Download CURRICULUM VITAE

Revised February 2009
CURRICULUM VITAE
John M. Greally M.B., Ph.D.
DATE & PLACE OF BIRTH
3 January 1965, Galway, Ireland.
ADDRESS
Department of Genetics, Price 322
Albert Einstein College of Medicine
1301 Morris Park Avenue
Bronx, NY 10461, USA
718 678 1234, fax 718 678 1016, [email protected]
http://greallylab.aecom.yu.edu/
EDUCATION
1982-1988
1995-1999
M.B., B.Ch., B.A.O. (Honours), National University of Ireland, Galway.
Ph.D. (Department of Microbiology), National University of Ireland, Galway.
RESEARCH INTERESTS
The lab‟s research program is focused on the epigenetic regulation of the mammalian genome.
Specific interests include: the physiology of the epigenome (genomic imprinting, X chromosome
inactivation, embryonic stem cell differentiation), epigenetic dysregulation in human disease,
bioinformatics, epigenomic technology development, comparative epigenomics and structural
epigenomics.
PROFESSIONAL EXPERIENCE
1988-1989
Intern, Departments of Medicine and Surgery,
University College Hospital, Galway, Ireland.
1989-1990
Postdoctoral fellow, Division of Medical Genetics, Children‟s Hospital of Pittsburgh.
1990-1993
Paediatric resident, Children‟s Hospital of Pittsburgh.
1993-1995
Postdoctoral Fellow, Department of Genetics, Yale University School of Medicine.
1995-1997
Postdoctoral Associate, Department of Genetics, Yale University School of Medicine.
1997-2000
Associate Research Scientist, Department of Genetics,
Yale University School of Medicine.
2001-2007
Assistant Professor, Department of Medicine (Hematology),
Albert Einstein College of Medicine (AECOM).
2002Secondary appointment, Department of Molecular Genetics, AECOM.
2002Member, Albert Einstein Cancer Center.
2003Faculty Supervisor, AECOM Genome Imaging Facility.
2003
BioLink USA-Ireland founder member, New York regional leader.
2004Faculty co-supervisor, AECOM Bioinformatics Shared Resource.
2004BioLink USA-Ireland, National Executive Committee, VP for Chapter Development.
2004Member, Marsupial Genome Sequencing International Consortium.
2005Faculty co-supervisor, AECOM NimbleGen Direct microarray service.
2005Co-program leader, Cell Growth and Differentiation Control,
Albert Einstein Cancer Center.
2005AACR Steering Committee for an International Human Epigenome Project
2007Associate Professor, Departments of Medicine (Hematology) and Molecular Genetics,
Albert Einstein College of Medicine.
2008
Director, Einstein Center for Epigenomics
2008
Chief, Division of Computational Genetics, Department of Genetics.
2009
Faculty Scholar for Epigenomics, Albert Einstein College of Medicine
PROFESSIONAL SOCIETIES
American Society of Human Genetics.
New York Academy of Sciences.
European Society for Human Genetics.
HONOURS & AWARDS
1982
Entrance scholarship to National University of Ireland, Galway.
1986
Dr. Reuben Berman travelling studentship.
1988
Dr. John F. Keenan travelling scholarship, National University of Ireland, Galway.
1995
Lucille P. Markey Physician-Scientist Fellowship Award.
1996
Mentored Clinical Scientist Development Award, NIH.
MEDICAL LICENSURE
New York, licence number 226186.
BOARD CERTIFICATION
1994
American Board of Paediatrics.
1996
American Board of Medical Genetics (recertified 2008).
TEACHING
1996
2000
2002 –
2002 –
2002 –
2003 –
2005
Visiting lecturer, Genetics 301, Case Western Reserve University.
Neuroscience 514b, Yale University.
Advanced Mammalian Genetics (AECOM; Morrow/Ozelius).
Gene Expression (AECOM; Query/Warner).
Critical Readings in Molecular Biology (AECOM; Michaeli).
Molecular and Cellular Foundations in Medicine (AECOM; Birshtein).
Bioinformatics (AECOM; Fiser)
TRAINEES
(i) Postdoctoral associates.
[current] Dr. Priti Tewari, Dr. Nirupama Narayanan, Dr. Rodoniki Athanasiadou
[former] Dr. Masako Suzuki (faculty, Einstein), Dr. Mayumi Oda (Keio University), Dr. Maria Figueroa
(Cornell University), Dr. Siobhan Dolan (Assistant Professor, Einstein), Dr. Shani Peretz (Peddie School,
NJ), Dr. Avril Friel (deceased).
(ii) Graduate students.
Mentor for: Reid Thompson (MSTP program), Marién Pascual de Pedro (University of Salamanca, Spain),
Esther Berko (MSTP program),
Former: Batbayar Khulan (PhD program), Jacob Glass (MSTP program).
Member of the student advisory committees for the following students:
Einstein: [current] Sandeep Wontakal, Andrea Silva.
[formerly] Pam Boimel, Rebecca Muhle, Romain Desprat, Richard Weldon, Lourdes Mendez, Elena
Avdievich, Michelle Lenzi, Francine Garrett, Jie Zhou, Elizabeth Spiteri.
Duke University: [current] Radhika Das (Randy Jirtle, mentor).
Cold Spring Harbor Laboratory: [former] Eyal Gruntman (Rob Martienssen, mentor).
SUNY Stony Brook: [former] Jasmin Roohi (Eli Hatchwell, mentor).
Yale University: [former] Helen Kwan (James McGrath, mentor).
PRESENTATIONS
1996
Department of Genetics, Case Western Reserve University.
1997
MRC Human Genetics Unit, Edinburgh.
Division of Developmental Biology, Babraham Institute, Cambridge.
Wellcome/CRC Institute of Cancer and Developmental Biology, University of Cambridge.
Departments of Microbiology and Immunology, Dartmouth University.
1998
Mount Sinai School of Medicine, New York.
2000
Clontech Laboratories Inc., Palo Alto.
Department of Human Genetics, University of Chicago.
Department of Human Genetics, Mount Sinai School of Medicine, New York.
Department of Cell Biology, Albert Einstein College of Medicine, New York.
Weill Medical College of Cornell University, New York.
2001
Session chair: “Imprinting/methylation”, American Society of Human Genetics (ASHG)
annual meeting, San Diego.
2002
Department of Genetics, Trinity College Dublin, Ireland.
2003
Department of Genetics, University of Pennsylvania.
Session chair and presenting speaker: “Epigenetics: Information Beyond the DNA
Sequence”, American Society of Human Genetics annual meeting, Los Angeles.
2004
2005
2006
2007
2008
New York State Society for Medical Oncologists and Hematologists.
Beckman Research Institute, City of Hope, Duarte, CA.
Department of Human Genetics, University of Pittsburgh.
AACR Workshop on the Human Epigenome, VA.
MRC Harwell conference on genomic imprinting, Oxford, UK.
Department of Animal Resource Sciences/Veterinary Medical Sciences, University of
Tokyo, Japan.
National Cancer Center Research Laboratories, Tokyo, Japan.
Genome Informatics, CSHL Meeting, NY
(Co-organizer) Genome-wide Epigenetics 2005, Tokyo, Japan.
Dept. Genetics, Sick Children‟s Hospital, Toronto, Canada.
Internal Faculty seminar, AECOM.
Early Detection Research Network (NCI), Philadelphia, PA.
Workshop on Epigenomics, AACR annual meeting, Washington, DC.
Bioinformatics course presenter, Philips Research, Briarcliff Manor, NY.
Department of Biomedical Sciences, Cornell University, Ithaca, NY.
Epigenetics Symposium, Fred Hutchinson Cancer Research Center, Seattle, WA.
Symposium, 50 years of 46 Chromosomes, NCI, Bethesda MD.
Genomic Analysis of Transcription Regulation, Sanger Centre, Cambridge UK.
Epigenetics and complex traits, ASHG annual meeting, New Orleans, LO.
Dept. Medicine (Hem/Onc), Mount Sinai School of Medicine, New York, NY.
Dept. Veterinary Integrative Biosciences, Texas A&M University, TX.
Dept. Pathology, Massachusetts General Hospital, Boston, MA.
Cancer Center, Columbia University, New York, NY.
Lake Shirakaba Conference, Grenada.
NCBES, National University of Ireland Galway, Galway, Ireland.
Dept. Genetics, Feinstein Institute, NSLIJ Hospital, NY.
Dept. Pathology, SUNY Stony Brook, NY.
Session chair (DNA Methylation) Gordon Research Conference on Epigenetics
School of Dentistry, U. Kentucky.
Center for Research on Reproduction and Women‟s Health, U. Penn., PA
Keynote speaker, Genes, Genomes and Pediatric Disease meeting, Children‟s Hospital of
Philadelphia, PA
Dept. Genetics, University of Pittsburgh, PA
Dept. Genetics, University of Iowa, IA
Roswell Park Cancer Institute, Buffalo, NY
Invited speaker, AACR special meeting in Cancer Epigenetics, Boston. MA.
Epigenomics workshop, National Institute for Aging, NIH, Bethesda MD
Plenary session speaker, American Society for Nephrology, Philadelphia PA
Peter MacCallum Cancer Center meeting, Melbourne Australia
Seminar speaker, U. Pennsylvania
th
2009
Plenary session speaker, 6 European conference on Biogerontology, Leiden,
Netherlands
Decoding the Epigenome, U. Tokyo, Japan
Center for Epigenetics, U. Florida FL
National Cancer Center, Tokyo Japan.
Japan Society for Regenerative Medicine, Tokyo Japan.
Mathematical Biology Institute, Ohio State University, Columbus OH
Karolinska Institutet, Stockholm Sweden
Pediatric grand rounds, Lincoln Hospital, Bronx NY
Pediatric Academic Societies meeting, Baltimore MD
PUBLICATIONS
Greally J.M., O‟Toole G., McCann H., Grimes H., O‟Connor B., Solan G., Walsh G. and Egan E.L.
Monoclonal gammopathies in the West of Ireland: a preliminary study. Irish J. Med. Sci. 1985 154 (3) 94101.
Greally J.M. The physiology of anti-idiotypic interactions: From clonal to paratopic selection. Clin.
Immunol. Immunopathol. 1991 60 1-12.
Greally J.M., Boone L.Y., Lenkey S.G., Wenger S.G. and Steele M.W. Acrometageria: a spectrum of
“premature aging” syndromes. Am. J. Med. Genet. 1992 44 334-339.
Soper R., Chaloupka J.C., Fayad P.B., Greally J.M., Shaywitz B.A., Awad I.A. and Pober B.R. Ischemic
stroke and intracranial multifocal cerebral arteriopathy in Williams syndrome. J. Pediatr. 1995 126(6) 9458.
Greally J.M., Neiswanger K., Cummins J.H., Boone L.Y., Lenkey S.G., Wenger S.L., Lewis J.L., Fischer
D., Paul R.A. and Steele M.W. A molecular anatomical analysis of mosaic trisomy 16. Hum. Genet. 1996
98 86-90.
Greally J.M., Guinness M.E., McGrath J. and Zemel S. Matrix-attachment regions in the mouse
chromosome 7F imprinted domain. Mamm. Genome 1997 8 805-810.
Greally J.M., Starr D.J., Hwang S., Song L., Jaarola M. and Zemel S. The mouse H19 locus mediates a
transition between imprinted and non-imprinted DNA replication patterns. Hum. Mol. Genet. 1998 7(1) 9196.
Lin X., State M.W., Greally J.M., Haas M. and Leckman J.F. Identification and chromosomal assignment
of the human homeodomain-containing gene Orthopedia (OTP). Genomics 1999 60 96-104.
Greally J.M., Gray T.A., Gabriel J.M., Song L., Zemel S. and Nicholls R.D. Conserved characteristics of
heterochromatin-forming DNA at the 15q11-q13 imprinting center. Proc. Natl. Acad. Sci. USA 1999 96
(25) 14430-14435.
Alami R., Greally J.M., Tanimoto K., Hwang S., Feng Y.-Q., Engel J.D., Fiering S. and Bouhassira E.E. globin YAC transgenes exhibit uniform expression levels but position effect variegation in mice. Hum. Mol.
Genet. 2000 9(4) 631-636.
Feng Y.-Q., Lorincz M., Fiering S., Greally J.M. and Bouhassira E.E.. Position effects are influenced by
the orientation of a transgene with respect to flanking chromatin. Mol. Cell. Biol. 2001 21(1) 298-309.
Henegariu O., Artan S., Greally J.M., Chen X.-N., Korenberg J.R., Vance G.H., Stubbs L., Bray-Ward P.
and Ward D.C. Cryptic translocation identification in human and mouse using several telomeric multiplex
FISH (TM-FISH) strategies. Lab. Invest. 2001 81 (4) 483-491.
Henegariu O., Dunai J., Chen X.-N., Korenberg J.R., Ward D.C. and Greally J.M. A triple color FISH
technique for mouse chromosome identification. Mamm. Genome 2001 12(6) 462-465.
Chai J.H., Locke D.P., Ohta T., Greally J.M. and Nicholls R.D. Retrotransposed genes such as Frat3 in
the mouse chromosome 7C Prader-Willi syndrome region acquire the imprinted status of their insertion
site. Mamm. Genome 2001 12 (11) 813-821.
Bayarsaihan D., Dunai J., Greally J.M., Kawasaki K., Sumiyama K., Enkhmandakh B., Shimizu N. and
Ruddle F. Genomic Organization of the Genes Gtf2ird1, Gtf2i, and Ncf1 at the Mouse Chromosome 5
Region Syntenic to the Human Chromosome 7q11.23 Williams Syndrome Critical Region. 2002 Genomics
79 (1) 137-143.
Kieffer L.J., Greally J.M., Landres I., Nag S., Nakajima Y., Kohwi-Shigematsu T. and Kavathas P.B.
Identification of a candidate regulatory region in the human CD8 gene complex by colocalization of DNase
I hypersensitive sites and matrix attachment regions which bind SATB1 and GATA-3. J. Immunol. 2002
168 (8) 3915-3922.
Suphapeetiporn K., Greally J.M., Walpita D., Ashley T. and Bale A.E. MEN1 tumor-suppressor protein
localizes to telomeres during meiosis. Genes, Chromosomes and Cancer 2002 35 (1) 81-85.
Neumeister P., Albanese C., Balent B., Greally J.M. and Pestell R.G. Senescence and epigenetic
dysregulation in cancer. Int. J. Biochem. Cell. Biol. 2002 34 (11) 1475-1490. [review]
Greally J.M. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in
the human genome. Proc. Natl. Acad. Sci. USA 2002 99 (1) 327-332.
Alami R., Fan Y., Pack S., Sonbuchner T., Besse A., Lin Q., Greally J.M., Skoultchi A.I. and Bouhassira
E.E. Mammalian linker histone subtypes differentially affect gene expression in vivo. Proc. Natl. Acad. Sci.
USA 2003 May 13;100(10):5920-5.
Brown C.J. and Greally J.M. A stain upon the silence: genes escaping X inactivation. Trends Genet.
2003 119 (8) 432-438. [review]
State M.W., Greally J.M., Cuker A., Bowers P., Hemegariu O., Morgan T., Gunel M., DiLuna M., King R.,
Nelson C., Donovan A., Leckman J.F., Hawkins T., Pauls D.L., Lifton R.P. and Ward D.C. Epigenetic
abnormalities associated with a chromosome 18(q21-22) inversion and a Gilles de la Tourette syndrome
phenotype. Proc. Natl. Acad. Sci. USA 2003 Apr 15;100(8):4684-9.
Chai J.-H., Locke D.P., Greally J.M., Knoll J.H.M., Ohta T., Dunai J., Yavor A., Eichler E.E. and Nicholls
R.D. Identification of four highly conserved genes between breakpoint hotspots BP1 and BP2 of the
Prader-Willi/Angelman syndromes deletion region that have undergone evolutionary transposition
mediated by flanking duplicons. Am. J. Hum. Genet. 2003 Oct;73(4):898-925.
Bayarsaihan D., Enkhmandakh B., Makeyev A, Greally J.M., Leckman J.F. and Ruddle F.H. Homez, a
homeobox leucine zipper gene specific to the vertebrate lineage. Proc. Natl. Acad. Sci. USA 2003 Sep
2;100(18):10358-63.
Tsuchiya K.D., Greally J.M., Yi Y., Noel K.P., Truong J.-P. and Disteche C.M. Comparative sequence and
X inactivation analysis of a domain of escape in human Xp11.2 and the conserved segment in mouse.
Genome Res. 2004 Jul; 14 (7): 1275-1284.
Fazzari M.J and Greally J.M. Epigenomics: beyond CpG islands. Nature Rev. Genet. 2004 5 446-455.
[review]
Stefan M., Claiborn K.C., Stasiek E., Chai J.H., Ohta T., Longnecker R., Greally J.M. and Nicholls R.D.
Genetic mapping of putative Chrna7 and Luzp2 neuronal transcriptional enhancers due to impact of a
transgene-insertion and 6.8 Mb deletion in a mouse model of Prader-Willi and Angelman syndromes.
BMC Genomics. 2005 Nov 9;6:157.
Kolas N.K., Svetlanov A., Lenzi M.L., Macaluso F.P., Lipkin S.M., Liskay R.M., Greally J., Edelmann W.,
Cohen P.E. Localization of MMR proteins on meiotic chromosomes in mice indicates distinct functions
during prophase I. J Cell Biol. 2005 Nov 7;171(3):447-58.
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. Applying whole-genome studies of epigenetic regulation to study human
disease. Cytogenet. Genome Res. 2006 114 (1) 1-15.
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.
Comparative isoschizomer profiling of cytosine methylation: The HELP assay. Genome Research 2006
Aug;16(8):1046-55.
Ikegami K., Iwatani M., Suzuki M., Tachibana M., Shinkai Y., Tanaka S., Greally J.M., Yagi S., Hattori N.,
Shiota K. Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem
cells. Genes Cells. 2007 Jan;12(1):1-11.
Polo J.M., Juszczynski P., Monti S., Cerchietti L., Ye K., Greally J.M., Shipp M. and Melnick A. A
transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6dependent diffuse large B-cell lymphomas. Proc. Natl. Acad. Sci. USA 2007 104(9):3207-12.
Mikkelsen T.S.,, Wakefield M.J., Aken B., Amemiya C.T., Chang J.L., Duke S., Garber M., Gentles A.J.,
Goodstadt L., Heger A., Jurka J., Kamal M., Mauceli E., Searle S.M.J., Sharpe T., Baker M.L., Batzer
M.A., Benos P.V., Belov K., Clamp M., Cook A., Cuff J., Das R., Davidow L., Deakin J.E., Fazzari M.J.,
Glass J.L., Grabherr M., Greally J.M., Gu W., Hore T., Huttley G.A., Jirtle R.L., Koina E., Lee J.T.,
Mahony S., Marra M.A., Miller R.D., Nicholls R.D., Oda M., Papenfuss A.T., Parra Z.E., Pollock D.D., Ray
D.A., Schein J.E., Speed T.P., Thompson K., VandeBerg J.L., Wade C.M., Walker J.A., Waters P.,
Webber C., Weidman J.R., Xie X., Zody M.C., Broad Institute Genome Sequencing Platform, Broad
Institute Whole Genome Assembly Team, Marshall Graves J.A., Ponting C.P., Breen M., Samollow P.B.,
Lander E.S., Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in
non-coding sequences Nature 2007 447 (7141) 167-77.
Gissot M., Kelly K.A., Ajioka J.W., Greally J.M., Kim K. Epigenomic modifications predict active promoters
and gene structure in Toxoplasma gondii. PLoS Pathogens 2007 3 (6) e77.
Greally, J.M. Genomics: Genomics: Encyclopaedia of humble DNA [News & Views] Nature 2007 Jun
14;447(7146):782-3.
Ferguson-Smith A.C., Greally J.M. Epigenetics: Perceptive enzymes [News & Views] Nature 2007 Sep
13;449(7159):148-9.
Ranuncolo SM, Polo JM, Dierov J, Singer M, Kuo T, Greally J, Green R, Carroll M, Melnick A. Bcl-6
mediates the germinal center B cell phenotype and lymphomagenesis through transcriptional repression
of the DNA-damage sensor ATR. Nature Immunol. 2007 Jul;8(7):705-14.
Sakamoto H., Suzuki M., Abe T., Hosoyama T., Himeno E., Tanaka S., Greally J.M., Hattori N., Yagi S.,
Shiota K. Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that
delineate developmental similarity. Genes Cells 2007 Oct;12(10):1123-1132.
Hatchwell E., Greally J.M. The role of epigenomic dysregulation in complex human disease. Trends in
Genetics 2007 Nov;23(11):588-95.
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. CG dinucleotide clustering is a speciesspecific property of the genome. Nucleic Acids Research 2007;35(20):6798-807.
Suzuki M., Sato S., Arai Y., Shinohara T., Tanaka S,. Greally J.M., Hattori N, Shiota K. A new class of
tissue-specifically methylated regions involving entire CpG islands in the mouse. Genes Cells. 2007
Dec;12(12):1305-14.
Gissot M., Choi S.W., Thompson R.F., Greally J.M., Kim K. Toxoplasma gondii and Cryptosporidium
parvum lack detectable DNA cytosine methylation. Eukaryot Cell. 2008 Jan 4
Figueroa M.E., Reimers M., Thompson R.F., Ye K., Li Y., Selzer R.R., Fridriksson J., Paietta E., Wiernik
P., Green R.D., Greally J.M., Melnick A. An integrative genomic and epigenomic approach for the study
of transcriptional regulation. PLoS ONE 2008 Mar 26;3(3):e1882.
Thompson R.F., Reimers M., Khulan B., Gissot M., Richmond T.A., Chen Q., Zheng X., Kim K., Greally
J.M. An analytical pipeline for genomic representations used for cytosine methylation studies.
Bioinformatics 2008 May 1;24(9):1161-7.
Jones P.A., Baylin S.B., Bernstein B.E., Feinberg A.P., Greally J.M., Jenuwein T., Martienssen R. and
Ushijima T. for the American Association for Cancer Research Human Epigenome Task Force, Pirrotta
V., Allis C.D., Elgin S.C., Rine J. and Wu C. for the European Union, Network of Excellence, Scientific
Advisory Board, Baylin S.B., Feinberg A.P. Moving AHEAD with an International Human Epigenome
Project. Nature 2008 Aug 7;454(7205):711-5. PMID: 18685699
Sohal D., Yeatts A., Ye K., Pellagatti A., Zhou L., Pahanish P., Mo Y., Bhagat T., Mariadason J.,
Boultwood J., Melnick A., Greally J.M., Verma A. Meta-analysis of microarray studies reveals a novel
hematopoietic progenitor cell signature and demonstrates feasibility of inter-platform data integration.
PLoS One 2008 Aug 13;3(8):e2965. PMID: 18698424
Lopes EC, Valls E, Figueroa ME, Mazur A, Meng FG, Chiosis G, Laird PW, Schreiber-Agus N, Greally
J.M., Prokhortchouk E, Melnick A. Kaiso contributes to DNA methylation-dependent silencing of tumor
suppressor genes in colon cancer cell lines. Cancer Res. 2008 Sep 15;68(18):7258-63. PMID: 18794111
Greally J. Journal club. A biologist considers a link between jumping genes and immune-system
enzymes. Nature. 2008 Dec 4;456(7222):549. PMID: 19052582
Jeddeloh JA, Greally J.M., Rando OJ. Reduced-representation methylation mapping. Genome Biol.
2008;9(8):231. PMID: 18771577
Figueroa ME, Wouters BJ, Skrabanek L, Glass J, Li Y, Erpelinck-Verschueren CA, Langerak AW,
Lowenberg B, Fazzari M, Greally J.M., Valk PJ, Melnick A, Delwel R. Genome wide epigenetic analysis
delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features. Blood. 2009
Jan 23. PMID: 19168792
Oda M. and Greally J.M. The HELP assay. Chapter in Methods for DNA Methylation Analysis, Jörg Tost
editor, Methods Mol. Biol. 2009 (Humana Press) 2009;507:77-87. PMID: 18987808
Figueroa ME, Skrabanek L, Li Y, Jiemjit A, Fandy TE, Paietta E, Fernandez H, Tallman MS, Greally JM,
Carraway H, Licht JD, Gore SD, Melnick A. MDS and secondary AML display unique patterns and
abundance of aberrant DNA methylation. Blood. 2009 Oct 15;114(16):3448-58. Epub 2009 Aug 3.
PubMed PMID: 19652201.
Figueroa ME, Melnick A, Greally JM. Genome-wide determination of DNA methylation by Hpa II tiny
fragment enrichment by ligation-mediated PCR (HELP) for the study of acute leukemias. Methods Mol
Biol. 2009;538:395-407. PubMed PMID: 19277580.
Thompson R.F., Suzuki M., Lau K.W. and Greally J.M. A pipeline for the quantitative analysis of CG
dinucleotide methylation using mass spectrometry. Bioinformatics 2009 Sep 1;25(17):2164-70. Epub
2009 Jun 26. PubMed PMID: 19561019.
Morey Kinney S.R., Zhang W., Pascual M., Greally J.M., Gillard B.M., Karasik E., Foster B.A., Karpf A.R.
Lack of Evidence for Green Tea Polyphenols as DNA Methylation Inhibitors in Murine Prostate. Cancer
Prev Res (Phila Pa). 2009 Nov 24. PMID: 19934341
Figueroa M.E., Lugthart S., Li Y., Erpelinck-Verschueren C., Deng X., Christos P.J., Schifano E., Booth J.,
van Putten W., Skrabanek L., Campagne F., Mazumdar M., Greally J.M., Valk P.J.M., Löwenberg B.,
Delwel R. and Melnick A. DNA methylation signatures identify biologically distinct subtypes in acute
myeloid leukemia. Cancer Cell 2010 Jan 19;17(1):13-27. PMID: 20060365
Glass J.L., Ferguson-Smith A.C. and Greally J.M. CG dinucleotide periodicities are distinctive at
retroelements and imprinted domains. Mammalian Genome 2009 Sep-Oct;20(9-10):633-43 PMID:
19921333
Einstein F., Thompson R.F., Bhagat T., Fazzari M.J., Verma A., Barzilai N., Greally J.M. Cytosine
methylation dysregulation in neonates following intrauterine growth restriction. PLoS ONE 2010 Jan
26;5(1):e8887. PMID: 20126273
Thompson R.F., Fazzari M.J. and Greally J.M. Experimental approaches to the study of epigenomic
dysregulation in aging. Exp. Gerontol. (in press) PubMed PMID: 20060885.
Goldberg A.D., Banaszynski L.A., Noh, K.-M., Lewis P.W., Elsaesser S.J., Dewell S., Law M., Guo X., Li
X., Wen D., Chapgier A., DeKelver R.C., Miller J.C., Lee Y.-L., Boydston E. A., Holmes M.C., Gregory
P.D., Greally J.M., Rafii S., Yang C., Scambler P.J., Garrick D., Gibbons R., Higgs D.R., Cristea I.M.,
Urnov F.D., Zheng D., Allis C.D. Distinct factors mediate histone variant H3.3 deposition at specific
genomic regions Cell 2010 Mar 5; 140 (5) 678-691
Thompson R.F., Fazzari M.J., Niu H., Barzilai N., Simmons R.A. and Greally J.M. Experimental IUGR
induces alterations in DNA methylation and gene expression in pancreatic islets of rats. J. Biol. Chem. (in
press).
Chow J.C., Ciaudo C., Fazzari M.J., Mise N., Servant N., Glass J.L., Attreed M., Avner P., Wutz A., Barillot
E., Greally J.M., Voinnet O., Heard E. LINE1 activity in facultative heterochromatin formation during Xchromosome inactivation. Cell 2010 (in press)
Manuscripts in review:
Oda M., Fazzari M.J., Thompson R.F., Glass J.L., Agarwal S., Koch C.M., Clelland G.K., Wilcox S., Beare
D.M., Andrews R.M., Dannenberg L., Zhang X., Selzer R.R., Richmond T.A., Green R.D., Dunham I., Ren
B. and Greally J.M. Cytosine methylation is targeted to transcribed sequences in the human genome.
Fazzari M.J. and Greally J.M. Classifier performance with varying feature set size: a decomposition of
error.
Fazzari M.J., Ahn H., Glass J.L., Greally J.M., Zhu W. Ensemble-based classification in genomics.
Suzuki M., Glass J.L., Thompson R.F., Khulan B., Desprat R., Olivier E.N., Selzer R.R., Richmond T.A.,
Green R.D., Bouhassira E.E., Greally J.M. Cis-expansion and contraction of cytosine hypomethylation
occurs with developmental gene activation and silencing.
Noh K.-M., Follenzi A., Miyawaki T., Greally J.M., Bennett M.V.L., Zukin R.S. REST-dependent
epigenetic remodeling of AMPA receptors is critical to ischemia induced neuronal death.
Non-peer reviewed:
Morton C.C., Christian S.L., Donlon T.A., Driscoll D.J., Fink J.K., Gabriel J.M., Gotway G., Greally J.M.,
Hitchins M.P., Howard H.C., Ji Y., Leonard S., Lerner T., Magenis E., Malcolm S., Ohta T., Rainier S.,
Rees M., Riley B., Robinson W.P., Saitoh S., Schultz R., Sell S., Sharp J.D., Talbot C., et al. Report of the
Fourth International Workshop on Human Chromosome 15 Mapping 1997. Cytogenet. Cell Genet. 1999
84 11-21.
Greally J.M. Genomic imprinting and chromatin insulation in Beckwith-Wiedemann syndrome. Mol.
Biotech. 1999 11 159-173.
Greally J.M. and Lombroso P.J. Genetics of childhood disorders: VIII. Making sense out of nonsense. J.
Am. Acad. Child Adolesc. Psychiatry 1999 38 1458-1461.
Greally J.M. and State M.W. Genetics of childhood disorders: XIII. Genomic imprinting: the indelible mark
of the gamete. J. Am. Acad. Child Adolesc. Psychiatry 2000 39 (4) 532-535.
Selected letters and abstracts:
Greally J.M. Imprinting and Angelman‟s syndrome [letter]. J. Med. Genet. 1990 27 (10) 663.
Kwan, H.C., Greally J.M. and McGrath J.M. The G protein stimulatory alpha subunit (Gnas) gene is
imprinted and maternally overexpressed in mouse [abstract]. Am. J. Hum. Genet. 1998 63 (4) A9.
Book chapters:
Figueroa, M.E., Melnick, A.M., Greally, J.M. (2007) Genome-wide determination of DNA methylation by
HELP (HpaII Tiny Fragment Enrichment by Ligation-Mediated PCR) for the study of acute leukemias, in
Childhood Leukemias (Chi Wai Eric So, P. D., Ed.), Humana Press, New Jersey.
Books:
Ferguson-Smith A.C., Greally J.M., and Martienssen R.A. (editors) Epigenomics. Springer 2009
Other:
Greally, J.M., Fazzari M.J. Bioinformatics and identification of imprinted genes in mammals. Genetics,
Genomics, Proteomics and Bioinformatics Online Wiley (http://www.wiley.com/legacy/wileychi/ggpb)
SOFTWARE PACKAGES
HELP, Bioconductor 2.6 (http://www.bioconductor.org/packages/2.6/bioc/html/HELP.html)
MassArray, Bioconductor 2.6 (http://bioconductor.org/packages/2.6/bioc/html/MassArray.html)
JOURNAL EDITORSHIPS AND REVIEWER ACTIVITIES
Editorial Board, Epigenetics and Chromatin (BioMed Central).
Assistant Editor, Translational OncoGenomics (Libertas Academica).
Former role as Executive Editor, Cytogenetic and Genome Research (Karger).
Reviewer: Nature, Nature Genetics, PNAS, J. Cell Biol., PLoS Genetics, Hum. Mol. Genet., Genome Res.,
Blood, Am. J. Hum. Genet., BMC Genomics, Biology of Reproduction, Trends in Genetics, Biotechniques.
GRANT REVIEW
Permanent: NIH GHD 2009-2013
Ad hoc: NIH (GCAT and GHD study sections ad hoc, NCI, NCRR), NSF, The Wellcome Trust (UK), the
National Health and Medical Research Council (Australia), Science Foundation Ireland.
UNIVERSITY GOVERNANCE AND SERVICE
2003- Faculty Supervisor, Genome Imaging Facility.
2003- Division of Research Information Technology subcommittee member.
2003- Division of Research committee member.
2003- Graduate Student qualifying examination committee.
2004- Faculty supervisor, Bioinformatics Shared Resource.
2005- Faculty co-supervisor, AECOM NimbleGen Direct microarray service.
2006 Dean‟s strategic planning task force (Human Genetics, Computational and Systems Biology
workgroups)
2007 Chair Search Committee, Department of Systems and Computational Biology
2007 Promotions Committee (Assistant to Associate Professor)
PATENTS
2007 Methods for determining cytosine methylation in DNA and uses thereof.
FUNDING
Active:
National Institutes of Health
R01 HD044078; Genomic analysis of mammalian imprinted loci.
Principal investigator.
4.1.05 – 3.31.10 $200,000
National Institutes of Health (NCI)
R01 CA125635; Mechanism of combined „epigenetic therapy‟ in myeloid malignancies
Subcontract with Johns Hopkins University (S. Gore PI)
7.1.07 – 6.30.11
High-Q Foundation.
Epigenetic remodeling of neuronal genes in Huntington‟s disease.
Co-principal investigator (Suzanne Zukin co-PI)
7.1.07 – 6.30.09
National Institutes of Health
R01 HG004401-01; Massively-parallel sequencing technology for the epigenome
Principal investigator.
6.1.07 – 5.31.10
Albert Einstein Center for AIDS Research
Feasibility studies to assess if histone modifications in C. neoformans regulate expression of
virulence associated genes.
Principal investigator
5.1.08-4.30.09
Expired (last 3 years):
National Institutes of Health, National Cancer Institute.
R21 CA122339-01; Epigenomic influences of diet on intestinal neoplasia.
Principal investigator.
National Institutes of Health
R21 CA110342-01
Co-investigator (Missak Haigentz PI)
Depsipeptide for the treatment of head and neck cancer.
4.1.05 – 3.31.07
American Diabetes Association.
Research Award.
Principal investigator.
Identification of type 2 diabetes mellitus candidate genes by imprinting analyses of 6q24.
1.1.04-12.31.06
National Institutes of Health, National Cancer Institute.
R03 CA111577; Genome-wide cytosine methylation analysis.
Principal investigator.
10.1.04 – 9.30.06
Albert Einstein Cancer Center
Pilot Project grant.
Principal investigator.
Epigenomics and rational cancer therapy.
5.1.05-4.30.06