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SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information.

Wijetunga NA, Johnston AD, Maekawa R, Delahaye F, Ulahannan N, Kim K, Greally JM.

BMC Bioinformatics. 2017 Jan 18;18(1):41. doi: 10.1186/s12859-017-1477-3.


Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts.

Zhang D, Wu B, Wang P, Wang Y, Lu P, Nechiporuk T, Floss T, Greally JM, Zheng D, Zhou B.

Nucleic Acids Res. 2017 Apr 7;45(6):3102-3115. doi: 10.1093/nar/gkw1258.


LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development.

Acosta D, Bagchi S, Broin PÓ, Hollern D, Racedo SE, Morrow B, Sellers RS, Greally JM, Golden A, Andrechek E, Wood T, Montagna C.

Sci Rep. 2016 Nov 3;6:35810. doi: 10.1038/srep35810.


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

Wijetunga NA, Pascual M, Tozour J, Delahaye F, Alani M, Adeyeye M, Wolkoff AW, Verma A, Greally JM.

Oncogene. 2017 Apr 6;36(14):2030-2044. doi: 10.1038/onc.2016.340. Epub 2016 Oct 10.


A polycomb-mediated epigenetic field defect precedes invasive cervical carcinoma.

Wijetunga NA, Ben-Dayan M, Tozour J, Burk RD, Schlecht NF, Einstein MH, Greally JM.

Oncotarget. 2016 Sep 20;7(38):62133-62143. doi: 10.18632/oncotarget.11390.


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

Birney E, Smith GD, Greally JM.

PLoS Genet. 2016 Jun 23;12(6):e1006105. doi: 10.1371/journal.pgen.1006105. eCollection 2016 Jun. Review.


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

Suzuki M, Maekawa R, Patterson NE, Reynolds DM, Calder BR, Reznik SE, Heo HJ, Einstein FH, Greally JM.

Clin Epigenetics. 2016 Jun 10;8:67. doi: 10.1186/s13148-016-0234-1. eCollection 2016.


Loss of MEN1 activates DNMT1 implicating DNA hypermethylation as a driver of MEN1 tumorigenesis.

Yuan Z, Sánchez Claros C, Suzuki M, Maggi EC, Kaner JD, Kinstlinger N, Gorecka J, Quinn TJ, Geha R, Corn A, Pastoriza J, Jing Q, Adem A, Wu H, Alemu G, Du YC, Zheng D, Greally JM, Libutti SK.

Oncotarget. 2016 Mar 15;7(11):12633-50. doi: 10.18632/oncotarget.7279.


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

Barnicle A, Seoighe C, Golden A, Greally JM, Egan LJ.

Physiol Genomics. 2016 Apr;48(4):257-73. doi: 10.1152/physiolgenomics.00046.2015. Epub 2016 Jan 26.


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

Nadel J, Athanasiadou R, Lemetre C, Wijetunga NA, Ó Broin P, Sato H, Zhang Z, Jeddeloh J, Montagna C, Golden A, Seoighe C, Greally JM.

Epigenetics Chromatin. 2015 Nov 16;8:46. doi: 10.1186/s13072-015-0040-6. eCollection 2015.


Development of a Targeted Multi-Disorder High-Throughput Sequencing Assay for the Effective Identification of Disease-Causing Variants.

Delio M, Patel K, Maslov A, Marion RW, McDonald TV, Cadoff EM, Golden A, Greally JM, Vijg J, Morrow B, Montagna C.

PLoS One. 2015 Jul 27;10(7):e0133742. doi: 10.1371/journal.pone.0133742. eCollection 2015.


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

Li Q, Suzuki M, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J, Richmond T, Rosenbaum H, Burgess D, Springer NM, Greally JM.

Nucleic Acids Res. 2015 Jul 13;43(12):e81. doi: 10.1093/nar/gkv244. Epub 2015 Mar 26.


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

Ramos MP, Wijetunga NA, McLellan AS, Suzuki M, Greally JM.

Epigenetics Chromatin. 2015 Mar 17;8:11. doi: 10.1186/s13072-015-0004-x. eCollection 2015.


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

Ulahannan N, Greally JM.

Epigenetics Chromatin. 2015 Jan 22;8:5. doi: 10.1186/1756-8935-8-5. eCollection 2015. Review.


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

Berko ER, Greally JM.

Epigenomics. 2015;7(1):1-4. doi: 10.2217/epi.14.86. No abstract available.


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

Rosenblum JM, Wijetunga NA, Fazzari MJ, Krailo M, Barkauskas DA, Gorlick R, Greally JM.

Epigenetics. 2015;10(1):31-9. doi: 10.4161/15592294.2014.989084. Epub 2015 Jan 23.


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

Wijetunga NA, Delahaye F, Zhao YM, Golden A, Mar JC, Einstein FH, Greally JM.

Nat Commun. 2014 Oct 20;5:5195. doi: 10.1038/ncomms6195.


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

Delahaye F, Wijetunga NA, Heo HJ, Tozour JN, Zhao YM, Greally JM, Einstein FH.

Nat Commun. 2014 Oct 10;5:5187. doi: 10.1038/ncomms6187.


DNA methylation is developmentally regulated for genes essential for cardiogenesis.

Chamberlain AA, Lin M, Lister RL, Maslov AA, Wang Y, Suzuki M, Wu B, Greally JM, Zheng D, Zhou B.

J Am Heart Assoc. 2014 Jun 19;3(3):e000976. doi: 10.1161/JAHA.114.000976.


Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival.

Hu CY, Mohtat D, Yu Y, Ko YA, Shenoy N, Bhattacharya S, Izquierdo MC, Park AS, Giricz O, Vallumsetla N, Gundabolu K, Ware K, Bhagat TD, Suzuki M, Pullman J, Liu XS, Greally JM, Susztak K, Verma A.

Clin Cancer Res. 2014 Aug 15;20(16):4349-60. doi: 10.1158/1078-0432.CCR-14-0494. Epub 2014 Jun 10.

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