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For: Kaur D, Lee SM, Goldberg D, Spix NJ, Hinoue T, Li HT, Dwaraka VB, Smith R, Shen H, Liang G, Renke N, Laird PW, Zhou W. Comprehensive Evaluation of The Infinium Human MethylationEPIC v2 BeadChip. Epigenetics Commun 2023;3:6. [PMID: 38455390 PMCID: PMC10919401 DOI: 10.1186/s43682-023-00021-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/18/2023] [Indexed: 03/09/2024]
Number Cited by Other Article(s)
1
Tiedemann RL, Hrit J, Du Q, Wiseman AK, Eden HE, Dickson BM, Kong X, Chomiak AA, Vaughan RM, Tibben BM, Hebert JM, David Y, Zhou W, Baylin SB, Jones PA, Clark SJ, Rothbart SB. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. Nucleic Acids Res 2024;52:13733-13756. [PMID: 39607687 DOI: 10.1093/nar/gkae1105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 10/04/2024] [Accepted: 10/25/2024] [Indexed: 11/29/2024]  Open
2
Jurkowska RZ. Role of epigenetic mechanisms in the pathogenesis of chronic respiratory diseases and response to inhaled exposures: From basic concepts to clinical applications. Pharmacol Ther 2024;264:108732. [PMID: 39426605 DOI: 10.1016/j.pharmthera.2024.108732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/15/2024] [Accepted: 10/11/2024] [Indexed: 10/21/2024]
3
Liu Y, Hrit JA, Chomiak AA, Stransky S, Hoffman JR, Tiedemann RL, Wiseman AK, Kariapper LS, Dickson BM, Worden EJ, Fry CJ, Sidoli S, Rothbart SB. DNA hypomethylation promotes UHRF1-and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states. Mol Cell 2024:S1097-2765(24)00914-6. [PMID: 39631394 DOI: 10.1016/j.molcel.2024.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 09/17/2024] [Accepted: 11/07/2024] [Indexed: 12/07/2024]
4
Lussier AA, Schuurmans IK, Großbach A, Maclsaac J, Dever K, Koen N, Zar HJ, Stein DJ, Kobor MS, Dunn EC. Technical variability across the 450K, EPICv1, and EPICv2 DNA methylation arrays: lessons learned for clinical and longitudinal studies. Clin Epigenetics 2024;16:166. [PMID: 39578866 PMCID: PMC11583407 DOI: 10.1186/s13148-024-01761-4] [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: 08/07/2024] [Accepted: 10/11/2024] [Indexed: 11/24/2024]  Open
5
Yang HH, Han MR. MethylCallR : a comprehensive analysis framework for Illumina Methylation Beadchip. Sci Rep 2024;14:27026. [PMID: 39506033 PMCID: PMC11541563 DOI: 10.1038/s41598-024-77914-5] [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: 08/12/2024] [Accepted: 10/28/2024] [Indexed: 11/08/2024]  Open
6
Dai L, Johnson-Buck A, Laird PW, Tewari M, Walter NG. Ultrasensitive Amplification-Free Quantification of a Methyl CpG-Rich Cancer Biomarker by Single-Molecule Kinetic Fingerprinting. Anal Chem 2024;96:17209-17216. [PMID: 39425638 DOI: 10.1021/acs.analchem.4c03002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2024]
7
Gabriel AAG, Racle J, Falquet M, Jandus C, Gfeller D. Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data. eLife 2024;13:RP94833. [PMID: 39383060 PMCID: PMC11464006 DOI: 10.7554/elife.94833] [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] [Indexed: 10/11/2024]  Open
8
Garma LD, Quintela-Fandino M. Applicability of epigenetic age models to next-generation methylation arrays. Genome Med 2024;16:116. [PMID: 39375688 PMCID: PMC11460231 DOI: 10.1186/s13073-024-01387-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 09/19/2024] [Indexed: 10/09/2024]  Open
9
Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retro-age: A unique epigenetic biomarker of aging captured by DNA methylation states of retroelements. Aging Cell 2024;23:e14288. [PMID: 39092674 PMCID: PMC11464121 DOI: 10.1111/acel.14288] [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: 02/15/2024] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024]  Open
10
Marijuan RP, Marin JJG. New insights into the impact of impaired epigenetic machinery on liver cancer malignant phenotype. Transl Cancer Res 2024;13:4514-4519. [PMID: 39430862 PMCID: PMC11483460 DOI: 10.21037/tcr-24-751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 09/12/2024] [Indexed: 10/22/2024]
11
Zhuang BC, Jude MS, Konwar C, Yusupov N, Ryan CP, Engelbrecht HR, Whitehead J, Halberstam AA, MacIsaac JL, Dever K, Tran TK, Korinek K, Zimmer Z, Lee NR, McDade TW, Kuzawa CW, Huffman KM, Belsky DW, Binder EB, Czamara D, Korthauer K, Kobor MS. Discrepancies in readouts between Infinium MethylationEPIC v2.0 and v1.0 reflected in DNA methylation-based tools: implications and considerations for human population epigenetic studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.600461. [PMID: 39005299 PMCID: PMC11245009 DOI: 10.1101/2024.07.02.600461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
12
Apsley AT, Ye Q, Caspi A, Chiaro C, Etzel L, Hastings WJ, Heim CC, Kozlosky J, Noll JG, Schreier HMC, Shenk CE, Sugden K, Shalev I. Cross-Tissue Comparison of Epigenetic Aging Clocks in Humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603774. [PMID: 39071385 PMCID: PMC11275734 DOI: 10.1101/2024.07.16.603774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
13
Chen BH, Zhou W. mLiftOver: harmonizing data across Infinium DNA methylation platforms. Bioinformatics 2024;40:btae423. [PMID: 38963309 PMCID: PMC11233119 DOI: 10.1093/bioinformatics/btae423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/07/2024] [Accepted: 07/03/2024] [Indexed: 07/05/2024]  Open
14
Puvvula J, Braun JM, DeFranco EA, Ho SM, Leung YK, Huang S, Zhang X, Vuong AM, Kim SS, Percy Z, Calafat AM, Botelho JC, Chen A. Gestational exposure to environmental chemicals and epigenetic alterations in the placenta and cord blood mononuclear cells. EPIGENETICS COMMUNICATIONS 2024;4:4. [PMID: 38962689 PMCID: PMC11217138 DOI: 10.1186/s43682-024-00027-7] [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: 12/21/2023] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
15
Goldberg DC, Cloud C, Lee SM, Barnes B, Gruber S, Kim E, Pottekat A, Westphal M, McAuliffe L, Majournie E, KalayilManian M, Zhu Q, Tran C, Hansen M, Parker JB, Kohli RM, Porecha R, Renke N, Zhou W. MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594606. [PMID: 38826316 PMCID: PMC11142114 DOI: 10.1101/2024.05.17.594606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
16
Hutarew G, Alinger-Scharinger B, Sotlar K, Kraus TFJ. Genome-Wide Methylation Analysis in Two Wild-Type Non-Small Cell Lung Cancer Subgroups with Negative and High PD-L1 Expression. Cancers (Basel) 2024;16:1841. [PMID: 38791918 PMCID: PMC11119885 DOI: 10.3390/cancers16101841] [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: 03/27/2024] [Revised: 04/25/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]  Open
17
Lee SM, Loo CE, Prasasya RD, Bartolomei MS, Kohli RM, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. Nucleic Acids Res 2024;52:e38. [PMID: 38407446 PMCID: PMC11040145 DOI: 10.1093/nar/gkae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024]  Open
18
Dai L, Johnson-Buck A, Laird PW, Tewari M, Walter NG. Ultrasensitive amplification-free quantification of a methyl CpG-rich cancer biomarker by single-molecule kinetic fingerprinting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.587997. [PMID: 38645159 PMCID: PMC11030368 DOI: 10.1101/2024.04.06.587997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
19
Peters TJ, Meyer B, Ryan L, Achinger-Kawecka J, Song J, Campbell EM, Qu W, Nair S, Loi-Luu P, Stricker P, Lim E, Stirzaker C, Clark SJ, Pidsley R. Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling. BMC Genomics 2024;25:251. [PMID: 38448820 PMCID: PMC10916044 DOI: 10.1186/s12864-024-10027-5] [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: 10/12/2023] [Accepted: 01/18/2024] [Indexed: 03/08/2024]  Open
20
Carreras-Gallo N, Dwaraka VB, Jima DD, Skaar DA, Mendez TL, Planchart A, Zhou W, Jirtle RL, Smith R, Hoyo C. Creation and Validation of the First Infinium DNA Methylation Array for the Human Imprintome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575646. [PMID: 38293193 PMCID: PMC10827131 DOI: 10.1101/2024.01.15.575646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
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