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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

The epigenome is studied 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 Resource, 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.

The research techniques include the development of novel molecular assays, and computational epigenomics research. 

 

 

Selected Publications

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

Greally JM, Jacobs MN.

ALTEX. 2013 Jun 20. doi:pii: S1868696X1302211X. [Epub ahead of print]

 

Bidding the CpG island goodbye.

Greally JM.

Elife. 2013;2:e00593. doi: 10.7554/eLife.00593. Epub 2013 Feb 26.

 

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

McLellan AS, Dubin RA, Jing Q, Broin PÓ, Moskowitz D, Suzuki M, Calder RB, Hargitai J, Golden A, Greally JM.

Genomics. 2012 Dec;100(6):345-51. doi: 10.1016/j.ygeno.2012.08.005. Epub 2012 Aug 27.

 

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.

 

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

Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, Agyiri F, Thompson RF, Glass JL, Jing Q, Sandstrom R, Fazzari MJ, Hansen RS, Stamatoyannopoulos JA, McLellan AS, Greally JM.

Genome Res. 2011 Nov;21(11):1833-40. doi: 10.1101/gr.116509.110. Epub 2011 Sep 28.

 

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

Pascual M, Suzuki M, Isidoro-Garcia M, Padrón J, Turner T, Lorente F, Dávila I, Greally JM.

Epigenetics. 2011 Sep 1;6(9):1131-7. doi: 10.4161/epi.6.9.16061. Epub 2011 Sep 1.

 

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

Thompson RF, Fazzari MJ, Niu H, Barzilai N, Simmons RA, Greally JM.

J Biol Chem. 2010 May 14;285(20):15111-8. doi: 10.1074/jbc.M109.095133. Epub 2010 Mar 1.

 

Cytosine methylation dysregulation in neonates following intrauterine growth restriction.

Einstein F, Thompson RF, Bhagat TD, Fazzari MJ, Verma A, Barzilai N, Greally JM.

PLoS One. 2010 Jan 26;5(1):e8887. doi: 10.1371/journal.pone.0008887.

 

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. doi: 10.1186/gb-2010-11-4-r36. Epub 2010 Apr 1.

 

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

McLellan AS, Dubin RA, Jing Q, Maqbool SB, Olea R, Westby G, Broin PÓ, Fazzari MJ, Zheng D, Suzuki M, Greally JM.

Epigenomics. 2009 Oct;1(1):33-8. doi: 10.2217/epi.09.9.

 

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

Thompson RF, Suzuki M, Lau KW, Greally JM.

Bioinformatics. 2009 Sep 1;25(17):2164-70. doi: 10.1093/bioinformatics/btp382. Epub 2009 Jun 26.

 

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

Glass JL, Fazzari MJ, Ferguson-Smith AC, Greally JM.

Mamm Genome. 2009 Sep-Oct;20(9-10):633-43. doi: 10.1007/s00335-009-9232-3. Epub 2009 Nov 17.

 

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

Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L, Green RD, Melnick A, Hatchwell E, Bouhassira EE, Verma A, Suzuki M, Greally JM.

Nucleic Acids Res. 2009 Jul;37(12):3829-39. doi: 10.1093/nar/gkp260. Epub 2009 Apr 22.

 

An analytical pipeline for genomic representations used for cytosine methylation studies.

Thompson RF, Reimers M, Khulan B, Gissot M, Richmond TA, Chen Q, Zheng X, Kim K, Greally JM.

Bioinformatics. 2008 May 1;24(9):1161-7. doi: 10.1093/bioinformatics/btn096. Epub 2008 Mar 18.

 

Epigenetics: perceptive enzymes.

Ferguson-Smith AC, Greally JM.

Nature. 2007 Sep 13;449(7159):148-9. No abstract available.

 

Genomics: Encyclopaedia of humble DNA.

Greally JM.

Nature. 2007 Jun 14;447(7146):782-3. No abstract available.

 

CG dinucleotide clustering is a species-specific property of the genome.

Glass JL, Thompson RF, Khulan B, Figueroa ME, Olivier EN, Oakley EJ, Van Zant G, Bouhassira EE, Melnick A, Golden A, Fazzari MJ, Greally JM.

Nucleic Acids Res. 2007;35(20):6798-807. Epub 2007 Oct 10.

 

Comparative isoschizomer profiling of cytosine methylation: the HELP assay.

Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM.

Genome Res. 2006 Aug;16(8):1046-55. Epub 2006 Jun 29.

 

Epigenomics: beyond CpG islands.

Fazzari MJ, Greally JM.

Nat Rev Genet. 2004 Jun;5(6):446-55. Review. No abstract available.

 

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.

Greally JM.

Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):327-32. Epub 2001 Dec 26.

 

 

More Information About Dr. John Greally

GreallyLab home page

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Contact

Albert Einstein College of Medicine
Michael F. Price Center
1301 Morris Park Avenue , Room 322
Bronx, NY 10461

Tel: 718.678.1234
Fax: 718.678.1016
john.greally@einstein.yu.edu

 
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Media Coverage

Nature.com features comments by Dr. John Greally about the Roadmap Epigenomics Project and its effort to identify and map all the chemical tags, known collectively as the human epigenome, that control the activities of genes.

More media coverage