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For: Condon DE, Tran PV, Lien YC, Schug J, Georgieff MK, Simmons RA, Won KJ. Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus. BMC Bioinformatics 2018;19:31. [PMID: 29402210 PMCID: PMC5800085 DOI: 10.1186/s12859-018-2037-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 01/23/2018] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
Balaramane D, Spill YG, Weber M, Bardet AF. MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets. Nucleic Acids Res 2024:gkae880. [PMID: 39420630 DOI: 10.1093/nar/gkae880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/13/2024] [Accepted: 09/30/2024] [Indexed: 10/19/2024]  Open
2
Donato L, Scimone C, Alibrandi S, Vadalà M, Castellucci M, Bonfiglio VME, Scalinci SZ, Abate G, D'Angelo R, Sidoti A. The genomic mosaic of mitochondrial dysfunction: Decoding nuclear and mitochondrial epigenetic contributions to maternally inherited diabetes and deafness pathogenesis. Heliyon 2024;10:e34756. [PMID: 39148984 PMCID: PMC11324998 DOI: 10.1016/j.heliyon.2024.e34756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 08/17/2024]  Open
3
Karaca M, Ince AG. Grafting based DNA methylation alteration of snoRNAs in upland cotton (Gossypium L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024;30:893-907. [PMID: 38974361 PMCID: PMC11222342 DOI: 10.1007/s12298-024-01469-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 07/09/2024]
4
Abnizova I, Stapel C, Boekhorst RT, Lee JTH, Hemberg M. Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation. BMC Biol 2024;22:78. [PMID: 38600550 PMCID: PMC11005181 DOI: 10.1186/s12915-024-01869-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024]  Open
5
Shokoohi F, Khaniki SH. Uncovering Alterations in Cancer Epigenetics via Trans-Dimensional Markov Chain Monte Carlo and Hidden Markov Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545168. [PMID: 37398181 PMCID: PMC10312753 DOI: 10.1101/2023.06.15.545168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
6
Ma Q, Oksenberg JR, Didonna A. Epigenetic control of ataxin-1 in multiple sclerosis. Ann Clin Transl Neurol 2022;9:1186-1194. [PMID: 35903875 PMCID: PMC9380165 DOI: 10.1002/acn3.51618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022]  Open
7
Gong T, Borgard H, Zhang Z, Chen S, Gao Z, Deng Y. Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies. SMALL METHODS 2022;6:e2101251. [PMID: 35064762 PMCID: PMC8963483 DOI: 10.1002/smtd.202101251] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/30/2021] [Indexed: 05/09/2023]
8
Lien YC, Pinney SE, Lu XM, Simmons RA. Identification of Novel Regulatory Regions Induced by Intrauterine Growth Restriction in Rat Islets. Endocrinology 2022;163:6459683. [PMID: 34894232 PMCID: PMC8743043 DOI: 10.1210/endocr/bqab251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 01/05/2023]
9
Sun X, Wang D, Zhu J, Sun S. A novel nonparametric computational strategy for identifying differential methylation regions. BMC Bioinformatics 2022;23:29. [PMID: 35012449 PMCID: PMC8750844 DOI: 10.1186/s12859-022-04563-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 01/03/2022] [Indexed: 11/26/2022]  Open
10
Peng X, Luo H, Kong X, Wang J. Metrics for evaluating differentially methylated region sets predicted from BS-seq data. Brief Bioinform 2021;23:6454651. [PMID: 34874989 DOI: 10.1093/bib/bbab475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 11/13/2022]  Open
11
Lee SD, Song J, LeBlanc VG, Marra MA. Integrative multi-omic analysis reveals neurodevelopmental gene dysregulation in CIC-knockout and IDH1 mutant cells. J Pathol 2021;256:297-309. [PMID: 34767259 PMCID: PMC9305137 DOI: 10.1002/path.5835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/22/2021] [Accepted: 11/09/2021] [Indexed: 11/18/2022]
12
Peng X, Li Y, Kong X, Zhu X, Ding X. Investigating Different DNA Methylation Patterns at the Resolution of Methylation Haplotypes. Front Genet 2021;12:697279. [PMID: 34262601 PMCID: PMC8273290 DOI: 10.3389/fgene.2021.697279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/01/2021] [Indexed: 11/15/2022]  Open
13
Weinberg DN, Rosenbaum P, Chen X, Barrows D, Horth C, Marunde MR, Popova IK, Gillespie ZB, Keogh MC, Lu C, Majewski J, Allis CD. Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands. Nat Genet 2021;53:794-800. [PMID: 33986537 PMCID: PMC8283687 DOI: 10.1038/s41588-021-00856-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
14
Cheng Y, Vechtova P, Fussy Z, Sterba J, Linhartová Z, Rodina M, Tučková V, Gela D, Samarin AM, Lebeda I, Xin M, Zhang S, Rahi D, Linhart O. Changes in Phenotypes and DNA Methylation of In Vitro Aging Sperm in Common Carp Cyprinus carpio. Int J Mol Sci 2021;22:5925. [PMID: 34073009 PMCID: PMC8198300 DOI: 10.3390/ijms22115925] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022]  Open
15
The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline. EPIGENOMES 2021;5:epigenomes5020012. [PMID: 34968299 PMCID: PMC8594691 DOI: 10.3390/epigenomes5020012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022]  Open
16
Bartoccetti M, van der Veer BK, Luo X, Khoueiry R, She P, Bajaj M, Xu J, Janiszewski A, Thienpont B, Pasque V, Koh KP. Regulatory Dynamics of Tet1 and Oct4 Resolve Stages of Global DNA Demethylation and Transcriptomic Changes in Reprogramming. Cell Rep 2021;30:2150-2169.e9. [PMID: 32075734 DOI: 10.1016/j.celrep.2020.01.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 12/12/2019] [Accepted: 01/21/2020] [Indexed: 01/05/2023]  Open
17
Shao J, Bai X, Pan T, Li Y, Jia X, Wang J, Lai S. Genome-Wide DNA Methylation Changes of Perirenal Adipose Tissue in Rabbits Fed a High-Fat Diet. Animals (Basel) 2020;10:E2213. [PMID: 33255930 PMCID: PMC7761299 DOI: 10.3390/ani10122213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 12/22/2022]  Open
18
Pinney SE, Joshi A, Yin V, Min SW, Rashid C, Condon DE, Wang PZ. Exposure to Gestational Diabetes Enriches Immune-Related Pathways in the Transcriptome and Methylome of Human Amniocytes. J Clin Endocrinol Metab 2020;105:5873862. [PMID: 32687192 PMCID: PMC7451504 DOI: 10.1210/clinem/dgaa466] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/15/2020] [Indexed: 12/13/2022]
19
Kreutz C, Can NS, Bruening RS, Meyberg R, Mérai Z, Fernandez-Pozo N, Rensing SA. A blind and independent benchmark study for detecting differeally methylated regions in plants. Bioinformatics 2020;36:3314-3321. [PMID: 32181821 DOI: 10.1093/bioinformatics/btaa191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/31/2020] [Accepted: 03/13/2020] [Indexed: 01/03/2023]  Open
20
Bansal A, Robles-Matos N, Wang PZ, Condon DE, Joshi A, Pinney SE. In utero Bisphenol A Exposure Is Linked with Sex Specific Changes in the Transcriptome and Methylome of Human Amniocytes. J Clin Endocrinol Metab 2020;105:5571768. [PMID: 31536135 PMCID: PMC7046022 DOI: 10.1210/clinem/dgz037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022]
21
Grehl C, Wagner M, Lemnian I, Glaser B, Grosse I. Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants. FRONTIERS IN PLANT SCIENCE 2020;11:176. [PMID: 32256504 PMCID: PMC7093021 DOI: 10.3389/fpls.2020.00176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/05/2020] [Indexed: 05/09/2023]
22
Yu YE, Xing Z, Do C, Pao A, Lee EJ, Krinsky-McHale S, Silverman W, Schupf N, Tycko B. Genetic and epigenetic pathways in Down syndrome: Insights to the brain and immune system from humans and mouse models. PROGRESS IN BRAIN RESEARCH 2019;251:1-28. [PMID: 32057305 PMCID: PMC7286740 DOI: 10.1016/bs.pbr.2019.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
23
Lien YC, Condon DE, Georgieff MK, Simmons RA, Tran PV. Dysregulation of Neuronal Genes by Fetal-Neonatal Iron Deficiency Anemia Is Associated with Altered DNA Methylation in the Rat Hippocampus. Nutrients 2019;11:nu11051191. [PMID: 31137889 PMCID: PMC6566599 DOI: 10.3390/nu11051191] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023]  Open
24
How to Design a Whole-Genome Bisulfite Sequencing Experiment. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2040021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
25
Georgieff MK, Ramel SE, Cusick SE. Nutritional influences on brain development. Acta Paediatr 2018;107:1310-1321. [PMID: 29468731 PMCID: PMC6045434 DOI: 10.1111/apa.14287] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/12/2018] [Accepted: 02/16/2018] [Indexed: 12/19/2022]
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