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Faculty Profile

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

Dr. John M. Greally

Professor, Department of Genetics

Professor, Department of Medicine (Hematology)

Professor, Department of Pediatrics

Faculty Scholar for Epigenomics, Department of Genetics


Professional Interests

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

Our main focus has been the study of the epigenome, as a regulator of transcriptional activity that can mediate memory of prior events, whether developmental cues or environmental perturbations. 

We study the normal physiology of the epigenome in mammalian cells, and perform epigenome-wide association studies of human diseases.

The research is 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 targeting mechanisms of DNA methylation, the role of non-canonical nucleic acid structures and the heritability of chromatin states. Our human disease research involves autism spectrum disorder, oncogenic viruses, and intrauterine effects on adult disease susceptibility.

We have been guided by our epigenomics studies to consider the broader possibility that mosaicism for cellular events is a much more common cause of human disease phenotypes than currently appreciated. We are therefore expanding our research interests to encompass genetic mosaicism, with an interest in isolated congential malformations and covert chromosomal aneuploidy.



Selected Publications

Ulahannan N, Greally JM

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

Epigenetics & Chromatin 2015, 8: 5. doi:10.1186/1756-8935-8-5


Ramos M-P, Wijetunga NA, McLellan AS, Suzuki M, Greally JM

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

Epigenetics & Chromatin 2015 Mar 17;8:11. doi:10.1186/s13072-015-0004-x. eCollection 2015. PubMed PMID: 25806086; PubMed Central PMCID: PMC4372267


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

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

Nucleic Acids Research 2015 Mar 26. pii: gkv244. [Epub ahead of print] PubMed PMID: 25813045.


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. 

Nature Communications (in press, 2014)

Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth. 
Delahaye F, Wijetunga NA, Heo HJ, Tozour JN, Zhao YM, Greally JM and Einstein FH.  
Nature Communications (in press, 2014)
Mosaic ectodermal epigenetic dysregulation in autism spectrum disorder.
Berko ER, Suzuki M, Beren F, Lemetre C, Alaimo C, 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 
PLOS Genet. 2014 10(5): e1004402. doi:10.1371/journal.pgen.1004402 PMID: 24875834
Astrogenomics: big data, old problems, old solutions? 
Golden A, Djorgovski SG, Greally JM 
Genome Biology 2013 Aug 13;14(8):129. [Epub ahead of print] PubMed PMID: 23953643.
Recommendations for the Design and Analysis of Epigenome-wide Association Studies. 
Michels KB, Binder A, Dedeurwaerder S, Epstein C, Greally J, Gut I, Houseman EA, Izzi B, Kelsey K, Meissner A, Milosavljevic A, Siegmund K, Bock C, Irizarry R.  
Nature Methods 2013 Sep 27;10(10):949-55. doi: 10.1038/nmeth.2632. PubMed PMID: 24076989

In vitro and in vivo testing methods of epigenomic endpoints for evaluating endocrine disruptors.
Greally JM and Jacobs MN. 
ALTEX. 2013 Jun 20 30(4):445-71. PubMed PMID: 23787785.
The Wasp System: an open source environment for managing and analyzing genomic data.
McLellan AS, Dubin RA, Jing Q, Ó Broin P, Moskowitz D, Suzuki M, Calder RB, Hargitai J, Golden AA, Greally JM.  
Genomics 2012 ec;100(6):345-51. doi: 10.1016/j.ygeno.2012.08.005. Epub 2012 Aug 27. PubMed PMID: 22944616.
The Einstein Genome Gateway using WASP - a high throughput multi-layered life sciences portal for XSEDE.
Golden A, McLellan AS, Dubin RA, Jing Q, O Broin P, Moskowitz D, Zhang Z, Suzuki M, Hargitai J, Calder RB, Greally JM.
Stud Health Technol Inform. 2012;175:182-91. PubMed PMID: 22942009. 
Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. 
Suzuki M., Oda M., Ramos M.-P., Pascual M., Lau K., Stasiek E., Agyiri F., Thompson R.F., Glass J.L., Jing Q., Sandstrom R., Fazzari M.J., Hansen R.S., Stamatoyannopoulos J.A., McLellan A.S., Greally J.M. 
Genome Res. 2011 21(11):1833-40. PMID: 21957152
Optimized design and data analysis of tag-based cytosine methylation assays.
Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally JM.
Genome Biol. 2010;11(4):R36. Epub 2010 Apr 1. PubMed PMID: 20359321; PubMed Central PMCID: PMC2884539
Experimental IUGR induces alterations in DNA methylation and gene expression in pancreatic islets of rats. 
Thompson R.F., Fazzari M.J., Niu H., Barzilai N., Simmons R.A. and Greally J.M. 
J. Biol. Chem. 2010 May 14;285(20):15111-8. Epub 2010 Mar 1.  PMID: 20194508
CG dinucleotide periodicities are distinctive at retroelements and imprinted domains.
Glass J.L., Ferguson-Smith A.C. and Greally J.M. 
Mammalian Genome  2009 Sep-Oct;20(9-10):633-43  PMID: 19921333
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. 
Thompson R.F., Suzuki M., Lau K.W. and Greally J.M.
Bioinformatics 2009 Sep 1;25(17):2164-70. Epub 2009 Jun 26. PubMed PMID: 19561019
An analytical pipeline for genomic representations used for cytosine methylation studies.
Thompson R.F., Reimers M., Khulan B., Gissot M., Richmond T.A., Chen Q., Zheng X., Kim K., Greally J.M. 
Bioinformatics 2008 May 1;24(9):1161-7.
CG dinucleotide clustering is a species-specific property of the genome.
Glass J.L., Thompson R.F., Khulan B., Figueroa M.E., Olivier E.N., Oakley E.J., Van Zant G., Bouhassira E.E., Melnick A., Golden A., Fazzari M.J. and Greally J.M.  
Nucleic Acids Research 2007;35(20):6798-807.
Comparative isoschizomer profiling of cytosine methylation: The HELP assay.
Khulan B., Thompson R.F., Ye K., Fazzari M.J., Suzuki M., Stasiek E., Figueroa M.E., Glass J.L., Chen Q., Montagna C., Hatchwell E., Selzer R.R., Richmond T.A., Green R.D., Melnick A., Greally J.M. 
Applying whole-genome studies of epigenetic regulation to study human disease.
Lieb J.D., Beck S., Bulyk M.L., Farnham P., Hattori N., Henikoff S., Liu X.S., Okumura K., Shiota K., Ushijima T. and Greally J.M. 
Cytogenet. Genome Res. 2006 114 (1) 1-15
Epigenomics: beyond CpG islands.
Fazzari M.J and Greally J.M.  
Nature Rev. Genet. 2004 5 446-455. 

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.
Greally J.M. 
Proc. Natl. Acad. Sci. USA 2002 99 (1) 327-332.

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Media Coverage

The New York Times features Dr. John Greally and the artist who works with Einstein’s genetic researchers to help visualize “big data.”

New York Daily News interviews Dr. John Greally about his study that found environmental influences may play a role in the development of autism.

More media coverage