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John M. Greally - Publications

Affiliations: 
Albert Einstein College of Medicine of Yeshiva University, NY, United States 
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186 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Sosa EA, Rosean S, O'Shea D, Raj SM, Seoighe C, Greally JM. Regulatory Landscape Enrichment Analysis (RLEA) using gaiaAssociation. Biorxiv : the Preprint Server For Biology. PMID 37905111 DOI: 10.1101/2023.10.11.561933  0.306
2022 Pelletier A, Carrier A, Zhao Y, Canouil M, Derhourhi M, Durand E, Berberian-Ferrato L, Greally J, Hughes F, Froguel P, Bonnefond A, Delahaye F. Epigenetic and Transcriptomic Programming of HSC Quiescence Signaling in Large for Gestational Age Neonates. International Journal of Molecular Sciences. 23. PMID 35806330 DOI: 10.3390/ijms23137323  0.35
2019 Kong Y, Rose CM, Cass AA, Williams AG, Darwish M, Lianoglou S, Haverty PM, Tong AJ, Blanchette C, Albert ML, Mellman I, Bourgon R, Greally J, Jhunjhunwala S, Chen-Harris H. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nature Communications. 10: 5228. PMID 31745090 DOI: 10.1038/S41467-019-13035-2  0.448
2019 Bhagat TD, Von Ahrens D, Dawlaty M, Zou Y, Baddour J, Achreja A, Zhao H, Yang L, Patel B, Kang C, Choudhary G, Gordon-Mitchell S, Aluri S, Bhattacharyya S, Sahu S, ... ... Greally J, et al. Lactate-mediated epigenetic reprogramming regulates formation of human pancreatic cancer-associated fibroblasts. Elife. 8. PMID 31663852 DOI: 10.7554/Elife.50663  0.401
2019 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. Nature Communications. 10: 3472. PMID 31375681 DOI: 10.1038/S41467-019-11412-5  0.432
2019 Bowler TG, Pradhan K, Kong Y, Bartenstein M, Morrone KA, Shridharan A, Kessel RM, Shastri A, Giricz O, Bhagat TD, Gordon-Mitchell S, Rohanizadegan M, Hooda L, Datt I, Przychodzen BP, ... ... Greally JM, et al. Misidentification of and other mutations in cancer due to highly homologous genomic regions. Leukemia & Lymphoma. 1-6. PMID 31288594 DOI: 10.1080/10428194.2019.1630620  0.359
2019 Sato H, Wu B, Delahaye F, Singer RH, Greally JM. Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains. The Journal of Cell Biology. PMID 31110057 DOI: 10.1083/Jcb.201811109  0.425
2019 Kong Y, Rastogi D, Seoighe C, Greally JM, Suzuki M. Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data. Plos One. 14: e0215987. PMID 31022271 DOI: 10.1371/Journal.Pone.0215987  0.415
2019 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. Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells. Nature Cell Biology. PMID 30988422 DOI: 10.1038/S41556-019-0308-3  0.322
2019 Piqué DG, Montagna C, Greally JM, Mar JC. A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma. British Journal of Cancer. PMID 30820027 DOI: 10.1038/S41416-019-0387-8  0.359
2019 Shenoy N, Bhagat TD, Cheville JC, Lohse C, Bhattacharyya S, Tischer A, Machha V, Gordon-Mitchell S, Choudhary GS, Wong LF, Gross L, Ressegue E, Leibovich BC, Boorjian SA, Steidl U, ... ... Greally JM, et al. Ascorbic acid-induced TET activation mitigates adverse hydroxymethylcystosine loss in renal cell carcinoma. The Journal of Clinical Investigation. PMID 30702441 DOI: 10.1172/Jci98747  0.387
2019 Nakahara F, Pinho S, Borger DK, Wei Q, Maryanovich M, Zahalka AH, Suzuki M, Cruz C, Wang Z, Xu C, Boulais P, Ma'ayan A, Greally JM, Frenette PS. Engineering a Hematopoietic Stem Cell Niche By Revitalizing Mesenchymal Stem Cells with Five Transcription Factors Blood. 134: 5004-5004. DOI: 10.1182/Blood-2019-125045  0.339
2019 Nakahara F, Borger D, Wei Q, Pinho S, Maryanovich M, Zahalka A, Suzuki M, Cruz C, Wang Z, Xu C, Boulais P, Ma'ayan A, Greally J, Frenette P. 2011 - ENGINEERING A HEMATOPOIETIC STEM CELL NICHE BY REVITALIZING MESENCHYMAL STEM CELLS Experimental Hematology. 76: S45. DOI: 10.1016/J.Exphem.2019.06.285  0.322
2018 Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM. Whole-genome bisulfite sequencing with improved accuracy and cost. Genome Research. PMID 30093547 DOI: 10.1101/Gr.232587.117  0.518
2018 Bartholdy B, Lajugie J, Yan Z, Zhang S, Mukhopadhyay R, Greally JM, Suzuki M, Bouhassira EE. Mechanisms of establishment and functional significance of DNA demethylation during erythroid differentiation. Blood Advances. 2: 1833-1852. PMID 30061308 DOI: 10.1182/Bloodadvances.2018015651  0.512
2018 Seoighe C, Tosh NJ, Greally JM. DNA methylation haplotypes as cancer markers. Nature Genetics. PMID 30054597 DOI: 10.1038/S41588-018-0185-X  0.427
2018 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, ... ... Greally JM, et al. The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma. Jci Insight. 3. PMID 30046005 DOI: 10.1172/Jci.Insight.120422  0.307
2018 Battachariyya S, Tytarenko R, Heuck C, Greally J, Verma A. Genome Wide Mapping of Methylated and Hydroxyl-Methylated Cytosines Using a Modified HpaII Tiny Fragment Enrichment by Ligation Mediated PCR Tagged Sequencing Protocol. Methods in Molecular Biology (Clifton, N.J.). 1792: 167-177. PMID 29797259 DOI: 10.1007/978-1-4939-7865-6_12  0.411
2018 Kong Y, Berko ER, Marckette A, Maqbool SB, Simões-Pires CA, Kronn DF, Ye QK, Suzuki M, Auton A, Greally J. Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq. Genome Research. PMID 29773658 DOI: 10.1101/Gr.226282.117  0.355
2018 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. Selective modulation of local linkages between active transcription and oxidative demethylation activity shapes cardiomyocyte-specific gene-body epigenetic status in mice. Bmc Genomics. 19: 349. PMID 29747586 DOI: 10.1186/S12864-018-4752-4  0.435
2018 Greally JM. The HELP-Based DNA Methylation Assays. Methods in Molecular Biology (Clifton, N.J.). 1708: 191-207. PMID 29224146 DOI: 10.1007/978-1-4939-7481-8_11  0.489
2018 Giricz O, Mo Y, Dahlman KB, Cotto-Rios XM, Vardabasso C, Nguyen H, Matusow B, Bartenstein M, Polishchuck-Lee V, Johnson DB, Bhagat TB, Shellooe R, Burton E, Habets G, Greally JM, et al. Abstract 2515: Aberrant expression of CSF1R in melanoma is driven through an endogenous viral promoter and it contributes to malignant growth and BRAF-inhibitor resistance Cancer Research. 78: 2515-2515. DOI: 10.1158/1538-7445.Am2018-2515  0.346
2017 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, et al. Development and validation of a targeted next generation DNA sequencing panel outperforming whole exome sequencing for the identification of clinically relevant genetic variants. Oncotarget. 8: 102033-102045. PMID 29254223 DOI: 10.18632/Oncotarget.22116  0.353
2017 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, et al. Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways. Genome Research. PMID 28986391 DOI: 10.1101/Gr.222794.117  0.435
2017 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, et al. Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop. Regulatory Toxicology and Pharmacology : Rtp. PMID 28958911 DOI: 10.1016/J.Yrtph.2017.09.002  0.308
2017 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. In Utero Exposure to a High-Fat Diet Programs Hepatic Hypermethylation and Gene Dysregulation and Development of Metabolic Syndrome in Male Mice. Endocrinology. 158: 2860-2872. PMID 28911167 DOI: 10.1210/En.2017-00334  0.445
2017 Bhagat T, Chen S, Bartenstein M, Barlowe TS, von Ahrens D, Choudhary GS, Tivnan P, Amin E, Marcondes AM, Sanders MA, Hoogenboezem RM, Kambhampati S, Ramachandra N, Mantzaris I, Sukrithan V, ... ... Greally J, et al. Wnt/ß-catenin activation by epigenetically aberrant stroma drives myelodysplastic syndrome. Cancer Research. PMID 28684528 DOI: 10.1158/0008-5472.Can-17-0282  0.392
2017 Do C, Shearer A, Suzuki M, Terry MB, Gelernter J, Greally JM, Tycko B. Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era. Genome Biology. 18: 120. PMID 28629478 DOI: 10.1186/S13059-017-1250-Y  0.432
2017 Barnicle A, Seoighe C, Greally JM, Golden A, Egan LJ. Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis. Epigenetics. 0. PMID 28557546 DOI: 10.1080/15592294.2017.1334023  0.493
2017 Lappalainen T, Greally JM. Associating cellular epigenetic models with human phenotypes. Nature Reviews. Genetics. 18: 441-451. PMID 28555657 DOI: 10.1038/Nrg.2017.32  0.429
2017 Wijetunga NA, Johnston AD, Maekawa R, Delahaye F, Ulahannan N, Kim K, Greally JM. SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. Bmc Bioinformatics. 18: 41. PMID 28100166 DOI: 10.1186/S12859-017-1477-3  0.402
2017 Giricz O, Mo Y, Hu CY, Yu Y, Pradhan K, Bartenstein M, Ramachandra N, Polishchuck V, Dahlman KB, Bhagat T, Nguyen H, Matusow B, Shellooe R, Burton E, Kenny P, ... Greally J, et al. Abstract 3332: Aberrant expression of CSF1R in melanoma is driven through an endogenous viral promoter and it contributes to malignant growth and the acquisition of resistance against BRAF inhibition Cancer Research. 77: 3332-3332. DOI: 10.1158/1538-7445.Am2017-3332  0.35
2016 Zhang D, Wu B, Wang P, Wang Y, Lu P, Nechiporuk T, Floss T, Greally JM, Zheng D, Zhou B. Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts. Nucleic Acids Research. PMID 27956497 DOI: 10.1093/Nar/Gkw1258  0.477
2016 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, ... ... Greally JM, et al. Notch pathway is activated via genetic and epigenetic alterations and is a therapeutic target in clear cell renal cancer. The Journal of Biological Chemistry. PMID 27909050 DOI: 10.1074/Jbc.M116.745208  0.403
2016 Acosta D, Bagchi S, Broin PÓ, Hollern D, Racedo SE, Morrow B, Sellers RS, Greally JM, Golden A, Andrechek E, Wood T, Montagna C. LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development. Scientific Reports. 6: 35810. PMID 27808166 DOI: 10.1038/Srep35810  0.332
2016 Wijetunga NA, Ben-Dayan M, Tozour J, Burk RD, Schlecht NF, Einstein MH, Greally JM. A polycomb-mediated epigenetic field defect precedes invasive cervical carcinoma. Oncotarget. PMID 27557505 DOI: 10.18632/Oncotarget.11390  0.423
2016 Henikoff S, Greally JM. Epigenetics, cellular memory and gene regulation. Current Biology : Cb. 26: R644-8. PMID 27458904 DOI: 10.1016/J.Cub.2016.06.011  0.35
2016 Khrapunov S, Tao Y, Cheng H, Padlan CF, Harris R, Galanopoulou AS, Greally JM, Girvin ME, Brenowitz MD. MeCP2 binding cooperativity inhibits DNA modification specific recognition. Biochemistry. PMID 27420643 DOI: 10.1021/Acs.Biochem.6B00451  0.324
2016 Wijetunga NA, Belbin TJ, Burk RD, Whitney K, Abadi M, Greally JM, Einstein MH, Schlecht NF. Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia. Gynecologic Oncology. PMID 27401842 DOI: 10.1016/J.Ygyno.2016.07.006  0.426
2016 Birney E, Smith GD, Greally JM. Epigenome-wide Association Studies and the Interpretation of Disease -Omics. Plos Genetics. 12: e1006105. PMID 27336614 DOI: 10.1371/Journal.Pgen.1006105  0.38
2016 Suzuki M, Maekawa R, Patterson NE, Reynolds DM, Calder BR, Reznik SE, Heo HJ, Einstein FH, Greally JM. Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus. Clinical Epigenetics. 8: 67. PMID 27293492 DOI: 10.1186/S13148-016-0234-1  0.375
2016 Yuan Z, Claros CS, 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, ... ... Greally JM, et al. Loss of MEN1 activates DNMT1 implicating DNA hypermethylation as a driver of MEN1 tumorigenesis. Oncotarget. PMID 26871472 DOI: 10.18632/Oncotarget.7279  0.4
2016 Barnicle A, Seoighe C, Golden A, Greally JM, Egan LJ. Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells. Physiological Genomics. physiolgenomics.0004. PMID 26812987 DOI: 10.1152/Physiolgenomics.00046.2015  0.416
2016 Giricz O, Mo Y, Hu CH, Dahlman K, Ramachandra N, Bartenstein M, Pradhan K, Bhagat T, Yu Y, Nguyen H, Burton E, Matusow B, Habets G, Shellooe R, Bollag G, ... ... Greally J, et al. Abstract 1885: Integrated epigenomic profiling reveals widespread demethylation in melanoma and points to the role of CSF1R-RUNX1 axis in resistance against BRAF inhibition Cancer Research. 76: 1885-1885. DOI: 10.1158/1538-7445.Am2016-1885  0.368
2016 Wijetunga NA, Pascual M, Tozour J, Delahaye F, Alani M, Adeyeye M, Wolkoff AW, Verma A, Greally JM. A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets Oncogene. DOI: 10.1038/Onc.2016.340  0.416
2015 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. RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships. Epigenetics & Chromatin. 8: 46. PMID 26579211 DOI: 10.1186/S13072-015-0040-6  0.358
2015 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. Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. Nucleic Acids Research. 43: e81. PMID 25813045 DOI: 10.1093/Nar/Gkv244  0.425
2015 Ramos MP, Wijetunga NA, McLellan AS, Suzuki M, Greally JM. DNA demethylation by 5-aza-2'-deoxycytidine is imprinted, targeted to euchromatin, and has limited transcriptional consequences. Epigenetics & Chromatin. 8: 11. PMID 25806086 DOI: 10.1186/S13072-015-0004-X  0.501
2015 Ulahannan N, Greally JM. Genome-wide assays that identify and quantify modified cytosines in human disease studies. Epigenetics & Chromatin. 8: 5. PMID 25788985 DOI: 10.1186/1756-8935-8-5  0.519
2015 Berko ER, Greally JM. How might epigenetic dysregulation in early embryonic life contribute to autism spectrum disorder? Epigenomics. 7: 1-4. PMID 25687459 DOI: 10.2217/Epi.14.86  0.43
2015 Rosenblum JM, Wijetunga NA, Fazzari MJ, Krailo M, Barkauskas DA, Gorlick R, Greally JM. Predictive properties of DNA methylation patterns in primary tumor samples for osteosarcoma relapse status. Epigenetics. 10: 31-9. PMID 25531418 DOI: 10.4161/15592294.2014.989084  0.502
2015 Giricz O, Mo Y, Hu C, Dahlman K, Bhattacharyya S, Nguyen H, Matusow B, Bhagat T, Yu Y, Shellooe R, Burton E, Habets G, Greally J, Paraic K, Sosman J, et al. Abstract PR06: Integrated epigenomic profiling reveals widespread demethylation in melanoma and reveals CSF-1 Receptor as an aberrant regulator of malignant growth and invasion Cancer Research. 74: 4781-4781. DOI: 10.1158/1538-7445.Mel2014-Pr06  0.428
2015 Chadwick LH, Sawa A, Yang IV, Baccarelli A, Breakefield XO, Deng HW, Dolinoy DC, Fallin MD, Holland NT, Houseman EA, Lomvardas S, Rao M, Satterlee JS, Tyson FL, Vijayanand P, ... Greally JM, et al. New insights and updated guidelines for epigenome-wide association studies Neuroepigenetics. 1: 14-19. DOI: 10.1016/J.Nepig.2014.10.004  0.398
2014 Wijetunga NA, Delahaye F, Zhao YM, Golden A, Mar JC, Einstein FH, Greally JM. The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences. Nature Communications. 5: 5195. PMID 25327398 DOI: 10.1038/Ncomms6195  0.439
2014 Delahaye F, Wijetunga NA, Heo HJ, Tozour JN, Zhao YM, Greally JM, Einstein FH. Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth Nature Communications. 5. PMID 25300954 DOI: 10.1038/Ncomms6187  0.343
2014 Pascual M, Roa S, García-Sánchez A, Sanz C, Hernandez-Hernandez L, Greally JM, Lorente F, Dávila I, Isidoro-García M. Genome-wide expression profiling of B lymphocytes reveals IL4R increase in allergic asthma. The Journal of Allergy and Clinical Immunology. 134: 972-5. PMID 24975796 DOI: 10.1016/J.Jaci.2014.05.015  0.308
2014 Chamberlain AA, Lin M, Lister RL, Maslov AA, Wang Y, Suzuki M, Wu B, Greally JM, Zheng D, Zhou B. DNA methylation is developmentally regulated for genes essential for cardiogenesis. Journal of the American Heart Association. 3: e000976. PMID 24947998 DOI: 10.1161/Jaha.114.000976  0.504
2014 Hu CY, Mohtat D, Yu Y, Ko YA, Shenoy N, Bhattacharya S, Izquierdo MC, Park AS, Giricz O, Vallumsetla N, Gundabolu K, Ware K, Bhagat TD, Suzuki M, Pullman J, ... ... Greally JM, et al. Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 20: 4349-60. PMID 24916699 DOI: 10.1158/1078-0432.Ccr-14-0494  0.466
2014 Berko ER, Suzuki M, Beren F, Lemetre C, Alaimo CM, Calder RB, Ballaban-Gil K, Gounder B, Kampf K, Kirschen J, Maqbool SB, Momin Z, Reynolds DM, Russo N, Shulman L, ... ... Greally JM, et al. Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. Plos Genetics. 10: e1004402. PMID 24875834 DOI: 10.1371/Journal.Pgen.1004402  0.475
2014 Khrapunov S, Warren C, Cheng H, Berko ER, Greally JM, Brenowitz M. Unusual characteristics of the DNA binding domain of epigenetic regulatory protein MeCP2 determine its binding specificity. Biochemistry. 53: 3379-91. PMID 24828757 DOI: 10.1021/Bi500424Z  0.36
2014 Bartholdy B, Christopeit M, Will B, Mo Y, Barreyro L, Yu Y, Bhagat TD, Okoye-Okafor UC, Todorova TI, Greally JM, Levine RL, Melnick A, Verma A, Steidl U. HSC commitment-associated epigenetic signature is prognostic in acute myeloid leukemia. The Journal of Clinical Investigation. 124: 1158-67. PMID 24487588 DOI: 10.1172/Jci71264  0.487
2014 Bhagat TD, Bartenstein M, Yu Y, Marcondes AMQ, Will B, Giricz O, Sohal DP, Mantzaris I, Wickrema A, Mcmahon C, Cecilia Y, Greally J, Mukherjee S, Steidl U, Deeg HJ, et al. Myelodysplastic Syndrome Marrow Stroma Shows Widespread Aberrant Hypermethylation That Is Abrogated By Treatment with Dnmt Inhibitors Blood. 124: 4379-4379. DOI: 10.1182/Blood.V124.21.4379.4379  0.514
2013 Dunican DS, Cruickshanks HA, Suzuki M, Semple CA, Davey T, Arceci RJ, Greally J, Adams IR, Meehan RR. Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. Genome Biology. 14: R146. PMID 24367978 DOI: 10.1186/Gb-2013-14-12-R146  0.5
2013 Auton A, Rui Li Y, Kidd J, Oliveira K, Nadel J, Holloway JK, Hayward JJ, Cohen PE, Greally JM, Wang J, Bustamante CD, Boyko AR. Genetic recombination is targeted towards gene promoter regions in dogs. Plos Genetics. 9: e1003984. PMID 24348265 DOI: 10.1371/Journal.Pgen.1003984  0.405
2013 Greally JM, Jacobs MN. In vitro and in vivo testing methods of epigenomic endpoints for evaluating endocrine disruptors. Altex. 30: 445-71. PMID 24173168 DOI: 10.14573/Altex.2013.4.445  0.352
2013 Ko YA, Mohtat D, Suzuki M, Park AS, Izquierdo MC, Han SY, Kang HM, Si H, Hostetter T, Pullman JM, Fazzari M, Verma A, Zheng D, Greally JM, Susztak K. Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development. Genome Biology. 14: R108. PMID 24098934 DOI: 10.1186/Gb-2013-14-10-R108  0.368
2013 Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA. Recommendations for the design and analysis of epigenome-wide association studies. Nature Methods. 10: 949-55. PMID 24076989 DOI: 10.1038/Nmeth.2632  0.35
2013 Golden A, Djorgovski S, Greally JM. Astrogenomics: big data, old problems, old solutions? Genome Biology. 14: 129. PMID 23953643 DOI: 10.1186/Gb-2013-14-8-129  0.395
2013 Bhattacharyya S, Yu Y, Suzuki M, Campbell N, Mazdo J, Vasanthakumar A, Bhagat TD, Nischal S, Christopeit M, Parekh S, Steidl U, Godley L, Maitra A, Greally JM, Verma A. Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer. Nucleic Acids Research. 41: e157. PMID 23861445 DOI: 10.1093/Nar/Gkt601  0.448
2013 Ikeda R, Shiura H, Numata K, Sugimoto M, Kondo M, Mise N, Suzuki M, Greally JM, Abe K. Large, male germ cell-specific hypomethylated DNA domains with unique genomic and epigenomic features on the mouse X chromosome. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 20: 549-65. PMID 23861320 DOI: 10.1093/Dnares/Dst030  0.523
2013 Rastogi D, Suzuki M, Greally JM. Differential epigenome-wide DNA methylation patterns in childhood obesity-associated asthma. Scientific Reports. 3: 2164. PMID 23857381 DOI: 10.1038/Srep02164  0.398
2013 Gendrel AV, Tang YA, Suzuki M, Godwin J, Nesterova TB, Greally JM, Heard E, Brockdorff N. Epigenetic functions of smchd1 repress gene clusters on the inactive X chromosome and on autosomes. Molecular and Cellular Biology. 33: 3150-65. PMID 23754746 DOI: 10.1128/Mcb.00145-13  0.444
2013 Reddington JP, Perricone SM, Nestor CE, Reichmann J, Youngson NA, Suzuki M, Reinhardt D, Dunican DS, Prendergast JG, Mjoseng H, Ramsahoye BH, Whitelaw E, Greally JM, Adams IR, Bickmore WA, et al. Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biology. 14: R25. PMID 23531360 DOI: 10.1186/Gb-2013-14-3-R25  0.485
2013 Suzuki M, Greally JM. Genome-wide DNA methylation analysis using massively parallel sequencing technologies. Seminars in Hematology. 50: 70-7. PMID 23507485 DOI: 10.1053/J.Seminhematol.2013.01.002  0.51
2013 Greally JM. DNA methylation: Bidding the CpG island goodbye. Elife. 2: e00593. PMID 23467495 DOI: 10.7554/Elife.00593  0.471
2013 Heuck CJ, Mehta J, Bhagat T, Gundabolu K, Yu Y, Khan S, Chrysofakis G, Schinke C, Tariman J, Vickrey E, Pulliam N, Nischal S, Zhou L, Bhattacharyya S, Meagher R, ... ... Greally J, et al. Myeloma is characterized by stage-specific alterations in DNA methylation that occur early during myelomagenesis. Journal of Immunology (Baltimore, Md. : 1950). 190: 2966-75. PMID 23408834 DOI: 10.4049/Jimmunol.1202493  0.474
2013 Wu W, Bhagat TD, Yang X, Song JH, Cheng Y, Agarwal R, Abraham JM, Ibrahim S, Bartenstein M, Hussain Z, Suzuki M, Yu Y, Chen W, Eng C, Greally J, et al. Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1, in Barrett's esophagus and esophageal adenocarcinoma. Gastroenterology. 144: 956-966.e4. PMID 23333711 DOI: 10.1053/J.Gastro.2013.01.019  0.431
2013 Yu Y, Mo Y, Ebenezer D, Bhattacharyya S, Liu H, Sundaravel S, Giricz O, Wontakal S, Cartier J, Caces B, Artz A, Nischal S, Bhagat T, Bathon K, Maqbool S, ... ... Greally J, et al. High resolution methylome analysis reveals widespread functional hypomethylation during adult human erythropoiesis. The Journal of Biological Chemistry. 288: 8805-14. PMID 23306203 DOI: 10.1074/Jbc.M112.423756  0.485
2013 Nischal S, Bhattacharyya S, Christopeit M, Yu Y, Zhou L, Bhagat TD, Sohal D, Will B, Mo Y, Suzuki M, Pardanani A, McDevitt M, Maciejewski JP, Melnick AM, Greally JM, et al. Methylome profiling reveals distinct alterations in phenotypic and mutational subgroups of myeloproliferative neoplasms. Cancer Research. 73: 1076-85. PMID 23066032 DOI: 10.1158/0008-5472.Can-12-0735  0.497
2013 Mo Y, Giricz O, Hu C, Dahlman K, Bhattacharyya S, Nguyen H, Matusow B, Bhagat T, Yu Y, Shellooe R, Burton E, Habets G, Greally J, Kenny P, Sosman J, et al. Abstract A26: Integrated epigenomic profiling reveals widespread demethylation in melanoma, and reveals aberrant CSF-1 receptor expression as a regulator of malignant growth and invasion inhibited by PLX3397 Cancer Research. 73. DOI: 10.1158/1538-7445.Tim2013-A26  0.374
2013 Bhattacharyya S, Yu Y, Suzuki M, Cambpell N, Mazdo J, Vasantkumar A, Bhagat TD, Nischal S, Steidl U, Godley L, Maitra A, Greally JM, Verma A. Abstract 4231: Genome wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer. Cancer Research. 73: 4231-4231. DOI: 10.1158/1538-7445.Am2013-4231  0.47
2013 Bhagat TD, Rattigan Y, Patel B, Mirte S, Yu Y, Sohal D, Bartenstein M, Giricz O, Gordon SA, Vallumsetla N, Polineni R, Walia M, Kenny P, Greally J, Banerjee D, et al. Abstract 1504: Pancreatic cancer associated fibroblasts are characterized by widespread epigenetic reprogramming that leads to aberrant expression of druggable target CXCR4. Cancer Research. 73: 1504-1504. DOI: 10.1158/1538-7445.Am2013-1504  0.468
2013 Bhagat TD, Bartenstein M, Yu Y, Marcondes AM, Sohal D, Greally J, Deeg HJ, Verma A. Abstract 1503: Myelodysplasia bone marrow stromal cells have widespread aberrant hypermethylation that is targeted by treatment with DNMT inhibitors. Cancer Research. 73: 1503-1503. DOI: 10.1158/1538-7445.Am2013-1503  0.452
2013 Delio M, Patel K, Maslov A, Golden A, Greally J, Morrow B, Vijg J, Montagna C. Abstract P2-12-09: Developing clinical sequencing assays at Einstein-Montefiore Cancer Research. 73. DOI: 10.1158/0008-5472.Sabcs13-P2-12-09  0.33
2012 Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker JR, Greally JM, Issa JP, Laird PW, Polyak K, Tycko B, Jones PA. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Research. 72: 6319-24. PMID 23188507 DOI: 10.1158/0008-5472.Can-12-3658  0.33
2012 Golden A, McLellan AS, Dubin RA, Jing Q, O Broin P, Moskowitz D, Zhang Z, Suzuki M, Hargitai J, Calder RB, Greally JM. The Einstein Genome Gateway using WASP - a high throughput multi-layered life sciences portal for XSEDE. Studies in Health Technology and Informatics. 175: 182-91. PMID 22942009 DOI: 10.3233/978-1-61499-054-3-182  0.328
2012 Das R, Anderson N, Koran MI, Weidman JR, Mikkelsen TS, Kamal M, Murphy SK, Linblad-Toh K, Greally JM, Jirtle RL. Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica. Bmc Genomics. 13: 394. PMID 22899817 DOI: 10.1186/1471-2164-13-394  0.444
2012 Will B, Zhou L, Vogler TO, Ben-Neriah S, Schinke C, Tamari R, Yu Y, Bhagat TD, Bhattacharyya S, Barreyro L, Heuck C, Mo Y, Parekh S, McMahon C, Pellagatti A, ... ... Greally JM, et al. Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterations. Blood. 120: 2076-86. PMID 22753872 DOI: 10.1182/Blood-2011-12-399683  0.337
2012 Hanoun M, Eisele L, Suzuki M, Greally JM, Hüttmann A, Aydin S, Scholtysik R, Klein-Hitpass L, Dührsen U, Dürig J. Epigenetic silencing of the circadian clock gene CRY1 is associated with an indolent clinical course in chronic lymphocytic leukemia. Plos One. 7: e34347. PMID 22470559 DOI: 10.1371/Journal.Pone.0034347  0.432
2012 Noh KM, Hwang JY, Follenzi A, Athanasiadou R, Miyawaki T, Greally JM, Bennett MV, Zukin RS. Repressor element-1 silencing transcription factor (REST)-dependent epigenetic remodeling is critical to ischemia-induced neuronal death. Proceedings of the National Academy of Sciences of the United States of America. 109: E962-71. PMID 22371606 DOI: 10.1073/Pnas.1121568109  0.411
2012 Jing Q, McLellan A, Greally JM, Suzuki M. Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays. Methods in Molecular Biology (Clifton, N.J.). 815: 79-87. PMID 22130985 DOI: 10.1007/978-1-61779-424-7_7  0.472
2012 Smith AC, Suzuki M, Thompson R, Choufani S, Higgins MJ, Chiu IW, Squire JA, Greally JM, Weksberg R. Maternal gametic transmission of translocations or inversions of human chromosome 11p15.5 results in regional DNA hypermethylation and downregulation of CDKN1C expression. Genomics. 99: 25-35. PMID 22079941 DOI: 10.1016/J.Ygeno.2011.10.007  0.68
2011 Pascual M, Suzuki M, Isidoro-Garcia M, Padrón J, Turner T, Lorente F, Dávila I, Greally JM. Epigenetic changes in B lymphocytes associated with house dust mite allergic asthma. Epigenetics : Official Journal of the Dna Methylation Society. 6: 1131-7. PMID 21975512 DOI: 10.4161/Epi.6.9.16061  0.459
2011 Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, Agyiri F, Thompson RF, Glass JL, Jing Q, Sandstrom R, Fazzari MJ, Hansen RS, Stamatoyannopoulos JA, McLellan AS, ... Greally JM, et al. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Research. 21: 1833-40. PMID 21957152 DOI: 10.1101/Gr.116509.110  0.735
2011 Thomas BJ, Rubio ED, Krumm N, Broin PO, Bomsztyk K, Welcsh P, Greally JM, Golden AA, Krumm A. Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene. Epigenetics & Chromatin. 4: 14. PMID 21812971 DOI: 10.1186/1756-8935-4-14  0.45
2011 Zhou L, Opalinska J, Sohal D, Yu Y, Mo Y, Bhagat T, Abdel-Wahab O, Fazzari M, Figueroa M, Alencar C, Zhang J, Kambhampati S, Parmar S, Nischal S, Hueck C, ... ... Greally JM, et al. Aberrant epigenetic and genetic marks are seen in myelodysplastic leukocytes and reveal Dock4 as a candidate pathogenic gene on chromosome 7q. The Journal of Biological Chemistry. 286: 25211-23. PMID 21532034 DOI: 10.1074/Jbc.M111.235028  0.419
2011 Alvarez H, Opalinska J, Zhou L, Sohal D, Fazzari MJ, Yu Y, Montagna C, Montgomery EA, Canto M, Dunbar KB, Wang J, Roa JC, Mo Y, Bhagat T, Ramesh KH, ... ... Greally JM, et al. Widespread hypomethylation occurs early and synergizes with gene amplification during esophageal carcinogenesis. Plos Genetics. 7: e1001356. PMID 21483804 DOI: 10.1371/Journal.Pgen.1001356  0.731
2011 Acosta D, Suzuki M, Connolly D, Thompson RF, Fazzari MJ, Greally JM, Montagna C. DNA methylation changes in murine breast adenocarcinomas allow the identification of candidate genes for human breast carcinogenesis. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 22: 249-59. PMID 21373886 DOI: 10.1007/S00335-011-9318-6  0.647
2011 Lugthart S, Figueroa ME, Bindels E, Skrabanek L, Valk PJ, Li Y, Meyer S, Erpelinck-Verschueren C, Greally J, Löwenberg B, Melnick A, Delwel R. Aberrant DNA hypermethylation signature in acute myeloid leukemia directed by EVI1. Blood. 117: 234-41. PMID 20855866 DOI: 10.1182/Blood-2010-04-281337  0.501
2010 Sharma A, Heuck CJ, Fazzari MJ, Mehta J, Singhal S, Greally JM, Verma A. DNA methylation alterations in multiple myeloma as a model for epigenetic changes in cancer. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 654-69. PMID 20890963 DOI: 10.1002/Wsbm.89  0.533
2010 Fazzari MJ, Greally JM. Introduction to epigenomics and epigenome-wide analysis. Methods in Molecular Biology (Clifton, N.J.). 620: 243-65. PMID 20652507 DOI: 10.1007/978-1-60761-580-4_7  0.531
2010 Shaknovich R, Geng H, Johnson NA, Tsikitas L, Cerchietti L, Greally JM, Gascoyne RD, Elemento O, Melnick A. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood. 116: e81-9. PMID 20610814 DOI: 10.1182/Blood-2010-05-285320  0.495
2010 Thompson RF, Atzmon G, Gheorghe C, Liang HQ, Lowes C, Greally JM, Barzilai N. Tissue-specific dysregulation of DNA methylation in aging. Aging Cell. 9: 506-18. PMID 20497131 DOI: 10.1111/J.1474-9726.2010.00577.X  0.767
2010 Suzuki M, Greally JM. DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR (HELP). Methods. 52: 218-222. PMID 20434563 DOI: 10.1016/J.Ymeth.2010.04.013  0.486
2010 Schinke C, Mo Y, Yu Y, Amiri K, Sosman J, Greally J, Verma A. Aberrant DNA methylation in malignant melanoma Melanoma Research. 20: 253-265. PMID 20418788 DOI: 10.1097/Cmr.0B013E328338A35A  0.481
2010 Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally JM. Optimized design and data analysis of tag-based cytosine methylation assays. Genome Biology. 11: R36. PMID 20359321 DOI: 10.1186/Gb-2010-11-4-R36  0.467
2010 Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X, Wen D, Chapgier A, DeKelver RC, Miller JC, Lee YL, ... ... Greally JM, et al. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell. 140: 678-91. PMID 20211137 DOI: 10.1016/J.Cell.2010.01.003  0.358
2010 Thompson RF, Fazzari MJ, Niu H, Barzilai N, Simmons RA, Greally JM. Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats. The Journal of Biological Chemistry. 285: 15111-8. PMID 20194508 DOI: 10.1074/Jbc.M109.095133  0.744
2010 Einstein F, Thompson RF, Bhagat TD, Fazzari MJ, Verma A, Barzilai N, Greally JM. Cytosine methylation dysregulation in neonates following intrauterine growth restriction. Plos One. 5: e8887. PMID 20126273 DOI: 10.1371/Journal.Pone.0008887  0.704
2010 Thompson RF, Fazzari MJ, Greally JM. Experimental approaches to the study of epigenomic dysregulation in ageing. Experimental Gerontology. 45: 255-68. PMID 20060885 DOI: 10.1016/J.Exger.2009.12.013  0.573
2010 Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ, Schifano E, Booth J, van Putten W, Skrabanek L, Campagne F, Mazumdar M, Greally JM, Valk PJ, Löwenberg B, et al. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell. 17: 13-27. PMID 20060365 DOI: 10.1016/J.Ccr.2009.11.020  0.479
2010 Nischal S, Zhou L, Yu Y, Bhagat T, Mo Y, Heuck C, Suzuki M, Maqbool S, Pardanani A, Greally J, Moliterno A, Verma A. Epigenomic Profiling of Myeloproliferative Diseases Reveal Idiopathic Myelofibrosis as An Epigenetically Distinct Subgroup and Highlights the Epigenetic Effects of Jak2V617F Mutation Blood. 116: 627-627. DOI: 10.1182/Blood.V116.21.627.627  0.476
2009 McLellan AS, Dubin RA, Jing Q, Maqbool SB, Olea R, Westby G, Broin PÓ, Fazzari MJ, Zheng D, Suzuki M, Greally JM. The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease. Epigenomics. 1: 33-8. PMID 22122636 DOI: 10.2217/Epi.09.9  0.385
2009 Morey Kinney SR, Zhang W, Pascual M, Greally JM, Gillard BM, Karasik E, Foster BA, Karpf AR. Lack of evidence for green tea polyphenols as DNA methylation inhibitors in murine prostate. Cancer Prevention Research (Philadelphia, Pa.). 2: 1065-75. PMID 19934341 DOI: 10.1158/1940-6207.Capr-09-0010  0.424
2009 Glass JL, Fazzari MJ, Ferguson-Smith AC, Greally JM. CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domains. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 20: 633-43. PMID 19921333 DOI: 10.1007/S00335-009-9232-3  0.493
2009 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. 114: 3448-58. PMID 19652201 DOI: 10.1182/Blood-2009-01-200519  0.504
2009 Thompson RF, Suzuki M, Lau KW, Greally JM. A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Bioinformatics (Oxford, England). 25: 2164-70. PMID 19561019 DOI: 10.1093/Bioinformatics/Btp382  0.701
2009 Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L, Green RD, Melnick A, Hatchwell E, Bouhassira EE, Verma A, ... ... Greally JM, et al. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Research. 37: 3829-39. PMID 19386619 DOI: 10.1093/Nar/Gkp260  0.698
2009 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 in Molecular Biology (Clifton, N.J.). 538: 395-407. PMID 19277580 DOI: 10.1007/978-1-59745-418-6_20  0.555
2009 Figueroa ME, Wouters BJ, Skrabanek L, Glass J, Li Y, Erpelinck-Verschueren CA, Langerak AW, Löwenberg B, Fazzari M, Greally JM, Valk PJ, Melnick A, Delwel R. Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features. Blood. 113: 2795-804. PMID 19168792 DOI: 10.1182/Blood-2008-08-172387  0.514
2009 Oda M, Greally JM. The HELP assay. Methods of Molecular Biology. 507: 77-87. PMID 18987808 DOI: 10.1007/978-1-59745-522-0_7  0.483
2009 Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ, Schifano E, Booth J, Skrabanek L, Campagne F, Mazumdar M, Greally J, Valk P, Lowenberg B, Delwel R, et al. DNA Methylation Profiling Predicts Clinical Outcomes and Reveals Unique Insights Into the Molecular Complexity of Acute Myeloid Leukemia. Blood. 114: 707-707. DOI: 10.1182/Blood.V114.22.707.707  0.438
2008 Lopes EC, Valls E, Figueroa ME, Mazur A, Meng FG, Chiosis G, Laird PW, Schreiber-Agus N, Greally JM, Prokhortchouk E, Melnick A. Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell lines. Cancer Research. 68: 7258-63. PMID 18794111 DOI: 10.1158/0008-5472.Can-08-0344  0.498
2008 Jeddeloh JA, Greally JM, Rando OJ. Reduced-representation methylation mapping. Genome Biology. 9: 231. PMID 18771577 DOI: 10.1186/Gb-2008-9-8-231  0.485
2008 Sohal D, Yeatts A, Ye K, Pellagatti A, Zhou L, Pahanish P, Mo Y, Bhagat T, Mariadason J, Boultwood J, Melnick A, Greally J, Verma A. Meta-analysis of microarray studies reveals a novel hematopoietic progenitor cell signature and demonstrates feasibility of inter-platform data integration. Plos One. 3: e2965. PMID 18698424 DOI: 10.1371/Journal.Pone.0002965  0.393
2008 Figueroa ME, Reimers M, Thompson RF, Ye K, Li Y, Selzer RR, Fridriksson J, Paietta E, Wiernik P, Green RD, Greally JM, Melnick A. An integrative genomic and epigenomic approach for the study of transcriptional regulation. Plos One. 3: e1882. PMID 18365023 DOI: 10.1371/Journal.Pone.0001882  0.709
2008 Thompson RF, Reimers M, Khulan B, Gissot M, Richmond TA, Chen Q, Zheng X, Kim K, Greally JM. An analytical pipeline for genomic representations used for cytosine methylation studies. Bioinformatics (Oxford, England). 24: 1161-7. PMID 18353789 DOI: 10.1093/Bioinformatics/Btn096  0.686
2008 Gissot M, Choi SW, Thompson RF, Greally JM, Kim K. Toxoplasma gondii and Cryptosporidium parvum lack detectable DNA cytosine methylation. Eukaryotic Cell. 7: 537-40. PMID 18178772 DOI: 10.1128/Ec.00448-07  0.691
2008 Figueroa ME, Greally J, Delwel R, Melnick AM. Genome-Wide Epigenetics in Myeloid Leukemias. Blood. 112: sci-35-sci-35. DOI: 10.1182/Blood.V112.11.Sci-35.Sci-35  0.549
2008 Sohal DP, Pellagati A, Zhou L, Mo Y, Opalinska JB, Alencar C, Heuck C, Wickrema A, Friedman E, Greally J, Ebert BL, Warner J, Boultwood J, Verma A. Downregulation of Ribosomal Proteins Is Seen in Non 5q- MDS Blood. 112: 854-854. DOI: 10.1182/Blood.V112.11.854.854  0.485
2008 Lugthart S, Figueroa ME, Valk PJ, Li Y, Erpelinck-Verschueren C, Greally J, Löwenberg B, Melnick A, Delwel R. Two Different EVI1 Expressing Poor-Risk AML Subgroups with Distinct Epigenetic Signatures Uncovered by Genome Wide DNA Methylation Profiling Blood. 112: 757-757. DOI: 10.1182/Blood.V112.11.757.757  0.514
2008 Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Christos PJ, Mazumdar M, Löwenberg B, Greally J, Valk PJ, Delwel R, Melnick A. Epigenetic Signatures Identify New Clinically Relevant Subtypes and Define Gene Regulatory Patterns in Patients with Acute Myeloid Leukemia (AML) Blood. 112: 756-756. DOI: 10.1182/Blood.V112.11.756.756  0.335
2008 Zhou L, Opalinska JB, Sohal DP, Mo Y, Kambhampati S, Parmar S, Alencar C, Heuck C, Vigoda I, Ng C, Pahanish P, Goel S, Schinke C, Cytryn L, Friedman E, ... ... Greally J, et al. Integrative Genomic Analysis Reveals Aberrant Epigenetic Marks in MDS That Can Be Seen in Peripheral Blood Leucocytes Blood. 112: 595-595. DOI: 10.1182/Blood.V112.11.595.595  0.538
2008 Bhagat TD, Spaulding E, Sohal D, Mo Y, Marcondes M, Zhou L, Thompson R, Greally J, Deeg HJ, Verma A. MDS Marrow Stroma Is Characterized by Distinct Epigenetic Alterations Blood. 112: 3635-3635. DOI: 10.1182/BLOOD.V112.11.3635.3635  0.373
2008 Einstein F, Thompson RF, Heo H, Budagov T, Atzmon G, Goffman D, Barzilai N, Montagna C, Greally JM. 600: Abnormal intrauterine growth induces global epigenetic changes in human stem cells American Journal of Obstetrics and Gynecology. 199: S173. DOI: 10.1016/J.Ajog.2008.09.630  0.678
2007 Suzuki M, Sato S, Arai Y, Shinohara T, Tanaka S, Greally JM, Hattori N, Shiota K. A new class of tissue-specifically methylated regions involving entire CpG islands in the mouse Genes to Cells. 12: 1305-1314. PMID 18076568 DOI: 10.1111/J.1365-2443.2007.01136.X  0.522
2007 Hatchwell E, Greally JM. The potential role of epigenomic dysregulation in complex human disease Trends in Genetics. 23: 588-595. PMID 17953999 DOI: 10.1016/J.Tig.2007.08.010  0.382
2007 Glass JL, Thompson RF, Khulan B, Figueroa ME, Olivier EN, Oakley EJ, Van Zant G, Bouhassira EE, Melnick A, Golden A, Fazzari MJ, Greally JM. CG dinucleotide clustering is a species-specific property of the genome. Nucleic Acids Research. 35: 6798-807. PMID 17932072 DOI: 10.1093/Nar/Gkm489  0.666
2007 Sakamoto H, Suzuki M, Abe T, Hosoyama T, Himeno E, Tanaka S, Greally JM, Hattori N, Yagi S, Shiota K. Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity. Genes to Cells. 12: 1123-1132. PMID 17903172 DOI: 10.1111/J.1365-2443.2007.01120.X  0.519
2007 Ferguson-Smith AC, Greally JM. Epigenetics: perceptive enzymes. Nature. 449: 148-9. PMID 17851501 DOI: 10.1038/449148A  0.443
2007 Greally JM. Genomics: Encyclopaedia of humble DNA Nature. 447: 782-783. PMID 17568731 DOI: 10.1038/447782A  0.437
2007 Gissot M, Kelly KA, Ajioka JW, Greally JM, Kim K. Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii. Plos Pathogens. 3: e77. PMID 17559302 DOI: 10.1371/Journal.Ppat.0030077  0.487
2007 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 Immunology. 8: 705-14. PMID 17558410 DOI: 10.1038/Ni1478  0.354
2007 Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, ... ... Greally JM, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 447: 167-77. PMID 17495919 DOI: 10.1038/Nature05805  0.372
2007 Polo JM, Juszczynski P, Monti S, Cerchietti L, Ye K, Greally JM, Shipp M, Melnick A. Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas. Proceedings of the National Academy of Sciences of the United States of America. 104: 3207-12. PMID 17360630 DOI: 10.1073/Pnas.0611399104  0.412
2007 Ikegami K, Iwatani M, Suzuki M, Tachibana M, Shinkai Y, Tanaka S, Greally JM, Yagi S, Hattori N, Shiota K. Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells. Genes to Cells : Devoted to Molecular & Cellular Mechanisms. 12: 1-11. PMID 17212651 DOI: 10.1111/J.1365-2443.2006.01029.X  0.489
2007 Sohal D, Yeatts A, Ye K, Pellagatti A, Zhou L, Pahanish P, Mariadason J, Melnick A, Greally J, Boultwood J, Verma A. Data Mining of Hematopoietic Stem Cell Microarray Studies Reveals a Novel Stem Cell Gene Expression Signature and Demonstrates Feasibility of Integrating Data from Different Labs and Different Microarray Platforms. Blood. 110: 4073-4073. DOI: 10.1182/Blood.V110.11.4073.4073  0.394
2007 Zhou L, Opalinska J, Sohal D, Thompson R, Li Y, Kotla V, Pahanish P, Parmar S, Kambhampati S, Figueroa M, Ye K, Friedman E, Wickrema A, Melnick A, Greally J, et al. Global Epigenomic Profiling Demonstrates That Myelodysplasia Is Characterized by a Distinct Epigenetic Signature with Aberrant DNA Methylation Changes Involving Various Malignant and Hematopoietic Pathways. Blood. 110: 2436-2436. DOI: 10.1182/Blood.V110.11.2436.2436  0.737
2007 Opalinska J, Daibata M, Sohal D, Zhou L, Thompson R, Pahanish P, Affer M, Figueroa M, Ye K, Greally J, Bai F, List A, Melnick A, Epling-Burnette P, Verma A. Integrated Epigenomic Profiling Reveals Aberrant DNA Hypomethylation in LGL and Demonstrates That a Combination of Genetic and Epigenetic Events Results in Leukemic Evolution in Model of Large Granular Lymphocytic Leukemia. Blood. 110: 2129-2129. DOI: 10.1182/Blood.V110.11.2129.2129  0.74
2007 Zhou D, Cui Q, Kim H, Thompson R, Greally J, Bouhassira EE, Gallagher RE. Increased Global Gene Promoter Methylation after Relapse (Rel) of Acute Promyelocytic Leukemia (APL) from All-trans Retinoic Acid (ATRA)-Containing Treatment Is Dissociated from Concurrent Gene Expression Changes. Blood. 110: 2121-2121. DOI: 10.1182/blood.v110.11.2121.2121  0.385
2007 Sohal D, Opalinska J, Zhou L, Pahanish P, Friedman E, Thompson R, Ye K, Figueroa M, Melnick A, Greally J, List A, Verma A. High Resolution Epigenomic Profiling of Loss of Heterozygosity in MDS Reveals an Important Role of DNA Methylation in Regulating Expression of Genes in the Deleted Regions of Chromosomes 5q, 7q and 20q. Blood. 110: 2120-2120. DOI: 10.1182/Blood.V110.11.2120.2120  0.72
2007 Opalinska J, Sohal D, Thompson R, Zhou L, Li Y, Pahanish P, Kotla V, Kambhampati S, Parmar S, Friedman E, Figueroa M, Ye K, Wickrema A, Melnick A, Greally J, et al. Global DNA Methylation Profiling Demonstrates That Idiopathic Myelofibrosis Is Characterized by a Distinct Epigenetic Signature with Aberrant Methylation Changes in Genes Involved in Inflammation and Hematopoiesis Blood. 110: 1536-1536. DOI: 10.1182/Blood.V110.11.1536.1536  0.74
2006 Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, ... Greally JM, et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Research. 16: 1046-55. PMID 16809668 DOI: 10.1101/Gr.5273806  0.72
2006 Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM. Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenetic and Genome Research. 114: 1-15. PMID 16717444 DOI: 10.1159/000091922  0.478
2006 Ryan M, Cerchietti L, Figueroa ME, Greally J, Melnick A. Sensitivity of Diffuse Large B-Cell Lymphomas to DNA Methyltransferase Inhibitors Is Associated with a Specific Epigenetic Signature. Blood. 108: 831-831. DOI: 10.1182/Blood.V108.11.831.831  0.456
2006 Figueroa ME, Ye K, Paietta E, Greally JM, Melnick AM. Epigenetic Signatures Accurately Distinguish Leukemia Subtypes and Provide a More Comprehensive Representation of Differentially Regulated Genes Than Gene Expression Profiling. Blood. 108: 735-735. DOI: 10.1182/Blood.V108.11.735.735  0.524
2006 Zhou D, Thompson R, Kim H, Greally J, Gallagher R. Lack of Increased Gene Promoter Methylation at Relapse in Acute Promyelocytic Leukemia (APL). Blood. 108: 4315-4315. DOI: 10.1182/BLOOD.V108.11.4315.4315  0.428
2006 Sohal D, Yeatts A, Opalinska J, Zhou L, Pahanish P, Ye K, Figueroa M, Mariadason J, Melnick A, Greally J, Verma A. Meta-Transcriptome of Bone Marrow Stem Cells Demonstrates Platform and Lab Dependant Variability in Gene Expression and Reveals a Novel Set of Enriched Genes. Blood. 108: 4189-4189. DOI: 10.1182/Blood.V108.11.4189.4189  0.391
2006 Opalinska J, Sohal D, Parmar S, Zhou L, Yeatts A, Pahanish P, Isulfi I, Ye K, Figueroa M, Melnick A, Greally J, Verma A. A High Resolution Epigenomic Map of Myelofibrosis Reveals Multiple Chromosomal Deletions and Amplifications Accompanied by a High Level of Functionally Important Methylation. Blood. 108: 2684-2684. DOI: 10.1182/Blood.V108.11.2684.2684  0.545
2006 Zhou L, Opalinska J, Sohal D, Parmar S, Pahanish P, Isulfi I, Ye K, Figueroa M, Greally J, Melnick A, Verma A. High Resolution Epigenomic Mapping of Myelodysplastic Syndrome Reveals a High Level of Functionally Important Methylation. Blood. 108: 2637-2637. DOI: 10.1182/Blood.V108.11.2637.2637  0.543
2006 Thompson RF, Figueroa ME, Melnick AM, Greally JM. Epigenetic Dysregulation of Candidate Cis-Regulatory Sequences in Hematological Malignancies. Blood. 108: 2229-2229. DOI: 10.1182/Blood.V108.11.2229.2229  0.715
2005 Stefan M, Claiborn KC, Stasiek E, Chai JH, Ohta T, Longnecker R, Greally JM, Nicholls RD. 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. 6: 157. PMID 16280085 DOI: 10.1186/1471-2164-6-157  0.305
2005 Kolas NK, Svetlanov A, Lenzi ML, Macaluso FP, Lipkin SM, Liskay RM, Greally J, Edelmann W, Cohen PE. Localization of MMR proteins on meiotic chromosomes in mice indicates distinct functions during prophase I. The Journal of Cell Biology. 171: 447-58. PMID 16260499 DOI: 10.1083/Jcb.200506170  0.316
2005 Figueroa ME, Ye KM, Paietta E, Greally JM, Melnick AM. An Integrated Epigenomic Analysis Approach To Determine the Molecular Basis of Acute Leukemias. Blood. 106: 3276-3276. DOI: 10.1182/Blood.V106.11.3276.3276  0.466
2004 Tsuchiya KD, Greally JM, Yi Y, Noel KP, Truong JP, Disteche CM. Comparative sequence and x-inactivation analyses of a domain of escape in human xp11.2 and the conserved segment in mouse. Genome Research. 14: 1275-84. PMID 15197169 DOI: 10.1101/Gr.2575904  0.35
2004 Fazzari MJ, Greally JM. EPIGENOMICS: BEYOND CpG ISLANDS Nature Reviews Genetics. 5: 446-455. PMID 15153997 DOI: 10.1038/Nrg1349  0.454
2003 Chai JH, Locke DP, Greally JM, Knoll JH, Ohta T, Dunai J, Yavor A, Eichler EE, Nicholls RD. 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. American Journal of Human Genetics. 73: 898-925. PMID 14508708 DOI: 10.1086/378816  0.396
2003 Bayarsaihan D, Enkhmandakh B, Makeyev A, Greally JM, Leckman JF, Ruddle FH. Homez, a homeobox leucine zipper gene specific to the vertebrate lineage. Proceedings of the National Academy of Sciences of the United States of America. 100: 10358-63. PMID 12925734 DOI: 10.1073/Pnas.1834010100  0.377
2003 Brown CJ, Greally JM. A stain upon the silence: genes escaping X inactivation Trends in Genetics. 19: 432-438. PMID 12902161 DOI: 10.1016/S0168-9525(03)00177-X  0.31
2003 Alami R, Fan Y, Pack S, Sonbuchner TM, Besse A, Lin Q, Greally JM, Skoultchi AI, Bouhassira EE. Mammalian linker-histone subtypes differentially affect gene expression in vivo. Proceedings of the National Academy of Sciences of the United States of America. 100: 5920-5. PMID 12719535 DOI: 10.1073/Pnas.0736105100  0.398
2003 State MW, Greally JM, Cuker A, Bowers PN, Henegariu O, Morgan TM, Gunel M, DiLuna M, King RA, Nelson C, Donovan A, Anderson GM, Leckman JF, Hawkins T, Pauls DL, et al. Epigenetic abnormalities associated with a chromosome 18(q21-q22) inversion and a Gilles de la Tourette syndrome phenotype. Proceedings of the National Academy of Sciences of the United States of America. 100: 4684-9. PMID 12682296 DOI: 10.1073/Pnas.0730775100  0.345
2002 Suphapeetiporn K, Greally JM, Walpita D, Ashley T, Bale AE. MEN1 tumor-suppressor protein localizes to telomeres during meiosis. Genes, Chromosomes & Cancer. 35: 81-5. PMID 12203793 DOI: 10.1002/Gcc.10113  0.319
2002 Neumeister P, Albanese C, Balent B, Greally J, Pestell RG. Senescence and epigenetic dysregulation in cancer. The International Journal of Biochemistry & Cell Biology. 34: 1475-90. PMID 12200040 DOI: 10.1016/S1357-2725(02)00079-1  0.499
2002 Kieffer LJ, Greally JM, Landres I, Nag S, Nakajima Y, Kohwi-Shigematsu T, Kavathas PB. 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. Journal of Immunology (Baltimore, Md. : 1950). 168: 3915-22. PMID 11937547 DOI: 10.4049/Jimmunol.168.8.3915  0.348
2002 Bayarsaihan D, Dunai J, Greally JM, Kawasaki K, Sumiyama K, Enkhmandakh B, Shimizu N, Ruddle FH. 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. Genomics. 79: 137-43. PMID 11827466 DOI: 10.1006/Geno.2001.6674  0.361
2002 Greally JM. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome Proceedings of the National Academy of Sciences of the United States of America. 99: 327-332. PMID 11756672 DOI: 10.1073/Pnas.012539199  0.452
2001 Chai JH, Locke DP, Ohta T, Greally JM, Nicholls RD. Retrotransposed genes such as Frat3 in the mouse Chromosome 7C Prader-Willi syndrome region acquire the imprinted status of their insertion site. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 12: 813-21. PMID 11845283 DOI: 10.1007/S00335-001-2083-1  0.431
2001 Feng YQ, Lorincz MC, Fiering S, Greally JM, Bouhassira EE. Position effects are influenced by the orientation of a transgene with respect to flanking chromatin. Molecular and Cellular Biology. 21: 298-309. PMID 11113204 DOI: 10.1128/Mcb.21.1.298-309.2001  0.441
2000 Alami R, Greally JM, Tanimoto K, Hwang S, Feng YQ, Engel JD, Fiering S, Bouhassira EE. β-globin YAC transgenes exhibit uniform expression levels but position effect variegation in mice Human Molecular Genetics. 9: 631-636. PMID 10699186 DOI: 10.1093/Hmg/9.4.631  0.359
1999 Greally JM, Gray TA, Gabriel JM, Song LQ, Zemel S, Nicholls RD. Conserved characteristics of heterochromatin-forming DNA at the 15q11- q13 imprinting center Proceedings of the National Academy of Sciences of the United States of America. 96: 14430-14435. PMID 10588722 DOI: 10.1073/Pnas.96.25.14430  0.363
1999 Greally JM, Lombroso PJ. Genetics of childhood disorders: VIII. Making sense out of nonsense. Journal of the American Academy of Child and Adolescent Psychiatry. 38: 1458-61. PMID 10560234 DOI: 10.1097/00004583-199911000-00022  0.418
1999 Greally JM. Genomic imprinting and chromatin insulation in Beckwith-Wiedemann syndrome. Molecular Biotechnology. 11: 159-173. PMID 10464770 DOI: 10.1007/Bf02915809  0.412
1999 Lin X, State MW, Vaccarino FM, Greally J, Hass M, Leckman JF. Identification, chromosomal assignment, and expression analysis of the human homeodomain-containing gene Orthopedia (OTP). Genomics. 60: 96-104. PMID 10458915 DOI: 10.1006/Geno.1999.5882  0.37
1998 Greally JM, Starr DJ, Hwang S, Song L, Jaarola M, Zemel S. The mouse H19 locus mediates a transition between imprinted and non-imprinted DNA replication patterns Human Molecular Genetics. 7: 91-95. PMID 9384608 DOI: 10.1093/Hmg/7.1.91  0.418
1997 Greally JM, Guinness ME, McGrath J, Zemel S. Matrix-attachment regions in the mouse chromosome 7F imprinted domain. Mammalian Genome. 8: 805-810. PMID 9337391 DOI: 10.1007/S003359900583  0.424
1996 Greally JM, Neiswanger K, Cummins JH, Boone LY, Lenkey SG, Wenger SL, Lewis JL, Fischer D, Paul RA, Steele MW. A molecular anatomical analysis of mosaic trisomy 16. Human Genetics. 98: 86-90. PMID 8682514 DOI: 10.1007/S004390050165  0.313
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