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1977 …2024

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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

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 : The 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

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

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 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

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

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

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
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

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

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
2015

Development of a targeted multi-disorder high-throughput sequencing assay for the effective identification of disease-causing variants

Delio, M., Patel, K., Maslov, A., Marion, R. W., McDonald, T. V., Cadoff, E. M., Golden, A., Greally, J. M., Vijg, J., Morrow, B. & Montagna, C., Jul 27 2015, In : PloS one. 10, 7, 0133742.

Research output: Contribution to journalArticle

10 Scopus citations

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

Ramos, M. P., Wijetunga, N. A., McLellan, A. S., Suzuki, M. & Greally, J. M., 2015, In : Epigenetics and Chromatin. 8, 1, 11.

Research output: Contribution to journalArticle

18 Scopus citations

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

Li, Q., Suzuki, M., Wendt, J., Patterson, N., Eichten, S. R., Hermanson, P. J., Green, D., Jeddeloh, J., Richmond, T., Rosenbaum, H., Burgess, D., Springer, N. M. & Greally, J. M., Jan 1 2015, In : Nucleic acids research. 43, 12, e81.

Research output: Contribution to journalArticle

35 Scopus citations

Predictive properties of DNA methylation patterns in primary tumor samples for osteosarcoma relapse status

Rosenblum, J. M., Ari Wijetunga, N. A., Fazzari, M. J., Krailo, M., Barkauskas, D. A., Gorlick, R. & Greally, J. M., Jan 23 2015, In : Epigenetics. 10, 1, p. 31-39 9 p.

Research output: Contribution to journalArticle

12 Scopus citations

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

Nadel, J., Athanasiadou, R., Lemetre, C., Wijetunga, N. A., Ó Broin, P., Sato, H., Zhang, Z., Jeddeloh, J., Montagna, C., Golden, A., Seoighe, C. & Greally, J. M., Nov 16 2015, In : Epigenetics and Chromatin. 8, 1, 40.

Research output: Contribution to journalArticle

52 Scopus citations
2014

DNA methylation is developmentally regulated for genes essential for cardiogenesis

Chamberlain, A. A., Lin, M., Lister, R. L., Maslov, A. A., Wang, Y., Suzuki, M., Wu, B., Greally, J. M., Zheng, D. & Zhou, B., Jan 1 2014, In : Journal of the American Heart Association. 3, 3, 000976.

Research output: Contribution to journalArticle

29 Scopus citations

Epigenetic effects of extreme intrauterine growth in humans

Greally, J. M., Jan 1 2014, In : Research and Perspectives in Endocrine Interactions. 12, p. 131-138 8 p.

Research output: Contribution to journalArticle

Genome-wide expression profiling of B lymphocytes reveals IL4R increase in allergic asthma

Pascual, M., Roa, S., García-Sánchez, A., Sanz, C., Hernandez-Hernandez, L., Greally, J. M., Lorente, F., Dávila, I. & Isidoro-García, M., Oct 1 2014, In : Journal of Allergy and Clinical Immunology. 134, 4, p. 972-975 4 p.

Research output: Contribution to journalArticle

13 Scopus citations

HSC commitment-associated epigenetic signature is prognostic in acute myeloid leukemia

Bartholdy, B., Christopeit, M., Will, B., Mo, Y., Barreyro, L., Yu, Y., Bhagat, T. D., Okoye-Okafor, U. C., Todorova, T. I., Greally, J. M., Levine, R. L., Melnick, A., Verma, A. & Steidl, U., Mar 3 2014, In : Journal of Clinical Investigation. 124, 3, p. 1158-1167 10 p.

Research output: Contribution to journalArticle

30 Scopus citations

Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival

Hu, C. Y., Mohtat, D., Yu, Y., Ko, Y. A., Shenoy, N., Bhattacharya, S., Izquierdo, M. C., Park, A. S. D., Giricz, O., Vallumsetla, N., Gundabolu, K., Ware, K., Bhagat, T. D., Suzuki, M., Pullman, J., Liu, X. S., Greally, J. M., Susztak, K. & Verma, A., Aug 15 2014, In : Clinical Cancer Research. 20, 16, p. 4349-4360 12 p.

Research output: Contribution to journalArticle

39 Scopus citations

Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder

Berko, E. R., Suzuki, M., Beren, F., Lemetre, C., Alaimo, C. M., Calder, R. B., Ballaban-Gil, K., Gounder, B., Kampf, K., Kirschen, J., Maqbool, S. B., Momin, Z., Reynolds, D. M., Russo, N., Shulman, L., Stasiek, E., Tozour, J., Valicenti-McDermott, M., Wang, S., Abrahams, B. S. & 9 others, Hargitai, J., Inbar, D., Zhang, Z., Buxbaum, J. D., Molholm, S., Foxe, J. J., Marion, R. W., Auton, A. & Greally, J. M., May 2014, In : PLoS genetics. 10, 5, e1004402.

Research output: Contribution to journalArticle

55 Scopus citations

Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth

Delahaye, F., Wijetunga, N. A., Heo, H. J., Tozour, J. N., Zhao, Y. M., Greally, J. M. & Einstein, F. H., 2014, In : Nature communications. 5, 5187.

Research output: Contribution to journalArticle

20 Scopus citations

The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences

Wijetunga, N. A., Delahaye, F., Zhao, Y. M., Golden, A., Mar, J. C., Einstein, F. H. & Greally, J. M., Oct 20 2014, In : Nature communications. 5, 6195.

Research output: Contribution to journalArticle

23 Scopus citations