• 8926 Citations
  • 50 h-Index
1977 …2025

Research output per year

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Publications

2020

AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX

Shieh, K. R., Kratschmer, C., Maier, K. E., Greally, J. M., Levy, M. & Golden, A., May 1 2020, In : Bioinformatics (Oxford, England). 36, 9, p. 2905-2906 2 p.

Research output: Contribution to journalArticle

2019

Aneuvis: Web-based exploration of numerical chromosomal variation in single cells

Piqué, D. G., Andriani, G. A., Maggi, E., Zimmerman, S. E., Greally, J. M., Montagna, C. & Mar, J. C., Jun 17 2019, In : BMC bioinformatics. 20, 1, 336.

Research output: Contribution to journalArticle

Open Access

A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma

Piqué, D. G., Montagna, C., Greally, J. M. & Mar, J. C., Apr 2 2019, In : British Journal of Cancer. 120, 7, p. 746-753 8 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Ascorbic acid–induced TET activation mitigates adverse hydroxymethylcytosine loss in renal cell carcinoma

Shenoy, N., Bhagat, T. D., Cheville, J., Lohse, C., Bhattacharyya, S., Tischer, A., Machha, V., Gordon-Mitchell, S., Choudhary, G., Wong, L. F., Gross, L. A., Ressigue, E., Leibovich, B., Boorjian, S. A., Steidl, U., Wu, X., Pradhan, K., Gartrell, B., Agarwal, B., Pagliaro, L. & 8 others, Suzuki, M., Greally, J. M., Rakheja, D., Houston Thompson, R., Susztak, K., Witzig, T., Zou, Y. & Verma, A., Apr 1 2019, In : Journal of Clinical Investigation. 129, 4, p. 1612-1625 14 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Chromatin organization in the female mouse brain fluctuates across the oestrous cycle

Jaric, I., Rocks, D., Greally, J. M., Suzuki, M. & Kundakovic, M., Dec 1 2019, In : Nature communications. 10, 1, 2851.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells

Nakahara, F., Borger, D. K., Wei, Q., Pinho, S., Maryanovich, M., Zahalka, A. H., Suzuki, M., Cruz, C. D., Wang, Z., Xu, C., Boulais, P. E., Ma’ayan, A., Greally, J. M. & Frenette, P. S., May 1 2019, In : Nature Cell Biology. 21, 5, p. 560-567 8 p.

Research output: Contribution to journalLetter

9 Scopus citations

Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding

Johnston, A. D., Simões-Pires, C. A., Thompson, T. V., Suzuki, M. & Greally, J. M., Dec 1 2019, In : Nature communications. 10, 1, 3472.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations
Open Access

Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data

Kong, Y., Rastogi, D., Seoighe, C., Greally, J. M. & Suzuki, M., Apr 1 2019, In : PLoS ONE. 14, 4, e0215987.

Research output: Contribution to journalArticle

Open Access

Lactate-mediated epigenetic reprogramming regulates formation of human pancreatic cancer-associated fibroblasts

Bhagat, T. D., Von Ahgrens, D., Dawlaty, M., Zou, Y., Baddour, J., Achreja, A., Zhao, H., Yang, L., Patel, B., Kwak, C., Choudhary, G. S., Gordon-Mitchell, S., Alluri, S., Bhattacharyya, S., Sahu, S., Yu, Y., Bartenstein, M., Giricz, O., Suzuki, M., Sohal, D. & 12 others, Gupta, S., Guerrero, P., Batra, S., Goggins, M., Steidl, U., Greally, J., Agarwal, B., Pradhan, K., Banerjee, D., Nagrath, D., Maitra, A. & Verma, A., Oct 2019, In : eLife. 8, e50663.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Misidentification of MLL3 and other mutations in cancer due to highly homologous genomic regions

Bowler, T. G., Pradhan, K., Kong, Y., Bartenstein, M., Morrone, K. A., Shridharan, A., Kessel, R. M., Shastri, A., Giricz, O., Bhagat, T. D., Gordon-Mitchell, S., Rohanizadegan, M., Hooda, L., Datt, I., Przychodzen, B. P., Parmar, S., Maqbool, S., Maciejewski, J. P., Steidl, U., Greally, J. M. & 1 others, Verma, A., Jan 1 2019, In : Leukemia and Lymphoma.

Research output: Contribution to journalArticle

Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains

Sato, H., Wu, B., Delahaye, F., Singer, R. H. & Greally, J. M., Jun 3 2019, In : Journal of Cell Biology. 218, 6, p. 1810-1823 14 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Transposable element expression in tumors is associated with immune infiltration and increased antigenicity

Kong, Y., Rose, C. M., Cass, A. A., Williams, A. G., Darwish, M., Lianoglou, S., Haverty, P. M., Tong, A. J., Blanchette, C., Albert, M. L., Mellman, I., Bourgon, R., Greally, J., Jhunjhunwala, S. & Chen-Harris, H., Dec 1 2019, In : Nature communications. 10, 1, 5228.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations
2018

A user's guide to the ambiguous word 'epigenetics'

Greally, J. M., Apr 1 2018, In : Nature Reviews Molecular Cell Biology. 19, 4, p. 207-208 2 p.

Research output: Contribution to journalComment/debate

27 Scopus citations

CDC42-related genes are upregulated in helper T cells from obese asthmatic children

Rastogi, D., Nico, J., Johnston, A. D., Tobias, T. A. M., Jorge, Y., Macian, F. & Greally, J. M., Feb 2018, In : Journal of Allergy and Clinical Immunology. 141, 2, p. 539-548.e7

Research output: Contribution to journalArticle

7 Scopus citations

Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq

Kong, Y., Berko, E. R., Marcketta, A., Maqbool, S. B., Simões-Pires, C. A., Kronn, D. F., Ye, K. Q., Suzuki, M., Auton, A. & Greally, J. M., Jul 2018, In : Genome research. 28, 7, p. 1039-1052 14 p.

Research output: Contribution to journalArticle

1 Scopus citations

DNA methylation haplotypes as cancer markers

Seoighe, C., Tosh, N. J. & Greally, J. M., Aug 1 2018, In : Nature Genetics. 50, 8, p. 1062-1063 2 p.

Research output: Contribution to journalLetter

2 Scopus citations

Genome wide mapping of methylated and hydroxyl-methylated cytosines using a modified hpaii tiny fragment enrichment by ligation mediated PCR tagged sequencing protocol

Battachariyya, S., Tytarenko, R., Heuck, C., Greally, J. M. & Verma, A. K., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 167-177 11 p. (Methods in Molecular Biology; vol. 1792).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

Intrauterine Hyperglycemia Is Associated with an Impaired Postnatal Response to Oxidative Damage

Tozour, J. N., Delahaye, F., Suzuki, M., Praiss, A., Zhao, Y., Cai, L., Heo, H. J., Greally, J. M. & Hughes, F., May 15 2018, In : Stem Cells and Development. 27, 10, p. 683-691 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

Mechanisms of establishment and functional significance of DNA demethylation during erythroid differentiation

Bartholdy, B., Lajugie, J., Yan, Z., Zhang, S., Mukhopadhyay, R., Greally, J. M., Suzuki, M. & Bouhassira, E. E., Aug 14 2018, In : Blood Advances. 2, 15, p. 1833-1852 20 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Selective modulation of local linkages between active transcription and oxidative demethylation activity shapes cardiomyocyte-specific gene-body epigenetic status in mice

Oda, M., Wakabayashi, S., Ari Wijetunga, N., Yuasa, S., Enomoto, H., Kaneda, R., Yoon, S. H., Mittal, N., Jing, Q., Suzuki, M., Greally, J. M., Fukuda, K. & Makino, S., May 10 2018, In : BMC Genomics. 19, 1, 349.

Research output: Contribution to journalArticle

The HELP-based DNA methylation assays

Greally, J. M., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., Vol. 1708. p. 191-207 17 p. (Methods in Molecular Biology; vol. 1708).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma

Giricz, O., Mo, Y., Dahlman, K. B., Cotto-Rios, X. M., Vardabasso, C., Nguyen, H., Matusow, B., Bartenstein, M., Polishchuk, V., Johnson, D. B., Bhagat, T. D., Shellooe, R., Burton, E., Tsai, J., Zhang, C., Habets, G., Greally, J. M., Yu, Y., Kenny, P. A., Fields, G. B. & 8 others, Pradhan, K., Stanley, E. R., Bernstein, E., Bollag, G., Gavathiotis, E., West, B. L., Sosman, J. A. & Verma, A. K., Jul 26 2018, In : JCI Insight. 3, 14

Research output: Contribution to journalArticle

Open Access

Whole-genome bisulfite sequencing with improved accuracy and cost

Suzuki, M., Liao, W., Wos, F., Johnston, A. D., DeGrazia, J., Ishii, J., Bloom, T., Zody, M. C., Germer, S. & Greally, J. M., Sep 1 2018, In : Genome Research. 28, 9, p. 1364-1371 8 p.

Research output: Contribution to journalArticle

8 Scopus citations
2017

Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways

Bhattacharyya, S., Pradhan, K., Campbell, N., Mazdo, J., Vasantkumar, A., Maqbool, S., Bhagat, T. D., Gupta, S., Suzuki, M., Yu, Y., Greally, J. M., Steidl, U., Bradner, J., Dawlaty, M., Godley, L., Maitra, A. & Verma, A., Nov 1 2017, In : Genome Research. 27, 11, p. 1830-1842 13 p.

Research output: Contribution to journalArticle

17 Scopus citations

Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop

Buesen, R., Chorley, B. N., da Silva Lima, B., Daston, G., Deferme, L., Ebbels, T., Gant, T. W., Goetz, A., Greally, J., Gribaldo, L., Hackermüller, J., Hubesch, B., Jennen, D., Johnson, K., Kanno, J., Kauffmann, H. M., Laffont, M., McMullen, P., Meehan, R., Pemberton, M. & 14 others, Perdichizzi, S., Piersma, A. H., Sauer, U. G., Schmidt, K., Seitz, H., Sumida, K., Tollefsen, K. E., Tong, W., Tralau, T., van Ravenzwaay, B., Weber, R. J. M., Worth, A., Yauk, C. & Poole, A., Dec 2017, In : Regulatory Toxicology and Pharmacology. 91, p. S3-S13

Research output: Contribution to journalArticle

41 Scopus citations

Associating cellular epigenetic models with human phenotypes

Lappalainen, T. & Greally, J. M., Jul 1 2017, In : Nature Reviews Genetics. 18, 7, p. 441-451 11 p.

Research output: Contribution to journalReview article

89 Scopus citations

Development and validation of a targeted next generation DNA sequencing panel outperforming whole exome sequencing for the identification of clinically relevant genetic variants

Miller, E. M., Patterson, N. E., Zechmeister, J. M., Bejerano-Sagie, M., Delio, M., Patel, K., Ravi, N., Quispe-Tintaya, W., Maslov, A., Simmons, N., Castaldi, M., Vijg, J., Karabakhtsian, R. G., Greally, J. M., Kuo, D. Y. S. & Montagna, C., Jan 1 2017, In : Oncotarget. 8, 60, p. 102033-102045 13 p.

Research output: Contribution to journalArticle

7 Scopus citations

Epigenetically aberrant stroma in MDS propagates disease via Wnt/β-catenin activation

Bhagat, T. D., Chen, S., Bartenstein, M., Barlowe, A. T., Von Ahrens, D., Choudhary, G. S., Tivnan, P., Amin, E., Marcondes, A. M., Sanders, M. A., Hoogenboezem, R. M., Kambhampati, S., Ramachandra, N., Mantzaris, I., Sukrithan, V., Laurence, R., Lopez, R., Bhagat, P., Giricz, O., Sohal, D. & 18 others, Wickrema, A., Yeung, C., Gritsman, K., Aplan, P., Hochedlinger, K., Yu, Y., Pradhan, K., Zhang, J., Greally, J. M., Mukherjee, S., Pellagatti, A., Boultwood, J., Will, B., Steidl, U., Raaijmakers, M. H. G. P., Deeg, H. J., Kharas, M. G. & Verma, A., Sep 15 2017, In : Cancer Research. 77, 18, p. 4846-4857 12 p.

Research output: Contribution to journalArticle

17 Scopus citations

Genetic-epigenetic interactions in cis: A major focus in the post-GWAS era

Do, C., Shearer, A., Suzuki, M., Terry, M. B., Gelernter, J., Greally, J. M. & Tycko, B., Jun 19 2017, In : Genome biology. 18, 1, 120.

Research output: Contribution to journalReview article

43 Scopus citations

Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis

Barnicle, A., Seoighe, C., Greally, J. M., Golden, A. & Egan, L. J., Aug 3 2017, In : Epigenetics. 12, 8, p. 591-606 16 p.

Research output: Contribution to journalArticle

10 Scopus citations

In utero exposure to a high-fat diet programs hepatic hypermethylation and gene dysregulation and development of metabolic syndrome in male mice

Seki, Y., Suzuki, M., Guo, X., Glenn, A. S., Vuguin, P. M., Fiallo, A., Du, Q., Ko, Y. A., Yu, Y., Susztak, K., Zheng, D., Greally, J. M., Katz, E. B. & Charron, M. J., Sep 1 2017, In : Endocrinology. 158, 9, p. 2860-2872 13 p.

Research output: Contribution to journalArticle

15 Scopus citations

Notch pathway is activated via genetic and epigenetic alterations and is a therapeutic target in clear cell renal cancer

Bhagat, T. D., Zou, Y., Huang, S., Park, J., Palmer, M. B., Hu, C., Li, W., Shenoy, N., Giricz, O., Choudhary, G., Yu, Y., Ko, Y. A., Izquierdo, M. C., Park, A. S. D., Vallumsetla, N., Laurence, R., Lopez, R., Suzuki, M., Pullman, J., Kaner, J. & 8 others, Gartrell, B., Hakimi, A. A., Greally, J. M., Patel, B., Benhadji, K., Pradhan, K., Verma, A. & Susztak, K., Jan 20 2017, In : Journal of Biological Chemistry. 292, 3, p. 837-846 10 p.

Research output: Contribution to journalArticle

11 Scopus citations

Population epigenetics

Greally, J. M., Feb 1 2017, In : Current Opinion in Systems Biology. 1, p. 84-89 6 p.

Research output: Contribution to journalReview article

5 Scopus citations

SMITE: An R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information

Wijetunga, N. A., Johnston, A. D., Maekawa, R., Delahaye, F., Ulahannan, N., Kim, K. & Greally, J. M., Jan 18 2017, In : BMC bioinformatics. 18, 1, 41.

Research output: Contribution to journalArticle

10 Scopus citations

The current state of epigenetic research inhumans promise and reality

Greally, J. M. & Drake, A. J., Feb 1 2017, In : JAMA Pediatrics. 171, 2, p. 103-104 2 p.

Research output: Contribution to journalComment/debate

6 Scopus citations
2016

Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

Suzuki, M., Maekawa, R., Patterson, N. E., Reynolds, D. M., Calder, B. R., Reznik, S. E., Heo, H. J., Einstein, F. H. & Greally, J. M., Jun 10 2016, In : Clinical Epigenetics. 8, 1, 67.

Research output: Contribution to journalArticle

3 Scopus citations

A polycomb-mediated epigenetic field defect precedes invasive cervical carcinoma

Wijetunga, N. A., Ben-Dayan, M., Tozour, J., Burk, R. D., Schlecht, N. F., Einstein, M. H. & Greally, J. M., Jan 1 2016, In : Oncotarget. 7, 38, p. 62133-62143 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets

Wijetunga, N. A., Pascual, M., Tozour, J., Delahaye, F., Alani, M., Adeyeye, M., Wolkoff, A. W., Verma, A. K. & Greally, J. M., Oct 10 2016, (Accepted/In press) In : Oncogene.

Research output: Contribution to journalArticle

13 Scopus citations

Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells

Barnicle, A., Seoighe, C., Golden, A., Greally, J. M. & Egan, L. J., Apr 1 2016, In : Physiological genomics. 48, 4, p. 257-273 17 p.

Research output: Contribution to journalArticle

4 Scopus citations

Epigenetics, cellular memory and gene regulation

Henikoff, S. & Greally, J. M., Jul 25 2016, In : Current Biology. 26, 14, p. R644-R648

Research output: Contribution to journalShort survey

60 Scopus citations

Epigenome-wide Association Studies and the Interpretation of Disease -Omics

Birney, E., Smith, G. D. & Greally, J. M., Jun 2016, In : PLoS genetics. 12, 6, e1006105.

Research output: Contribution to journalReview article

92 Scopus citations

LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation

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., Jul 28 2016, In : Cell. 166, 3, p. 782 1 p.

Research output: Contribution to journalEditorial

Loss of MEN1 activates DNMT1 implicating DNA hypermethylation as a driver of MEN1 tumorigenesis

Yuan, Z., Claros, C. S., Suzuki, M., Maggi, E. C., Kaner, J. D., Kinstlinger, N., Gorecka, J., Quinn, T. J., Geha, R., Corn, A., Pastoriza, J., Jing, Q., Adem, A., Wu, H., Alemu, G., Du, Y. C., Zheng, D., Greally, J. M. & Libutti, S. K., Mar 15 2016, In : Oncotarget. 7, 11, p. 12633-12650 18 p.

Research output: Contribution to journalArticle

11 Scopus citations

LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development

Acosta, D., Bagchi, S., Broin, P., Hollern, D., Racedo, S. E., Morrow, B., Sellers, R. S., Greally, J. M., Golden, A., Andrechek, E., Wood, T. & Montagna, C., Nov 3 2016, In : Scientific reports. 6, 35810.

Research output: Contribution to journalArticle

4 Scopus citations

MeCP2 Binding Cooperativity Inhibits DNA Modification-Specific Recognition

Khrapunov, S., Tao, Y., Cheng, H., Padlan, C., Harris, R., Galanopoulou, A. S., Greally, J. M., Girvin, M. E. & Brenowitz, M., Aug 9 2016, In : Biochemistry. 55, 31, p. 4275-4285 11 p.

Research output: Contribution to journalArticle

3 Scopus citations

Neuroepigenomics and Human Disease

Greally, J. M. & Nestler, E. J., Jun 21 2016, Genomics, Circuits, and Pathways in Clinical Neuropsychiatry. Elsevier Inc., p. 73-91 19 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts

Zhang, D., Wu, B., Wang, P., Wang, Y., Lu, P., Nechiporuk, T., Floss, T., Greally, J. M., Zheng, D. & Zhou, B., 2016, In : Nucleic Acids Research. 45, 6, p. 3102-3115 14 p.

Research output: Contribution to journalArticle

13 Scopus citations

Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia

Wijetunga, N. A., Belbin, T. J., Burk, R. D., Whitney, K. D., Abadi, M., Greally, J. M., Einstein, M. H. & Schlecht, N. F., Sep 1 2016, In : Gynecologic Oncology. 142, 3, p. 566-573 8 p.

Research output: Contribution to journalArticle

17 Scopus citations

Pediatric obesity-related asthma: The role of metabolic dysregulation

Vijayakanthi, N., Greally, J. M. & Rastogi, D., May 1 2016, In : Pediatrics. 137, 5, e20150812.

Research output: Contribution to journalArticle

32 Scopus citations