, Braydon;
- Ryan, Lauren;
- Achinger‑Kawecka, Joanna;
- Song, Jenny;
- Campbell, Elyssa M.;
- Wenjia Qu;
- Nair, Shalima;
- Loi‑Luu, Phuc;
- Stricker, Phillip;
- Lim, Elgene;
- Stirzaker, Clare;
- Clark, Susan J.;
- Pidsley, Ruth
Publication type:
Article
DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer.
Published in:
Nature Communications, 2015, v. 6, n. 7, p. 7758, doi. 10.1038/ncomms8758
By:
- Stone, Andrew;
- Zotenko, Elena;
- Locke, Warwick J.;
- Korbie, Darren;
- Millar, Ewan K. A.;
- Pidsley, Ruth;
- Stirzaker, Clare;
- Graham, Peter;
- Trau, Matt;
- Musgrove, Elizabeth A.;
- Nicholson, Robert I.;
- Gee, Julia M. W.;
- Clark, Susan J.
Publication type:
Article
Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value.
Published in:
Nature Communications, 2015, v. 6, n. 2, p. 5899, doi. 10.1038/ncomms6899
By:
- Stirzaker, Clare;
- Zotenko, Elena;
- Song, Jenny Z.;
- Qu, Wenjia;
- Nair, Shalima S.;
- Locke, Warwick J.;
- Stone, Andrew;
- Armstong, Nicola J.;
- Robinson, Mark D.;
- Dobrovic, Alexander;
- Avery-Kiejda, Kelly A.;
- Peters, Kate M.;
- French, Juliet D.;
- Stein, Sandra;
- Korbie, Darren J.;
- Trau, Matt;
- Forbes, John F.;
- Scott, Rodney J.;
- Brown, Melissa A.;
- Francis, Glenn D.
Publication type:
Article
BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach.
Published in:
Genome Biology, 2014, v. 15, n. 1, p. 1, doi. 10.1186/gb-2014-15-2-r35
By:
- Riebler, Andrea;
- Menigatti, Mirco;
- Song, Jenny Z.;
- Statham, Aaron L.;
- Stirzaker, Clare;
- Mahmud, Nadiya;
- Mein, Charles A.;
- Clark, Susan J.;
- Robinson, Mark D.
Publication type:
Article
Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels.
Published in:
Clinical Epigenetics, 2020, v. 12, n. 1, p. 1, doi. 10.1186/s13148-020-00880-y
By:
- Lam, Dilys;
- Luu, Phuc-Loi;
- Song, Jenny Z.;
- Qu, Wenjia;
- Risbridger, Gail P.;
- Lawrence, Mitchell G.;
- Lu, Jennifer;
- Trau, Matt;
- Korbie, Darren;
- Clark, Susan J.;
- Pidsley, Ruth;
- Stirzaker, Clare
Publication type:
Article
Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer.
Published in:
Clinical Epigenetics, 2020, v. 12, n. 1, p. 1, doi. 10.1186/s13148-020-00836-2
By:
- Lawrence, Mitchell G.;
- Pidsley, Ruth;
- Niranjan, Birunthi;
- Papargiris, Melissa;
- Pereira, Brooke A.;
- Richards, Michelle;
- Teng, Linda;
- Norden, Sam;
- Ryan, Andrew;
- Frydenberg, Mark;
- Stirzaker, Clare;
- Taylor, Renea A.;
- Risbridger, Gail P.;
- Clark, Susan J.
Publication type:
Article
The DNA methylation landscape in cancer.
Published in:
Essays in Biochemistry, 2019, v. 63, n. 6, p. 797, doi. 10.1042/EBC20190037
By:
- Skvortsova, Ksenia;
- Stirzaker, Clare;
- Taberlay, Phillippa
Publication type:
Article
Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer.
Published in:
Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01393-8
By:
- Valdés-Mora, Fátima;
- Gould, Cathryn M.;
- Colino-Sanguino, Yolanda;
- Wenjia Qu;
- Song, Jenny Z.;
- Taylor, Kylie M.;
- Buske, Fabian A.;
- Statham, Aaron L.;
- Nair, Shalima S.;
- Armstrong, Nicola J.;
- Kench, James G.;
- Lee, Kenneth M. L.;
- Horvath, Lisa G.;
- Qiu, Minru;
- Ilinykh, Alexei;
- Yeo-Teh, Nicole S.;
- Gallego-Ortega, David;
- Stirzaker, Clare;
- Clark, Susan J.
Publication type:
Article
Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling.
Published in:
Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-1066-1
By:
- Pidsley, Ruth;
- Zotenko, Elena;
- Peters, Timothy J.;
- Lawrence, Mitchell G.;
- Risbridger, Gail P.;
- Molloy, Peter;
- Van Djik, Susan;
- Muhlhausler, Beverly;
- Stirzaker, Clare;
- Clark, Susan J.
Publication type:
Article
Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning.
Published in:
Human Molecular Genetics, 2009, v. 18, n. 16, p. 3098, doi. 10.1093/hmg/ddp251
By:
- Hinshelwood, Rebecca A.;
- Melki, John R.;
- Huschtscha, Lily I.;
- Paul, Cheryl;
- Song, Jenny Z.;
- Stirzaker, Clare;
- Reddel, Roger R.;
- Clark, Susan J.
Publication type:
Article
Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups.
Published in:
Epigenetics & Chromatin, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13072-019-0258-9
By:
- Giles, Katherine A.;
- Gould, Cathryn M.;
- Du, Qian;
- Skvortsova, Ksenia;
- Song, Jenny Z.;
- Maddugoda, Madhavi P.;
- Achinger-Kawecka, Joanna;
- Stirzaker, Clare;
- Clark, Susan J.;
- Taberlay, Phillippa C.
Publication type:
Article
Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements.
Published in:
Bioinformatics, 2019, v. 35, n. 4, p. 560, doi. 10.1093/bioinformatics/bty675
By:
- Peters, Timothy J;
- Pidsley, Ruth;
- Nair, Shalima;
- Qu, Wenjia;
- Song, Jenny;
- Giles, Katherine A;
- Statham, Aaron L;
- French, Hugh J;
- Bradford, Stephen T;
- Stirzaker, Clare;
- Clark, Susan J;
- Varinli, Hilal;
- Speirs, Helen;
- Speed, Terence P
Publication type:
Article
Repitools: an R package for the analysis of enrichment-based epigenomic data.
Published in:
Bioinformatics, 2010, v. 26, n. 13, p. 1662, doi. 10.1093/bioinformatics/btq247
By:
- Statham, Aaron L.;
- Strbenac, Dario;
- Coolen, Marcel W.;
- Stirzaker, Clare;
- Clark, Susan J.;
- Robinson, Mark D.
Publication type:
Article
Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-019-14098-x
By:
- Achinger-Kawecka, Joanna;
- Valdes-Mora, Fatima;
- Luu, Phuc-Loi;
- Giles, Katherine A.;
- Caldon, C. Elizabeth;
- Qu, Wenjia;
- Nair, Shalima;
- Soto, Sebastian;
- Locke, Warwick J.;
- Yeo-Teh, Nicole S.;
- Gould, Cathryn M.;
- Du, Qian;
- Smith, Grady C.;
- Ramos, Irene R.;
- Fernandez, Kristine F.;
- Hoon, Dave S.;
- Gee, Julia M. W.;
- Stirzaker, Clare;
- Clark, Susan J.
Publication type:
Article
Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-019-13753-7
By:
- Khoury, Amanda;
- Achinger-Kawecka, Joanna;
- Bert, Saul A.;
- Smith, Grady C.;
- French, Hugh J.;
- Luu, Phuc-Loi;
- Peters, Timothy J.;
- Du, Qian;
- Parry, Aled J.;
- Valdes-Mora, Fatima;
- Taberlay, Phillippa C.;
- Stirzaker, Clare;
- Statham, Aaron L.;
- Clark, Susan J.
Publication type:
Article

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