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List of works by Susan Clark

A Read/Write Mechanism Connects p300 Bromodomain Function to H2A.Z Acetylation

scientific article published on 31 October 2019

A bioengineered microenvironment to quantitatively measure the tumorigenic properties of cancer-associated fibroblasts in human prostate cancer.

scientific article published on 2 April 2013

Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning

scientific article

Abstract A4: Whole genome sequencing of free circulating DNA from plasma of HGSOC patients

Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer.

scientific article published on 7 November 2017

Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer

scientific article published on 25 July 2011

Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis

scientific article published on April 2007

Advances in Prognostic Methylation Biomarkers for Prostate Cancer

scientific article published on 15 October 2020

Alterations in Three-Dimensional Organization of the Cancer Genome and Epigenome.

scientific article published on 19 April 2017

Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer

scientific article published on 18 March 2020

Alterations in the p16(INK4a) and p53 tumor suppressor genes of hTERT-immortalized human fibroblasts.

scientific article published on April 2004

Androgen receptor expression predicts breast cancer survival: the role of genetic and epigenetic events ⬇️

scientific article published on April 2, 2012

BCL-2 hypermethylation is a potential biomarker of sensitivity to antimitotic chemotherapy in endocrine-resistant breast cancer

scientific article published on 16 July 2013

BRG1 promotes transcriptional patterns that are permissive to proliferation in cancer cells

BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

scientific article (publication date: 11 February 2014)

Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data

scientific article published on 06 August 2020

Bisulfite Sequencing in Preimplantation Embryos: DNA Methylation Profile of the Upstream Region of the Mouse ImprintedH19Gene ⬇️

scientific article published on July 15, 1998

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

scientific article

Bisulphite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq).

scientific article published in January 2018

COBRA-Seq: Sensitive and Quantitative Methylome Profiling

scientific article published on 23 October 2015

Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate

scientific article published on 01 November 2021

Cancer-specific region of hypermethylation identified within the HIC1 putative tumour suppressor gene in acute myeloid leukaemia

scientific article published on 01 June 1999

Chromatin remodeler mutations in human cancers: epigenetic implications

scientific article

Circulating microRNAs are associated with docetaxel chemotherapy outcome in castration-resistant prostate cancer

scientific article

Collagen and calcium-binding EGF domains 1 is frequently inactivated in ovarian cancer by aberrant promoter hypermethylation and modulates cell migration and survival

scientific article

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

scientific article published on January 2011

Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA.

scientific article

Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels

scientific article published on 22 June 2020

Concordant epigenetic silencing of transforming growth factor-beta signaling pathway genes occurs early in breast carcinogenesis.

scientific article published on December 2007

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity

scientific article

Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains

scientific article published on 07 January 2020

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis.

scientific article published on May 2015

Coordinated epigenetic repression of the miR-200 family and miR-205 in invasive bladder cancer.

scientific article

Copy-number-aware differential analysis of quantitative DNA sequencing data

scientific article

CpNpG methylation in mammalian cells ⬇️

scientific article published on May 1, 1995

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling.

scientific article published on 07 October 2016

Cytosines adjacent to methylated CpG sites can be partially resistant to conversion in genomic bisulfite sequencing leading to methylation artifacts.

scientific article published in November 1998

DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns

scientific article published on 01 February 2019

DNA methylation analysis in mammalian cells

scientific article published in June 2002

DNA methylation and gene silencing in cancer: which is the guilty party?

scientific article

DNA methylation changes in leukaemia

scientific article

DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment

scientific article published on 29 January 2008

DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer.

scientific article

DNA methylation profile of triple negative breast cancer-specific genes comparing lymph node positive patients to lymph node negative patients

scientific article published on 27 September 2016

DNA methylation: Bisulphite modification and analysis

scientific article published on 01 January 2006

DNA methylation: bisulphite modification and analysis.

scientific article

De novo identification of differentially methylated regions in the human genome.

scientific article published on 27 January 2015

Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA.

scientific article published on November 1997

Development and protective efficacy of a recombinant-DNA derived fimbrial vaccine against enterotoxic colibacillosis in neonatal piglets.

scientific article

Direct Cloning of Polymerase Chain Reaction Products in an Xcml T-Vector

scientific article published on 01 January 1994

Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription

scientific article

Disruption of the 3D cancer genome blueprint.

scientific article published on 12 December 2016

Dynamics of bivalent chromatin domains upon drug induced reactivation and resilencing in cancer cells

scientific article published in September 2011

ELF5 Drives Lung Metastasis in Luminal Breast Cancer through Recruitment of Gr1+ CD11b+ Myeloid-Derived Suppressor Cells

scientific article (publication date: December 2015)

ELF5 modulates the estrogen receptor cistrome in breast cancer

scientific article published on 02 January 2020

ELF5 suppresses estrogen sensitivity and underpins the acquisition of antiestrogen resistance in luminal breast cancer.

scientific article

Enduring epigenetic landmarks define the cancer microenvironment

scientific article published on 12 April 2018

Epigenetic architecture and miRNA: reciprocal regulators.

scientific article published on December 2010

Epigenetic deregulation across chromosome 2q14.2 differentiates normal from prostate cancer and provides a regional panel of novel DNA methylation cancer biomarkers.

scientific article

Epigenetic inactivation of a cluster of genes flanking MLH1 in microsatellite-unstable colorectal cancer

scientific article

Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band.

scientific article

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer

scientific article published on 16 January 2020

Epigenetics in Prostate Cancer: Biologic and Clinical Relevance ⬇️

scientific article published on June 22, 2011

Epigenome remodelling in breast cancer: insights from an early in vitro model of carcinogenesis

scientific article

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation

scientific article

Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements

scientific article published on 01 February 2019

Exploring and exploiting the aberrant DNA methylation profile of endocrine-resistant breast cancer

scientific article published on 01 December 2013

GWAS of DNA methylation variation within imprinting control regions suggests parent-of-origin association

scientific article published on 3 June 2013

Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas

scientific article published on 18 July 2016

Genome-wide DNA methylation profiling in triple-negative breast cancer reveals epigenetic signatures with important clinical value

scientific article published on 26 May 2015

Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines

scientific article

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements

scientific article

Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten.

scientific article

H2A.Z acetylation and transcription: ready, steady, go!

scientific article published on 18 April 2016

Human histone genes are interspersed with members of the Alu family and with other transcribed sequences

article

Hypermethylation of the Inhibin -Subunit Gene in Prostate Carcinoma

article

Hypermethylation of the prostacyclin synthase (PTGIS) promoter is a frequent event in colorectal cancer and associated with aneuploidy

scientific article published in November 2005

Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells.

scientific article published in February 2002

Identification and resolution of artifacts in bisulfite sequencing.

scientific article published in June 2002

Identification of DNA methylation biomarkers with potential to predict response to neoadjuvant chemotherapy in triple-negative breast cancer

scientific article published on 18 December 2021

Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins

scientific article

Increased DNA methyltransferase expression in leukaemia

scientific article published on 01 March 1998

Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups

scientific article published on 12 February 2019

Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers

scientific article published on 9 December 2011

Lineage specific methylation of the Elf5 promoter in mammary epithelial cells.

scientific article

Long-range epigenetic silencing at 2q14.2 affects most human colorectal cancers and may have application as a non-invasive biomarker of disease.

scientific article published on 21 April 2009

Long-range regulators of the lncRNA HOTAIR enhance its prognostic potential in breast cancer

scientific article published on 04 July 2016

Low O6-methylguanine-DNA methyltransferase (MGMT) expression and response to temozolomide in aggressive pituitary tumours.

scientific article published on 03 December 2008

Mapping the regulatory sequences controlling 93 breast cancer-associated miRNA genes leads to the identification of two functional promoters of the Hsa-mir-200b cluster, methylation of which is associated with metastasis or hormone receptor status i

scientific article

MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection

scientific article published on 26 December 2020

Methyl-CpG-binding domain proteins: readers of the epigenome

scientific article published on 30 April 2015

Methylated Glutathione S-transferase 1 (mGSTP1) is a potential plasma free DNA epigenetic marker of prognosis and response to chemotherapy in castrate-resistant prostate cancer

scientific article published on 21 August 2014

Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma

scientific article

Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes

scientific article published on 02 July 2019

Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value.

scientific article published on 02 February 2015

MicroRNA alterations and associated aberrant DNA methylation patterns across multiple sample types in oral squamous cell carcinoma.

scientific article

MicroRNA profiling of the pubertal mouse mammary gland identifies miR-184 as a candidate breast tumour suppressor gene

scientific article published on 13 June 2015

Mining cancer methylomes: prospects and challenges

scientific article published on 21 December 2013

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression.

scientific article published on 4 June 2019

Multiple H4 histone mRNAs of HeLa cells are encoded in different genes

scientific article published in Nature

Multiplex bisulfite PCR resequencing of clinical FFPE DNA.

scientific article

Mutation and methylation analysis of TP53 in adrenal carcinogenesis.

scientific article

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

scientific article

Nucleotide-Level Profiling of m5C RNA Methylation

scientific article published on 01 January 2016

Organization of human histone genes ⬇️

scientific article published on March 1, 1982

Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation

scientific article

Profiling the tyrosine phosphoproteome of different mouse mammary tumour models reveals distinct, model-specific signalling networks and conserved oncogenic pathways.

scientific article

Prognostic and diagnostic significance of DNA methylation patterns in high grade serous ovarian cancer

scientific article published on 22 November 2011

Prostate cancer epigenetic biomarkers: next-generation technologies.

scientific article published on 19 May 2014

Protocol matters: which methylome are you actually studying?

scientific article

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

scientific article

Regional activation of the cancer genome by long-range epigenetic remodeling

scientific article published on 13 December 2012

Repitools: an R package for the analysis of enrichment-based epigenomic data

scientific article

Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer

scientific article published in Nature Communications

Sequence-specific methylation of the mouse H19 gene in embryonic cells deficient in the Dnmt-1 gene

scientific article published in January 1998

Sequencing 5-methylcytosine residues in genomic DNA.

scientific article published on June 1994

Serum Free Methylated Glutathione S-transferase 1 DNA Levels, Survival, and Response to Docetaxel in Metastatic, Castration-resistant Prostate Cancer: Post Hoc Analyses of Data from a Phase 3 Trial

scientific article published on 19 November 2018

Sp1 binding is inhibited by (m)Cp(m)CpG methylation.

scientific article published on August 1997

Telomere-Driven Karyotypic Complexity Concurs with p16INK4a Inactivation in TP53-Competent Immortal Endothelial Cells

scientific article published on 01 November 2006

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.

scientific article published on 06 April 2016

Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells.

scientific article published on June 2004

Transient exposure to miR-203 enhances the differentiation capacity of established pluripotent stem cells

scientific article published on 02 July 2020

Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients

scientific article published on 11 December 2020

Wool fibre crimp is determined by mitotic asymmetry and position of final keratinisation and not ortho- and para-cortical cell segmentation ⬇️

scientific article published on June 1, 2009

ZNF300P1 encodes a lincRNA that regulates cell polarity and is epigenetically silenced in type II epithelial ovarian cancer

scientific article

miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA

scientific article

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