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Items: 1 to 50 of 234

1.

High-efficiency genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells using a single-stranded donor oligonucleotide strategy.

Johnston AD, Simões-Pires CA, Suzuki M, Greally JM.

Commun Biol. 2019 Aug 14;2:312. doi: 10.1038/s42003-019-0559-3. eCollection 2019.

2.

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

Johnston AD, Simões-Pires CA, Thompson TV, Suzuki M, Greally JM.

Nat Commun. 2019 Aug 2;10(1):3472. doi: 10.1038/s41467-019-11412-5.

3.

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

Bowler TG, Pradhan K, Kong Y, Bartenstein M, Morrone KA, Sridharan A, Kessel RM, Shastri A, Giricz O, Bhagat TD, Gordon-Mitchell S, Rohanizadegan M, Hooda L, Datt I, Przychodzen BP, Parmar S, Maqbool S, Maciejewski JP, Steidl U, Greally JM, Verma A.

Leuk Lymphoma. 2019 Jul 10:1-6. doi: 10.1080/10428194.2019.1630620. [Epub ahead of print]

PMID:
31288594
4.

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

Jaric I, Rocks D, Greally JM, Suzuki M, Kundakovic M.

Nat Commun. 2019 Jun 28;10(1):2851. doi: 10.1038/s41467-019-10704-0.

5.

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

Piqué DG, Andriani GA, Maggi E, Zimmerman SE, Greally JM, Montagna C, Mar JC.

BMC Bioinformatics. 2019 Jun 17;20(1):336. doi: 10.1186/s12859-019-2842-1.

6.

Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains.

Sato H, Wu B, Delahaye F, Singer RH, Greally JM.

J Cell Biol. 2019 Jun 3;218(6):1810-1823. doi: 10.1083/jcb.201811109. Epub 2019 May 20.

PMID:
31110057
7.

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

Kong Y, Rastogi D, Seoighe C, Greally JM, Suzuki M.

PLoS One. 2019 Apr 25;14(4):e0215987. doi: 10.1371/journal.pone.0215987. eCollection 2019.

8.

Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells.

Nakahara F, Borger DK, Wei Q, Pinho S, Maryanovich M, Zahalka AH, Suzuki M, Cruz CD, Wang Z, Xu C, Boulais PE, Ma'ayan A, Greally JM, Frenette PS.

Nat Cell Biol. 2019 May;21(5):560-567. doi: 10.1038/s41556-019-0308-3. Epub 2019 Apr 15.

9.

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

Piqué DG, Montagna C, Greally JM, Mar JC.

Br J Cancer. 2019 Apr;120(7):746-753. doi: 10.1038/s41416-019-0387-8. Epub 2019 Mar 1.

10.

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

Shenoy N, Bhagat TD, Cheville J, Lohse C, Bhattacharyya S, Tischer A, Machha V, Gordon-Mitchell S, Choudhary G, Wong LF, Gross L, Ressigue E, Leibovich B, Boorjian SA, Steidl U, Wu X, Pradhan K, Gartrell B, Agarwal B, Pagliaro L, Suzuki M, Greally JM, Rakheja D, Thompson RH, Susztak K, Witzig T, Zou Y, Verma A.

J Clin Invest. 2019 Mar 4;130:1612-1625. doi: 10.1172/JCI98747. eCollection 2019 Mar 4.

11.

Whole-genome bisulfite sequencing with improved accuracy and cost.

Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM.

Genome Res. 2018 Sep;28(9):1364-1371. doi: 10.1101/gr.232587.117. Epub 2018 Aug 9.

12.

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

Bartholdy B, Lajugie J, Yan Z, Zhang S, Mukhopadhyay R, Greally JM, Suzuki M, Bouhassira EE.

Blood Adv. 2018 Aug 14;2(15):1833-1852. doi: 10.1182/bloodadvances.2018015651.

13.

DNA methylation haplotypes as cancer markers.

Seoighe C, Tosh NJ, Greally JM.

Nat Genet. 2018 Aug;50(8):1062-1063. doi: 10.1038/s41588-018-0185-x. No abstract available.

PMID:
30054597
14.

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 KB, Cotto-Rios XM, Vardabasso C, Nguyen H, Matusow B, Bartenstein M, Polishchuk V, Johnson DB, Bhagat TD, Shellooe R, Burton E, Tsai J, Zhang C, Habets G, Greally JM, Yu Y, Kenny PA, Fields GB, Pradhan K, Stanley ER, Bernstein E, Bollag G, Gavathiotis E, West BL, Sosman JA, Verma AK.

JCI Insight. 2018 Jul 26;3(14). pii: 120422. doi: 10.1172/jci.insight.120422. eCollection 2018 Jul 26.

15.

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, Verma A.

Methods Mol Biol. 2018;1792:167-177. doi: 10.1007/978-1-4939-7865-6_12.

PMID:
29797259
16.

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

Kong Y, Berko ER, Marcketta A, Maqbool SB, Simões-Pires CA, Kronn DF, Ye KQ, Suzuki M, Auton A, Greally JM.

Genome Res. 2018 Jul;28(7):1039-1052. doi: 10.1101/gr.226282.117. Epub 2018 May 17.

17.

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 SH, Mittal N, Jing Q, Suzuki M, Greally JM, Fukuda K, Makino S.

BMC Genomics. 2018 May 10;19(1):349. doi: 10.1186/s12864-018-4752-4.

18.

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

Tozour JN, Delahaye F, Suzuki M, Praiss A, Zhao Y, Cai L, Heo HJ, Greally JM, Hughes F.

Stem Cells Dev. 2018 May 15;27(10):683-691. doi: 10.1089/scd.2017.0232. Epub 2018 Apr 26.

19.

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

Greally JM.

Nat Rev Mol Cell Biol. 2018 Apr;19(4):207-208. doi: 10.1038/nrm.2017.135. Epub 2018 Jan 17. No abstract available.

PMID:
29339796
20.

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

Miller EM, Patterson NE, Zechmeister JM, Bejerano-Sagie M, Delio M, Patel K, Ravi N, Quispe-Tintaya W, Maslov A, Simmons N, Castaldi M, Vijg J, Karabakhtsian RG, Greally JM, Kuo DYS, Montagna C.

Oncotarget. 2017 Oct 26;8(60):102033-102045. doi: 10.18632/oncotarget.22116. eCollection 2017 Nov 24.

21.

The HELP-Based DNA Methylation Assays.

Greally JM.

Methods Mol Biol. 2018;1708:191-207. doi: 10.1007/978-1-4939-7481-8_11.

PMID:
29224146
22.

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 TD, Gupta S, Suzuki M, Yu Y, Greally JM, Steidl U, Bradner J, Dawlaty M, Godley L, Maitra A, Verma A.

Genome Res. 2017 Nov;27(11):1830-1842. doi: 10.1101/gr.222794.117. Epub 2017 Oct 6.

23.

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

Buesen R, Chorley BN, da Silva Lima B, Daston G, Deferme L, Ebbels T, Gant TW, Goetz A, Greally J, Gribaldo L, Hackermüller J, Hubesch B, Jennen D, Johnson K, Kanno J, Kauffmann HM, Laffont M, McMullen P, Meehan R, Pemberton M, Perdichizzi S, Piersma AH, Sauer UG, Schmidt K, Seitz H, Sumida K, Tollefsen KE, Tong W, Tralau T, van Ravenzwaay B, Weber RJM, Worth A, Yauk C, Poole A.

Regul Toxicol Pharmacol. 2017 Dec;91 Suppl 1:S3-S13. doi: 10.1016/j.yrtph.2017.09.002. Epub 2017 Sep 25. Review.

24.

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 AS, Vuguin PM, Fiallo A, Du Q, Ko YA, Yu Y, Susztak K, Zheng D, Greally JM, Katz EB, Charron MJ.

Endocrinology. 2017 Sep 1;158(9):2860-2872. doi: 10.1210/en.2017-00334.

25.

Epigenetically Aberrant Stroma in MDS Propagates Disease via Wnt/β-Catenin Activation.

Bhagat TD, Chen S, Bartenstein M, Barlowe AT, Von Ahrens D, Choudhary GS, Tivnan P, Amin E, Marcondes AM, Sanders MA, Hoogenboezem RM, Kambhampati S, Ramachandra N, Mantzaris I, Sukrithan V, Laurence R, Lopez R, Bhagat P, Giricz O, Sohal D, Wickrema A, Yeung C, Gritsman K, Aplan P, Hochedlinger K, Yu Y, Pradhan K, Zhang J, Greally JM, Mukherjee S, Pellagatti A, Boultwood J, Will B, Steidl U, Raaijmakers MHGP, Deeg HJ, Kharas MG, Verma A.

Cancer Res. 2017 Sep 15;77(18):4846-4857. doi: 10.1158/0008-5472.CAN-17-0282. Epub 2017 Jul 6.

26.

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

Do C, Shearer A, Suzuki M, Terry MB, Gelernter J, Greally JM, Tycko B.

Genome Biol. 2017 Jun 19;18(1):120. doi: 10.1186/s13059-017-1250-y. Review.

27.

Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis.

Barnicle A, Seoighe C, Greally JM, Golden A, Egan LJ.

Epigenetics. 2017 Aug;12(8):591-606. doi: 10.1080/15592294.2017.1334023. Epub 2017 May 30.

28.

Associating cellular epigenetic models with human phenotypes.

Lappalainen T, Greally JM.

Nat Rev Genet. 2017 Jul;18(7):441-451. doi: 10.1038/nrg.2017.32. Epub 2017 May 30. Review.

PMID:
28555657
29.

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

Rastogi D, Nico J, Johnston AD, Tobias TAM, Jorge Y, Macian F, Greally JM.

J Allergy Clin Immunol. 2018 Feb;141(2):539-548.e7. doi: 10.1016/j.jaci.2017.04.016. Epub 2017 May 4. Erratum in: J Allergy Clin Immunol. 2018 Dec;142(6):2014.

30.

Population Epigenetics.

Greally JM.

Curr Opin Syst Biol. 2017 Feb;1:84-89. doi: 10.1016/j.coisb.2017.01.004. Epub 2017 Jan 27.

31.

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

Wijetunga NA, Johnston AD, Maekawa R, Delahaye F, Ulahannan N, Kim K, Greally JM.

BMC Bioinformatics. 2017 Jan 18;18(1):41. doi: 10.1186/s12859-017-1477-3.

32.

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 JM, Zheng D, Zhou B.

Nucleic Acids Res. 2017 Apr 7;45(6):3102-3115. doi: 10.1093/nar/gkw1258.

33.

The Current State of Epigenetic Research in Humans: Promise and Reality.

Greally JM, Drake AJ.

JAMA Pediatr. 2017 Feb 1;171(2):103-104. doi: 10.1001/jamapediatrics.2016.3508. No abstract available.

PMID:
27918756
34.

Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer.

Bhagat TD, Zou Y, Huang S, Park J, Palmer MB, Hu C, Li W, Shenoy N, Giricz O, Choudhary G, Yu Y, Ko YA, Izquierdo MC, Park AS, Vallumsetla N, Laurence R, Lopez R, Suzuki M, Pullman J, Kaner J, Gartrell B, Hakimi AA, Greally JM, Patel B, Benhadji K, Pradhan K, Verma A, Susztak K.

J Biol Chem. 2017 Jan 20;292(3):837-846. doi: 10.1074/jbc.M116.745208. Epub 2016 Dec 1.

35.

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

Acosta D, Bagchi S, Broin PÓ, Hollern D, Racedo SE, Morrow B, Sellers RS, Greally JM, Golden A, Andrechek E, Wood T, Montagna C.

Sci Rep. 2016 Nov 3;6:35810. doi: 10.1038/srep35810.

36.

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

Wijetunga NA, Pascual M, Tozour J, Delahaye F, Alani M, Adeyeye M, Wolkoff AW, Verma A, Greally JM.

Oncogene. 2017 Apr 6;36(14):2030-2044. doi: 10.1038/onc.2016.340. Epub 2016 Oct 10.

37.

A polycomb-mediated epigenetic field defect precedes invasive cervical carcinoma.

Wijetunga NA, Ben-Dayan M, Tozour J, Burk RD, Schlecht NF, Einstein MH, Greally JM.

Oncotarget. 2016 Sep 20;7(38):62133-62143. doi: 10.18632/oncotarget.11390.

38.

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

Chow JC, Ciaudo C, Fazzari MJ, Mise N, Servant N, Glass JL, Attreed M, Avner P, Wutz A, Barillot E, Greally JM, Voinnet O, Heard E.

Cell. 2016 Jul 28;166(3):782. doi: 10.1016/j.cell.2016.07.013. No abstract available.

39.

Epigenetics, cellular memory and gene regulation.

Henikoff S, Greally JM.

Curr Biol. 2016 Jul 25;26(14):R644-8. doi: 10.1016/j.cub.2016.06.011.

40.

MeCP2 Binding Cooperativity Inhibits DNA Modification-Specific Recognition.

Khrapunov S, Tao Y, Cheng H, Padlan C, Harris R, Galanopoulou AS, Greally JM, Girvin ME, Brenowitz M.

Biochemistry. 2016 Aug 9;55(31):4275-85. doi: 10.1021/acs.biochem.6b00451. Epub 2016 Jul 28.

41.

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

Wijetunga NA, Belbin TJ, Burk RD, Whitney K, Abadi M, Greally JM, Einstein MH, Schlecht NF.

Gynecol Oncol. 2016 Sep;142(3):566-73. doi: 10.1016/j.ygyno.2016.07.006. Epub 2016 Jul 9.

42.

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

Birney E, Smith GD, Greally JM.

PLoS Genet. 2016 Jun 23;12(6):e1006105. doi: 10.1371/journal.pgen.1006105. eCollection 2016 Jun. Review.

43.

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

Suzuki M, Maekawa R, Patterson NE, Reynolds DM, Calder BR, Reznik SE, Heo HJ, Einstein FH, Greally JM.

Clin Epigenetics. 2016 Jun 10;8:67. doi: 10.1186/s13148-016-0234-1. eCollection 2016.

44.

Pediatric Obesity-Related Asthma: The Role of Metabolic Dysregulation.

Vijayakanthi N, Greally JM, Rastogi D.

Pediatrics. 2016 May;137(5). pii: e20150812. doi: 10.1542/peds.2015-0812. Epub 2016 Apr 8. Review.

45.

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

Yuan Z, Sánchez Claros C, Suzuki M, Maggi EC, Kaner JD, Kinstlinger N, Gorecka J, Quinn TJ, Geha R, Corn A, Pastoriza J, Jing Q, Adem A, Wu H, Alemu G, Du YC, Zheng D, Greally JM, Libutti SK.

Oncotarget. 2016 Mar 15;7(11):12633-50. doi: 10.18632/oncotarget.7279.

46.

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

Barnicle A, Seoighe C, Golden A, Greally JM, Egan LJ.

Physiol Genomics. 2016 Apr;48(4):257-73. doi: 10.1152/physiolgenomics.00046.2015. Epub 2016 Jan 26.

47.

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

Nadel J, Athanasiadou R, Lemetre C, Wijetunga NA, Ó Broin P, Sato H, Zhang Z, Jeddeloh J, Montagna C, Golden A, Seoighe C, Greally JM.

Epigenetics Chromatin. 2015 Nov 16;8:46. doi: 10.1186/s13072-015-0040-6. eCollection 2015.

48.

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 RW, McDonald TV, Cadoff EM, Golden A, Greally JM, Vijg J, Morrow B, Montagna C.

PLoS One. 2015 Jul 27;10(7):e0133742. doi: 10.1371/journal.pone.0133742. eCollection 2015.

49.

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

Li Q, Suzuki M, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J, Richmond T, Rosenbaum H, Burgess D, Springer NM, Greally JM.

Nucleic Acids Res. 2015 Jul 13;43(12):e81. doi: 10.1093/nar/gkv244. Epub 2015 Mar 26.

50.

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

Ramos MP, Wijetunga NA, McLellan AS, Suzuki M, Greally JM.

Epigenetics Chromatin. 2015 Mar 17;8:11. doi: 10.1186/s13072-015-0004-x. eCollection 2015.

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