Rosean S, Sosa EA, O'Shea D, Raj SM, Seoighe C, Greally JM. Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization. BMC Bioinformatics 2024 May 7;25(1):179. doi: 10.1186/s12859-024-05794-7. PMID: 38714913; PMCID: PMC11075237.Johnston AD, Simões-Pires CA, Thompson TV, Suzuki M, Greally JM. Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding. Nat Commun. 2019 Aug 2;10(1):3472. doi:10.1038/s41467-019-11412-5. PMID: 31375681; PMCID: PMC6677801.
Kong Y, Rose CM, Cass AA, Williams AG, Darwish M, Lianoglou S, Haverty PM, Tong AJ, Blanchette C, Albert ML, Mellman I, Bourgon R, Greally J, Jhunjhunwala S, Chen-Harris H. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat Commun. 2019 Nov 19;10(1):5228. doi: 10.1038/s41467-019-13035-2. PMID: 31745090; PMCID:PMC6864081.
Sato H, Wu B, Delahaye F, Singer RH, Greally JM. Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains. J Cell Biol. 2019 Jun 3;218(6):1810-1823. doi: 10.1083/jcb.201811109. Epub 2019 May 20. PMID:31110057; PMCID: PMC6548134.
Nakahara F, Borger DK, Wei Q, Pinho S, Maryanovich M, Zahalka AH, Suzuki M, Cruz CD, Wang Z, Xu C, Boulais PE, Ma'ayan A, Greally JM, Frenette PS. Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells. Nat Cell Biol. 2019 May;21(5):560-567. doi: 10.1038/s41556-019-0308-3. Epub 2019 Apr 15. PMID: 30988422; PMCID: PMC6499646.
Kong Y, Berko ER, Marcketta A, Maqbool SB, Simões-Pires CA, Kronn DF, Ye KQ, Suzuki M, Auton A, Greally JM. Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq. Genome Res. 2018 Jul;28(7):1039-1052. doi: 10.1101/gr.226282.117. Epub 2018 May 17. PMID:29773658; PMCID: PMC6028128.
Greally JM. A user's guide to the ambiguous word 'epigenetics'. Nat Rev Mol Cell Biol. 2018 Apr;19(4):207-208. doi: 10.1038/nrm.2017.135. Epub 2018 Jan 17. PMID: 29339796.
Lappalainen T, Greally JM. Associating cellular epigenetic models with human phenotypes. Nat Rev Genet. 2017 Jul;18(7):441-451. doi: 10.1038/nrg.2017.32. Epub 2017 May 30. PMID: 28555657.
Wijetunga NA, Johnston AD, Maekawa R, Delahaye F, Ulahannan N, Kim K, Greally JM. SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. BMC Bioinformatics. 2017 Jan 18;18(1):41. doi: 10.1186/s12859-017-1477-3. PMID: 28100166; PMCID: PMC5242055.
Wijetunga NA, Pascual M, Tozour J, Delahaye F, Alani M, Adeyeye M, Wolkoff AW, Verma A, Greally JM. A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets. Version 2. Oncogene. 2017 Apr 6;36(14):2030-2044. doi: 10.1038/onc.2016.340. Epub 2016 Oct 10. PMID: 27721404; PMCID: PMC5383522.
Wijetunga NA, Ben-Dayan M, Tozour J, Burk RD, Schlecht NF, Einstein MH, Greally JM. A polycomb-mediated epigenetic field defect precedes invasive cervical carcinoma. Oncotarget. 2016 Sep 20;7(38):62133-62143. doi:10.18632/oncotarget.11390. PMID: 27557505; PMCID: PMC5308716.
Henikoff S, Greally JM. Epigenetics, cellular memory and gene regulation. Curr Biol. 2016 Jul 25;26(14):R644-8. doi: 10.1016/j.cub.2016.06.011. PMID:27458904.
Birney E, Smith GD, Greally JM. Epigenome-wide Association Studies and the Interpretation of Disease -Omics. PLoS Genet. 2016 Jun 23;12(6):e1006105. doi:10.1371/journal.pgen.1006105. PMID: 27336614; PMCID: PMC4919098.
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. RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships. Epigenetics Chromatin. 2015 Nov 16;8:46. doi: 10.1186/s13072-015-0040-6. PMID: 26579211; PMCID: PMC4647656.
Wijetunga NA, Delahaye F, Zhao YM, Golden A, Mar JC, Einstein FH, Greally JM. The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences. Nat Commun. 2014 Oct 20;5:5195. doi:10.1038/ncomms6195. PMID: 25327398; PMCID: PMC4300104.
Delahaye F, Wijetunga NA, Heo HJ, Tozour JN, Zhao YM, Greally JM, Einstein FH. Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth. Nat Commun. 2014 Oct 10;5:5187. doi: 10.1038/ncomms6187. PMID: 25300954; PMCID: PMC4197137.
Berko ER, Suzuki M, Beren F, Lemetre C, Alaimo CM, Calder RB, Ballaban-Gil K, Gounder B, Kampf K, Kirschen J, Maqbool SB, Momin Z, Reynolds DM, Russo N, Shulman L, Stasiek E, Tozour J, Valicenti-McDermott M, Wang S, Abrahams BS, Hargitai J, Inbar D, Zhang Z, Buxbaum JD, Molholm S, Foxe JJ, Marion RW, Auton A, Greally JM. Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. PLoS Genet. 2014 May 29;10(5):e1004402. doi:10.1371/journal.pgen.1004402. PMID: 24875834; PMCID: PMC4038484.
Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct;10(10):949-55. doi:10.1038/nmeth.2632. PMID: 24076989.
