Faculty Profile

Dr. John M. Greally, Ph.D., M.B.,B.Ch.

John M. Greally, Ph.D., M.B.,B.Ch.

Professor, Department of Genetics

Professor, Department of Medicine (Hematology)

Professor, Department of Pediatrics (Pediatric Genetic Medicine)

Chief, Division of Genomics, Department of Genetics

Director, Center for Epigenomics

Faculty Scholar for Epigenomics

Faculty Advisor, Computational Genomics Core, Department of Genetics

Faculty Advisor, Epigenetics Shared Facility, Department of Genetics

Areas of Research: Regulation of transcription, the influence of DNA sequence variation on transcriptional regulation, non-canonical nucleic acid structures, epigenetic models of mammalian phenotypes, data visualisation

Professional Interests

Our research is based on understanding models of genetic susceptibility to human disease, especially those affecting children.

We focus on understanding phenotypes, through genetic or environmental influences that change the innate properties of a canonical cell type, or perturbations that alter cell lineage choices during differentiation.

We define this field as somatic cellular genomics, invoilving the study of the normal physiology of transcriptional regulation in mammalian cells, and mosaic somatic mutations.

Our studies are facilitated by Einstein's Center for Epigenomics, its Epigenomics Shared Facility and the Computational Epigenomics Group, where the development of the Wasp System software cyberecosystem is nurtured.

Our basic research involves the study of the effects of environmental and genetic influences on stem cell differentiation, with a focus on liver and blood diseases. 

Selected Publications

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. eCollection 2015. PubMed PMID: 26579211; PubMed Central PMCID: PMC4647656.  Awarded Epigenetics & ChromatinPaper of the Year 2015.

Birney E, Davey Smith G, Greally JM  Epigenome-wide association studies and the interpretation of disease –omics. (review). PLoS Genet. 2016 Jun 23;12(6):e1006105. doi:10.1371/journal.pgen.1006105. eCollection 2016 Jun. Review. PubMed PMID: 27336614.

Wijetunga NA, Ben-Dayan M, Burk RD, Schlecht NF, Einstein MH, Greally JM  A polycomb-mediated epigenetic field defect precedes invasive cervical carcinoma.  2016 Oncotarget 2016 Aug 19. doi: 10.18632/oncotarget.11390. [Epub ahead of print] PubMed PMID: 27557505.

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.  Oncogene 2016 Oct 10. doi: 10.1038/onc.2016.340. PubMed PMID: 27721404.

Wijetunga NA, Maekawa R, Johnston A, Delahaye F, Ulahannan N, Kim K and Greally JM  SMITE: an R 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. PubMed PMID: 28100166; PubMed Central PMCID: PMC5242055.

Lappalainen T, GreallyJM Associating cellular epigenetic models with human phenotypes. Nature Reviews in Genetics 2017 May 30. doi: 10.1038/nrg.2017.32. Epub 2017 May 30. Review. PubMed PMID: 28555657.

Greally JM A user’s guide to the ambiguous word ‘epigenetics’.  Nature Reviews Molecular Cell Biology 2018 doi:10.1038/nrm.2017.135.

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 May 17. doi: 10.1101/gr.226282.117. [Epub ahead of print] PubMed PMID: 29773658.

Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM. Whole-genome bisulfite sequencing with improved accuracy and cost. Genome Res. 2018 Aug 9. doi: 10.1101/gr.232587.117. PubMed PMID: 30093547.

Seoighe C, Tosh NJ, Greally JM DNA methylation haplotypes as cancer markers. Nature Genetics 2018 Aug;50(8):1062-1063. doi: 10.1038/s41588-018-0185-x. PubMed PMID: 30054597.

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 and Paul S. Frenette.  Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells.  Nature Cell Biol. 2019 Apr 15. doi: 10.1038/s41556-019-0308-3.

Sato H, Wu B, Delahaye F, Singer RH, Greally JM  Re-targeting of MacroH2A following mitosis to cytogenetic-scale heterochromatic domains. Journal of Cell Biology 2019 Jun 3;218(6):1810-1823. doi: 10.1083/jcb.201811109.

Kong Y, Rastogi D, Seoighe C, Greally JM, Suzuki M  Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data.  PLOS ONE 2019 Apr 25;14(4):e0215987. doi: 10.1371/journal.pone.0215987. eCollection 2019. PubMed PMID: 31022271.

Jaric I, Rocks D, Greally JM, Suzuki M and Kundakovic M Chromatin organization in the female brain fluctuates across the oestrous cycle.  Nature Communications 2019 Jun 28;10(1):2851. doi: 10.1038/s41467-019-10704-0. PubMed PMID: 31253786; PubMed Central PMCID: PMC6598989.

Johnston AD, Simoes-Pires CA, Thompson TV, Suzuki M, Greally JM  Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding Nature Communications (2019, in press).

Johnston AD, Simoes-Pires CA, Suzuki M, Greally JM  High efficiency genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells.  Communications Biology (2019, in press).


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Research Information

In the News

Parents’ Emotional Trauma May Change Their Children’s Biology. Studies in Mice Show How

John Greally, D.Med., Ph.D., comments on recent studies that claim trauma can be passed down to future generations through epigenetic changes. Dr. Greally is director of the Center for Epigenomics and professor and chief of computational genetics.

The New York Times interviews Dr. John Greally about epigenetics and whether humans can inherit trauma.

More media coverage