| Year |
Citation |
Score |
| 2024 |
Sayaman RW, Miyano M, Carlson EG, Senapati P, Zirbes A, Shalabi SF, Todhunter ME, Seewaldt VE, Neuhausen SL, Stampfer MR, Schones DE, LaBarge M. Luminal epithelial cells integrate variable responses to aging into stereotypical changes that underlie breast cancer susceptibility. Elife. 13. PMID 39545637 DOI: 10.7554/eLife.95720 |
0.658 |
|
| 2024 |
Vidal CM, Alva-Ornelas JA, Chen NZ, Senapati P, Tomsic J, Robles VM, Resto C, Sanchez N, Sanchez A, Hyslop T, Emwas N, Aljaber D, Bachelder N, Martinez E, Ann D, ... ... Schones D, et al. Insulin Resistance in Women Correlates with Chromatin Histone Lysine Acetylation, Inflammatory Signaling, and Accelerated Aging. Cancers. 16. PMID 39123463 DOI: 10.3390/cancers16152735 |
0.71 |
|
| 2023 |
Shin H, Leung A, Costello KR, Senapati P, Kato H, Moore RE, Lee M, Lin D, Tang X, Pirrotte P, Bouman Chen Z, Schones DE. Inhibition of DNMT1 methyltransferase activity via glucose-regulated -GlcNAcylation alters the epigenome. Elife. 12. PMID 37470704 DOI: 10.7554/eLife.85595 |
0.791 |
|
| 2023 |
Senapati P, Miyano M, Sayaman RW, Basam M, Leung A, LaBarge MA, Schones DE. Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells. Genome Research. PMID 37463750 DOI: 10.1101/gr.277511.122 |
0.789 |
|
| 2023 |
Dror E, Fagnocchi L, Wegert V, Apostle S, Grimaldi B, Gruber T, Panzeri I, Heyne S, Höffler KD, Kreiner V, Ching R, Tsai-Hsiu Lu T, Semwal A, Johnson B, Senapati P, ... ... Schones D, et al. Epigenetic dosage identifies two major and functionally distinct β cell subtypes. Cell Metabolism. PMID 36948185 DOI: 10.1016/j.cmet.2023.03.008 |
0.652 |
|
| 2021 |
Costello KR, Leung A, Trac C, Lee M, Basam M, Popsilik JA, Schones DE. Sequence features of retrotransposons allow for epigenetic variability. Elife. 10. PMID 34668484 DOI: 10.7554/eLife.71104 |
0.803 |
|
| 2020 |
Ishak Gabra MB, Yang Y, Li H, Senapati P, Hanse EA, Lowman XH, Tran TQ, Zhang L, Doan LT, Xu X, Schones DE, Fruman DA, Kong M. Dietary glutamine supplementation suppresses epigenetically-activated oncogenic pathways to inhibit melanoma tumour growth. Nature Communications. 11: 3326. PMID 32620791 DOI: 10.1038/S41467-020-17181-W |
0.678 |
|
| 2020 |
Jokela TA, Schones D, LaBarge MA. Abstract P6-03-04: Microenvironment-induced epigenetic reprogramming imposes drug-tolerant states in breast cancer cells Cancer Research. 80. DOI: 10.1158/1538-7445.Sabcs19-P6-03-04 |
0.625 |
|
| 2019 |
Senapati P, Kato H, Lee M, Leung A, Thai C, Sanchez A, Gallagher EJ, LeRoith D, Seewaldt VL, Ann DK, Schones DE. Hyperinsulinemia promotes aberrant histone acetylation in triple-negative breast cancer. Epigenetics & Chromatin. 12: 44. PMID 31315653 DOI: 10.1186/S13072-019-0290-9 |
0.739 |
|
| 2018 |
Cheng CT, Qi Y, Wang YC, Chi KK, Chung Y, Ouyang C, Chen YR, Oh ME, Sheng X, Tang Y, Liu YR, Lin HH, Kuo CY, Schones D, Vidal CM, et al. Arginine starvation kills tumor cells through aspartate exhaustion and mitochondrial dysfunction. Communications Biology. 1: 178. PMID 30393775 DOI: 10.1038/s42003-018-0178-4 |
0.744 |
|
| 2018 |
Leung A, Trac C, Kato H, Costello KR, Chen Z, Natarajan R, Schones DE. LTRs activated by Epstein-Barr virus-induced transformation of B cells alter the transcriptome. Genome Research. PMID 30381291 DOI: 10.1101/Gr.233585.117 |
0.784 |
|
| 2018 |
Das S, Reddy MA, Senapati P, Stapleton K, Lanting L, Wang M, Amaram V, Ganguly R, Zhang L, Devaraj S, Schones DE, Natarajan R. Diabetes Mellitus-Induced Long Noncoding RNA Regulates Macrophage Functions and Inflammation via Nuclear Mechanisms. Arteriosclerosis, Thrombosis, and Vascular Biology. PMID 29930005 DOI: 10.1161/Atvbaha.117.310663 |
0.641 |
|
| 2018 |
Li S, Ali S, Duan X, Liu S, Du J, Liu C, Dai H, Zhou M, Zhou L, Yang L, Chu P, Li L, Bhatia R, Schones DE, Wu X, et al. JMJD1B Demethylates H4R3me2s and H3K9me2 to Facilitate Gene Expression for Development of Hematopoietic Stem and Progenitor Cells. Cell Reports. 23: 389-403. PMID 29641999 DOI: 10.1016/J.Celrep.2018.03.051 |
0.56 |
|
| 2018 |
Costello KR, Schones DE. Chromatin modifications in metabolic disease: Potential mediators of long-term disease risk. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 29369528 DOI: 10.1002/Wsbm.1416 |
0.752 |
|
| 2017 |
Das S, Senapati P, Chen Z, Reddy MA, Ganguly R, Lanting L, Mandi V, Bansal A, Leung A, Zhang S, Jia Y, Wu X, Schones DE, Natarajan R. Regulation of angiotensin II actions by enhancers and super-enhancers in vascular smooth muscle cells. Nature Communications. 8: 1467. PMID 29133788 DOI: 10.1038/S41467-017-01629-7 |
0.7 |
|
| 2017 |
Du J, Tian J, Ding L, Trac C, Xia B, Sun S, Schones DE, Huang W. Vertical sleeve gastrectomy reverses diet-induced gene-regulatory changes impacting lipid metabolism. Scientific Reports. 7: 5274. PMID 28706189 DOI: 10.1038/S41598-017-05349-2 |
0.441 |
|
| 2016 |
Pan M, Reid MA, Lowman XH, Kulkarni RP, Tran TQ, Liu X, Yang Y, Hernandez-Davies JE, Rosales KK, Li H, Hugo W, Song C, Xu X, Schones DE, Ann DK, et al. Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation. Nature Cell Biology. PMID 27617932 DOI: 10.1038/Ncb3410 |
0.434 |
|
| 2016 |
Du J, Leung A, Trac C, Lee M, Parks BW, Lusis AJ, Natarajan R, Schones DE. Chromatin variation associated with liver metabolism is mediated by transposable elements. Epigenetics & Chromatin. 9: 28. PMID 27398095 DOI: 10.1186/S13072-016-0078-0 |
0.614 |
|
| 2016 |
Chen Z, Miao F, Paterson AD, Lachin JM, Zhang L, Schones DE, Wu X, Wang J, Tompkins JD, Genuth S, Braffett BH, Riggs AD, Natarajan R. Epigenomic profiling reveals an association between persistence of DNA methylation and metabolic memory in the DCCT/EDIC type 1 diabetes cohort. Proceedings of the National Academy of Sciences of the United States of America. PMID 27162351 DOI: 10.1073/Pnas.1603712113 |
0.37 |
|
| 2016 |
Leung A, Trac C, Du J, Natarajan R, Schones DE. Persistent chromatin modifications induced by high fat diet. The Journal of Biological Chemistry. PMID 27006400 DOI: 10.1074/Jbc.M115.711028 |
0.456 |
|
| 2016 |
Chimge NO, Little GH, Baniwal SK, Adisetiyo H, Xie Y, Zhang T, O'Laughlin A, Liu ZY, Ulrich P, Martin A, Mhawech-Fauceglia P, Ellis MJ, Tripathy D, Groshen S, Liang C, ... ... Schones DE, et al. RUNX1 prevents oestrogen-mediated AXIN1 suppression and β-catenin activation in ER-positive breast cancer. Nature Communications. 7: 10751. PMID 26916619 DOI: 10.1038/Ncomms10751 |
0.304 |
|
| 2015 |
Schones DE, Leung A, Natarajan R. Chromatin Modifications Associated With Diabetes and Obesity. Arteriosclerosis, Thrombosis, and Vascular Biology. 35: 1557-61. PMID 26044585 DOI: 10.1161/Atvbaha.115.305041 |
0.361 |
|
| 2015 |
Li Z, Dai H, Martos SN, Xu B, Gao Y, Li T, Zhu G, Schones DE, Wang Z. Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells. Genome Biology. 16: 115. PMID 26032981 DOI: 10.1186/S13059-015-0685-2 |
0.748 |
|
| 2014 |
Jose CC, Xu B, Jagannathan L, Trac C, Mallela RK, Hattori T, Lai D, Koide S, Schones DE, Cuddapah S. Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Proceedings of the National Academy of Sciences of the United States of America. 111: 14631-6. PMID 25246589 DOI: 10.1073/Pnas.1406923111 |
0.808 |
|
| 2014 |
Schones DE, Chen X, Trac C, Setten R, Paddison PJ. G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors. Epigenetics & Chromatin. 7: 23. PMID 25237399 DOI: 10.1186/1756-8935-7-23 |
0.39 |
|
| 2014 |
Leung A, Parks BW, Du J, Trac C, Setten R, Chen Y, Brown K, Lusis AJ, Natarajan R, Schones DE. Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. The Journal of Biological Chemistry. 289: 23557-67. PMID 25006255 DOI: 10.1074/Jbc.M114.581439 |
0.508 |
|
| 2014 |
Little GH, Baniwal SK, Adisetiyo H, Groshen S, Chimge NO, Kim SY, Khalid O, Hawes D, Jones JO, Pinski J, Schones DE, Frenkel B. Differential effects of RUNX2 on the androgen receptor in prostate cancer: synergistic stimulation of a gene set exemplified by SNAI2 and subsequent invasiveness. Cancer Research. 74: 2857-68. PMID 24648349 DOI: 10.1158/0008-5472.Can-13-2003 |
0.336 |
|
| 2013 |
Byeon B, Wang W, Barski A, Ranallo RT, Bao K, Schones DE, Zhao K, Wu C, Wu WH. The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter-proximal nucleosomes. The Journal of Biological Chemistry. 288: 23182-93. PMID 23779104 DOI: 10.1074/Jbc.M113.471979 |
0.769 |
|
| 2013 |
Zhang S, Schones DE, Malicet C, Rochman M, Zhou M, Foisner R, Bustin M. High mobility group protein N5 (HMGN5) and lamina-associated polypeptide 2α (LAP2α) interact and reciprocally affect their genome-wide chromatin organization. The Journal of Biological Chemistry. 288: 18104-9. PMID 23673662 DOI: 10.1074/Jbc.C113.469544 |
0.419 |
|
| 2013 |
Xu B, Schones DE, Wang Y, Liang H, Li G. A structural-based strategy for recognition of transcription factor binding sites. Plos One. 8: e52460. PMID 23320072 DOI: 10.1371/Journal.Pone.0052460 |
0.705 |
|
| 2013 |
Xu B, Schones DE, Wang Y, Liang H, Li G. Correction: A Structural-Based Strategy for Recognition of Transcription Factor Binding Sites Plos One. 8. DOI: 10.1371/Annotation/0312E1Be-336D-430A-Aa90-101Bbb44F8Db |
0.661 |
|
| 2012 |
Leung A, Schones DE, Natarajan R. Using epigenetic mechanisms to understand the impact of common disease causing alleles. Current Opinion in Immunology. 24: 558-63. PMID 22857822 DOI: 10.1016/J.Coi.2012.07.004 |
0.34 |
|
| 2011 |
Abuhatzira L, Shamir A, Schones DE, Schäffer AA, Bustin M. The chromatin-binding protein HMGN1 regulates the expression of methyl CpG-binding protein 2 (MECP2) and affects the behavior of mice. The Journal of Biological Chemistry. 286: 42051-62. PMID 22009741 DOI: 10.1074/Jbc.M111.300541 |
0.421 |
|
| 2011 |
Schones DE, Cui K, Cuddapah S. Genome-wide approaches to studying yeast chromatin modifications. Methods in Molecular Biology (Clifton, N.J.). 759: 61-71. PMID 21863481 DOI: 10.1007/978-1-61779-173-4_4 |
0.783 |
|
| 2011 |
Hu G, Schones DE, Cui K, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo NP, Huang S, Zhao K. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Research. 21: 1650-8. PMID 21795385 DOI: 10.1101/Gr.121145.111 |
0.652 |
|
| 2011 |
Cuddapah S, Schones DE, Cui K, Roh TY, Barski A, Wei G, Rochman M, Bustin M, Zhao K. Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions. Molecular and Cellular Biology. 31: 700-9. PMID 21173166 DOI: 10.1128/Mcb.00740-10 |
0.817 |
|
| 2010 |
Gan Q, Schones DE, Ho Eun S, Wei G, Cui K, Zhao K, Chen X. Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis. Genome Biology. 11: R42. PMID 20398323 DOI: 10.1186/Gb-2010-11-4-R42 |
0.623 |
|
| 2009 |
Cuddapah S, Barski A, Cui K, Schones DE, Wang Z, Wei G, Zhao K. Native chromatin preparation and Illumina/Solexa library construction. Cold Spring Harbor Protocols. 2009: pdb.prot5237. PMID 20147195 DOI: 10.1101/Pdb.Prot5237 |
0.78 |
|
| 2009 |
Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K. Chromatin poises miRNA- and protein-coding genes for expression. Genome Research. 19: 1742-51. PMID 19713549 DOI: 10.1101/Gr.090951.109 |
0.802 |
|
| 2009 |
Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell. 138: 1019-31. PMID 19698979 DOI: 10.1016/J.Cell.2009.06.049 |
0.828 |
|
| 2009 |
Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L. Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. Plos One. 4: e6589. PMID 19668381 DOI: 10.1371/Journal.Pone.0006589 |
0.578 |
|
| 2009 |
Araki Y, Wang Z, Zang C, Wood WH, Schones D, Cui K, Roh TY, Lhotsky B, Wersto RP, Peng W, Becker KG, Zhao K, Weng NP. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells. Immunity. 30: 912-25. PMID 19523850 DOI: 10.1016/J.Immuni.2009.05.006 |
0.829 |
|
| 2009 |
Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (Oxford, England). 25: 1952-8. PMID 19505939 DOI: 10.1093/Bioinformatics/Btp340 |
0.741 |
|
| 2009 |
Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. Determination of enriched histone modifications in non-genic portions of the human genome. Bmc Genomics. 10: 143. PMID 19335899 DOI: 10.1186/1471-2164-10-143 |
0.77 |
|
| 2009 |
Wang Z, Schones DE, Zhao K. Characterization of human epigenomes. Current Opinion in Genetics & Development. 19: 127-34. PMID 19299119 DOI: 10.1016/J.Gde.2009.02.001 |
0.718 |
|
| 2009 |
Zhu J, Davidson TS, Wei G, Jankovic D, Cui K, Schones DE, Guo L, Zhao K, Shevach EM, Paul WE. Down-regulation of Gfi-1 expression by TGF-beta is important for differentiation of Th17 and CD103+ inducible regulatory T cells. The Journal of Experimental Medicine. 206: 329-41. PMID 19188499 DOI: 10.1084/Jem.20081666 |
0.58 |
|
| 2009 |
Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, Schones DE, Peng W, Sun HW, Paul WE, O'Shea JJ, et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity. 30: 155-67. PMID 19144320 DOI: 10.1016/J.Immuni.2008.12.009 |
0.777 |
|
| 2009 |
Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell. 4: 80-93. PMID 19128795 DOI: 10.1016/J.Stem.2008.11.011 |
0.803 |
|
| 2009 |
Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Research. 19: 24-32. PMID 19056695 DOI: 10.1101/Gr.082800.108 |
0.798 |
|
| 2008 |
Liao W, Schones DE, Oh J, Cui Y, Cui K, Roh TY, Zhao K, Leonard WJ. Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression. Nature Immunology. 9: 1288-96. PMID 18820682 DOI: 10.1038/Ni.1656 |
0.689 |
|
| 2008 |
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics. 40: 897-903. PMID 18552846 DOI: 10.1038/Ng.154 |
0.816 |
|
| 2008 |
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell. 132: 887-98. PMID 18329373 DOI: 10.1016/J.Cell.2008.02.022 |
0.815 |
|
| 2008 |
Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nature Reviews. Genetics. 9: 179-91. PMID 18250624 DOI: 10.1038/Nrg2270 |
0.669 |
|
| 2008 |
Eguchi J, Yan QW, Schones DE, Kamal M, Hsu CH, Zhang MQ, Crawford GE, Rosen ED. Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metabolism. 7: 86-94. PMID 18177728 DOI: 10.1016/J.Cmet.2007.11.002 |
0.563 |
|
| 2007 |
Mignone JL, Roig-Lopez JL, Fedtsova N, Schones DE, Manganas LN, Maletic-Savatic M, Keyes WM, Mills AA, Gleiberman A, Zhang MQ, Enikolopov G. Neural potential of a stem cell population in the hair follicle. Cell Cycle (Georgetown, Tex.). 6: 2161-70. PMID 17873521 DOI: 10.4161/Cc.6.17.4593 |
0.47 |
|
| 2007 |
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-Resolution Profiling of Histone Methylations in the Human Genome Cell. 129: 823-837. PMID 17512414 DOI: 10.1016/J.Cell.2007.05.009 |
0.826 |
|
| 2007 |
Schones DE, Smith AD, Zhang MQ. Statistical significance of cis-regulatory modules. Bmc Bioinformatics. 8: 19. PMID 17241466 DOI: 10.1186/1471-2105-8-19 |
0.57 |
|
| 2007 |
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. Response: Mapping Nucleosome Positions Using ChIP-Seq Data Cell. 131: 832-833. DOI: 10.1016/J.Cell.2007.11.018 |
0.828 |
|
| 2005 |
Schones DE, Sumazin P, Zhang MQ. Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (Oxford, England). 21: 307-13. PMID 15319260 DOI: 10.1093/Bioinformatics/Bth480 |
0.502 |
|
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