John M. Greally

<p>Our research is based on understanding models of genetic susceptibility to human disease, especially those affecting children.</p>
<p>We focus on understanding phenotypes, through genetic or environmental influences that change the innate properties of a canonical cell type, or how those influences alter cell lineage choices during differentiation.</p>
<p>Our studies are facilitated by Einstein's Center for Epigenomics, its Epigenomics Shared Facility and the Computational Epigenomics Group.</p>
<p>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.</p>
<p>Our lab is focusing on stem cell systems to understand mechanisms of cellular memory, and to reveal the functional variants in the non-coding majority of the human genome.</p>
<p>Our clinical research program is centered on the New York Center for Rare Diseases, where we contribute to advanced diagnostics through long-read sequencing and advanced phenotyping and analytical tools.</p>

<p class="MsoNormal" style="line-height: 15.6pt;"><span style="font-size: 9.0pt;">Dr. Greally began his career as a pediatrician who subspecialized in clinical genetics, seeing patients with genetic syndromes, birth defects and developmental problems. Now, Dr. Greally seeks to understand how genetic disease is caused not by DNA mutations, but due to abnormalities in how genes are switched off and on &ndash; a field known as epigenomics.&nbsp;</span></p>
<p class="MsoNormal" style="line-height: 15.6pt;"><span style="font-size: 9.0pt;">Dr. Greally&rsquo;s research focuses on epigenetic abnormalities in human diseases such as breast cancer, type 2 diabetes, viral hepatitis, and allergies and on epigenetic regulation of stem cell differentiation. He also serves on the editorial board of the journal<span>&nbsp;</span><em>Epigenetics &amp; Chromatin</em>.&nbsp;</span></p>

<p>Rosean S, Sosa EA, O'Shea D, Raj SM, Seoighe C, <strong>Greally JM</strong>. Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization. <strong><em>BMC Bioinformatics</em></strong>. 2024 May 7;25(1):179. doi: 10.1186/s12859-024-05794-7. PMID: 38714913; PMCID: PMC11075237.</p>
<p>Pearson NM, Stolte C, Shi K, Beren F, Abul-Husn NS, Bertier G, Brown K, Diaz GA, Odgis JA, Suckiel SA, Horowitz CR, Wasserstein M, Gelb BD, Kenny EE, Gagnon C, Jobanputra V, Bloom T, Greally JM. GenomeDiver: a platform for phenotype-guided medical genomic diagnosis. Genet Med. 2021 Oct;23(10):1998-2002. doi: 10.1038/s41436-021-01219-5. Epub 2021 Jun 10. PMID: 34113009; PMCID: PMC8488006.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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. </p>

<p>John M. Greally, DMed, PhD, MB, BCh, BAO, is Chief of the Division of Genomics in the Department of Genetics, Director of the Center for Epigenomics and Professor of Genetics and Pediatrics at Montefiore Einstein. Dr. Greally is a specialist in clinical genetics, with an emphasis on rare diseases and congenital conditions. He has expertise in medical genomics, the use of advanced genomic technologies to diagnose genetic conditions.</p><p>Dr. Greally obtained his Bachelor&rsquo;s degree in Medicine, Surgery and Obstetrics in 1988 from the National University of Ireland in Galway, Ireland. He received his Doctorate of Philosophy in 1999 and his Doctorate of Medicine in 2016 from the same institution.</p><p>Building on his clinical focus, Dr. Greally runs a research program that uses genomic technologies, advanced data analysis techniques and stem cell systems to understand the mechanisms of human genetic diseases, with a focus on rare DNA sequence variants in the non-coding majority of the human genome. He is focused on improving our ability to diagnose rare diseases and on the equitable provision of genomics services to populations of all ancestries. He has also initiated a startup business, Latent Genomics, to allow the effective use of medical genomics in clinical care.</p><p>Dr. Greally holds a United States Patent titled <em>Methods for determining cytosine methylation in DNA and uses thereof</em>. His work has been published in numerous peer-reviewed journals, chapters and books, and he has presented nationally and internationally. He sits on the editorial board of <em>Epigenetics and Chromatin</em> (BioMed Central) and is a section editor for Epigenetics at <em>PLOS Genetics</em>.</p><p>Dr. Greally is board certified in pediatrics by the American Board of Pediatrics and in clinical genetics and genomics by the American Board of Medical Genetics. He is a member of the American Society of Human Genetics and a fellow of the American College of Medical Genetics and Genomics. Dr. Greally has been appointed president of the New York Celtic Medical Society from 2021 to 2023, and in 2014 he won Mentor of the Year in Basic Science from Montefiore Einstein.</p>