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List of works by John Greally

A new class of tissue-specifically methylated regions involving entire CpG islands in the mouse.

scientific article published on December 2007

A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry

scientific article

A polycomb-mediated epigenetic field defect precedes invasive cervical carcinoma

scientific article published on 19 August 2016

A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets

scientific article published on 10 October 2016

A stain upon the silence: genes escaping X inactivation

scientific article

Aberrant DNA hypermethylation signature in acute myeloid leukemia directed by EVI1.

scientific article

Aberrant DNA methylation in malignant melanoma

scientific article

Aberrant epigenetic and genetic marks are seen in myelodysplastic leukocytes and reveal Dock4 as a candidate pathogenic gene on chromosome 7q

scientific article

Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene

scientific article

Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus.

scientific article published on 10 June 2016

An analytical pipeline for genomic representations used for cytosine methylation studies

scientific article

An integrative genomic and epigenomic approach for the study of transcriptional regulation

scientific article

Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays

scientific article

CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domains

scientific article

Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity

scientific article published on 01 October 2007

Chromatin organization in the female mouse brain fluctuates across the oestrous cycle

scientific article published on 28 June 2019

Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica

scientific article

Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development

scientific article

Cytosine methylation dysregulation in neonates following intrauterine growth restriction

scientific article

DNA demethylation by 5-aza-2'-deoxycytidine is imprinted, targeted to euchromatin, and has limited transcriptional consequences

scientific article published on 17 March 2015

DNA methylation alterations in multiple myeloma as a model for epigenetic changes in cancer

scientific article

DNA methylation changes in murine breast adenocarcinomas allow the identification of candidate genes for human breast carcinogenesis

scientific article published on 04 March 2011

DNA methylation haplotypes as cancer markers

scientific article published on 01 August 2018

DNA methylation is developmentally regulated for genes essential for cardiogenesis

scientific article

DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR (HELP)

scientific article published on 29 April 2010

DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma

scientific article

DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia.

scientific article

DNA methylation: Bidding the CpG island goodbye

scientific article published on 26 February 2013

Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells.

scientific article published on 26 January 2016

Differential epigenome-wide DNA methylation patterns in childhood obesity-associated asthma

scientific article published on January 2013

Distinct factors control histone variant H3.3 localization at specific genomic regions

scientific article

Encyclopaedia of humble DNA

scientific article published in Nature

Epigenetic changes in B lymphocytes associated with house dust mite allergic asthma

scientific article published in September 2011

Epigenetic functions of smchd1 repress gene clusters on the inactive X chromosome and on autosomes

scientific journal article

Epigenetics, cellular memory and gene regulation.

scientific article

Epigenome-wide Association Studies and the Interpretation of Disease -Omics

scientific article

Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii

scientific article

Epigenomics: beyond CpG islands.

scientific article published on June 2004

Experimental approaches to the study of epigenomic dysregulation in ageing

scientific article

Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats.

scientific article

Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding

scientific article published on 02 August 2019

Genetic recombination is targeted towards gene promoter regions in dogs.

scientific article

Genome-wide DNA methylation analysis using massively parallel sequencing technologies

scientific article published on January 2013

Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells

scientific journal article

Genome-wide assays that identify and quantify modified cytosines in human disease studies

scientific article

Genome-wide determination of DNA methylation by Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP) for the study of acute leukemias

scientific article published in January 2009

Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features.

scientific article

Genome-wide expression profiling of B lymphocytes reveals IL4R increase in allergic asthma.

scientific article published on 26 June 2014

High-efficiency genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells using a single-stranded donor oligonucleotide strategy

scientific article published on 14 August 2019

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers.

scientific article published on 22 April 2009

How might epigenetic dysregulation in early embryonic life contribute to autism spectrum disorder?

scientific article published on January 2015

In vitro and in vivo testing methods of epigenomic endpoints for evaluating endocrine disruptors.

scientific article published on January 2013

Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data

scientific article published on 25 April 2019

Introduction to epigenomics and epigenome-wide analysis

scientific article published on January 2010

Journal club

journal article; published in Nature on 2008-12-04

Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell lines

scientific article published on September 2008

LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation

scientific article published in July 2016

LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation

scientific article published on June 2010

Lack of evidence for green tea polyphenols as DNA methylation inhibitors in murine prostate

scientific article published on 24 November 2009

Lactate-mediated epigenetic reprogramming regulates formation of human pancreatic cancer-associated fibroblasts

scientific article published on 01 November 2019

Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome.

scientific article

Lsh regulates LTR retrotransposon repression independently of Dnmt3b function

scientific article

Maternal gametic transmission of translocations or inversions of human chromosome 11p15.5 results in regional DNA hypermethylation and downregulation of CDKN1C expression

scientific article

MeCP2 Binding Cooperativity Inhibits DNA Modification-Specific Recognition.

scientific article published on 15 July 2016

Meta-analysis of microarray studies reveals a novel hematopoietic progenitor cell signature and demonstrates feasibility of inter-platform data integration

scientific article published on 13 August 2008

Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder

scientific article

Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer

scientific article published on December 2016

Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia

scientific article published on 9 July 2016

Optimized design and data analysis of tag-based cytosine methylation assays

scientific article (publication date: 2010)

Pediatric Obesity-Related Asthma: The Role of Metabolic Dysregulation

scientific article published on 8 April 2016

Perceptive enzymes

scientific article published in Nature

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

scientific article published on 26 March 2015

Predictive properties of DNA methylation patterns in primary tumor samples for osteosarcoma relapse status

scientific article

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships.

scientific article

Re-targeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains

Recommendations for the design and analysis of epigenome-wide association studies

scientific article published on October 2013

Reduced-representation methylation mapping

scientific article published on September 2008

Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains

scientific article published on 20 May 2019

Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth

scientific article

Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterations

scientific article

The Current State of Epigenetic Research in Humans: Promise and Reality

scientific article

The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease

scientific article published on October 2009

The HELP assay

scientific article

The Wasp System: an open source environment for managing and analyzing genomic data.

scientific article

The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences

scientific article

Toxoplasma gondii and Cryptosporidium parvum lack detectable DNA cytosine methylation

scientific article published on 4 January 2008

Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas.

scholarly article

Transposable element expression in tumors is associated with immune infiltration and increased antigenicity

scientific article published on 19 November 2019

Unusual characteristics of the DNA binding domain of epigenetic regulatory protein MeCP2 determine its binding specificity

scientific article published on 23 May 2014

Whole-genome bisulfite sequencing with improved accuracy and cost

scientific article published on 09 August 2018

Widespread Hypomethylation Occurs Early and Synergizes with Gene Amplification during Esophageal Carcinogenesis ⬇️

scientific article published on March 31, 2011

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