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For: Pott S. Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells. eLife 2017;6:e23203. [PMID: 28653622 PMCID: PMC5487215 DOI: 10.7554/elife.23203] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 05/26/2017] [Indexed: 12/23/2022]  Open
Number Cited by Other Article(s)
1
Xiao Y, Jin W, Ju L, Fu J, Wang G, Yu M, Chen F, Qian K, Wang X, Zhang Y. Tracking single-cell evolution using clock-like chromatin accessibility loci. Nat Biotechnol 2025;43:784-798. [PMID: 38724668 DOI: 10.1038/s41587-024-02241-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 04/10/2024] [Indexed: 05/18/2025]
2
Wang J, Ye F, Chai H, Jiang Y, Wang T, Ran X, Xia Q, Xu Z, Fu Y, Zhang G, Wu H, Guo G, Guo H, Ruan Y, Wang Y, Xing D, Xu X, Zhang Z. Advances and applications in single-cell and spatial genomics. SCIENCE CHINA. LIFE SCIENCES 2025;68:1226-1282. [PMID: 39792333 DOI: 10.1007/s11427-024-2770-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 10/10/2024] [Indexed: 01/12/2025]
3
Theunis K, Vanuytven S, Claes I, Geurts J, Rambow F, Brown D, Van Der Haegen M, Marin-Bejar O, Rogiers A, Van Raemdonck N, Leucci E, Demeulemeester J, Sifrim A, Marine JC, Voet T. Single-cell genome and transcriptome sequencing without upfront whole-genome amplification reveals cell state plasticity of melanoma subclones. Nucleic Acids Res 2025;53:gkaf173. [PMID: 40138718 PMCID: PMC11941470 DOI: 10.1093/nar/gkaf173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 02/07/2025] [Accepted: 02/21/2025] [Indexed: 03/29/2025]  Open
4
Liu Z, Gu A, Bao Y, Lin GN. Epigenetic Impacts of Non-Coding Mutations Deciphered Through Pre-Trained DNA Language Model at Single-Cell Resolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2413571. [PMID: 39888214 PMCID: PMC11924033 DOI: 10.1002/advs.202413571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 01/20/2025] [Indexed: 02/01/2025]
5
Nichols RV, Rylaarsdam LE, O'Connell BL, Shipony Z, Iremadze N, Acharya SN, Adey AC. Atlas-scale single-cell DNA methylation profiling with sciMETv3. CELL GENOMICS 2025;5:100726. [PMID: 39719707 PMCID: PMC11770211 DOI: 10.1016/j.xgen.2024.100726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 10/25/2024] [Accepted: 11/26/2024] [Indexed: 12/26/2024]
6
Liu T, Conesa A. Profiling the epigenome using long-read sequencing. Nat Genet 2025;57:27-41. [PMID: 39779955 DOI: 10.1038/s41588-024-02038-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 11/19/2024] [Indexed: 01/11/2025]
7
Laisné M, Lupien M, Vallot C. Epigenomic heterogeneity as a source of tumour evolution. Nat Rev Cancer 2025;25:7-26. [PMID: 39414948 DOI: 10.1038/s41568-024-00757-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2024] [Indexed: 10/18/2024]
8
Xiong X, Wang X, Liu CC, Shao ZM, Yu KD. Deciphering breast cancer dynamics: insights from single-cell and spatial profiling in the multi-omics era. Biomark Res 2024;12:107. [PMID: 39294728 PMCID: PMC11411917 DOI: 10.1186/s40364-024-00654-1] [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: 06/28/2024] [Accepted: 09/10/2024] [Indexed: 09/21/2024]  Open
9
Zeng X, Yang X, Zhong Z, Lin X, Chen Q, Jiang S, Mo M, Lin S, Zhang H, Zhu Z, Li J, Song J, Yang C. AMAR-seq: Automated Multimodal Sequencing of DNA Methylation, Chromatin Accessibility, and RNA Expression with Single-Cell Resolution. Anal Chem 2024. [PMID: 39250680 DOI: 10.1021/acs.analchem.4c02765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
10
Stuart T. Progress in multifactorial single-cell chromatin profiling methods. Biochem Soc Trans 2024;52:1827-1839. [PMID: 39023855 PMCID: PMC11668300 DOI: 10.1042/bst20231471] [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: 06/30/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
11
Schwaiger M, Mohn F, Bühler M, Kaaij LJT. guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel. BMC Genomics 2024;25:732. [PMID: 39075377 PMCID: PMC11288131 DOI: 10.1186/s12864-024-10625-3] [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: 06/13/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024]  Open
12
Wang X, Li F, Zhang Y, Imoto S, Shen HH, Li S, Guo Y, Yang J, Song J. Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects. Brief Bioinform 2024;25:bbae446. [PMID: 39276327 PMCID: PMC11401448 DOI: 10.1093/bib/bbae446] [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: 04/02/2024] [Revised: 08/08/2024] [Accepted: 08/27/2024] [Indexed: 09/16/2024]  Open
13
Rhaman MS, Ali M, Ye W, Li B. Opportunities and Challenges in Advancing Plant Research with Single-cell Omics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzae026. [PMID: 38996445 PMCID: PMC11423859 DOI: 10.1093/gpbjnl/qzae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 07/14/2024]
14
Yu H, Zheng Y, Yang X. scDM: A deep generative method for cell surface protein prediction with diffusion model. J Mol Biol 2024;436:168610. [PMID: 38754773 DOI: 10.1016/j.jmb.2024.168610] [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: 01/03/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
15
Liu Z, Hu Y, Xie H, Chen K, Wen L, Fu W, Zhou X, Tang F. Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers. Cancer Discov 2024;14:1082-1105. [PMID: 38445965 DOI: 10.1158/2159-8290.cd-23-1445] [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: 11/30/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
16
Fabyanic EB, Hu P, Qiu Q, Berríos KN, Connolly DR, Wang T, Flournoy J, Zhou Z, Kohli RM, Wu H. Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Nat Biotechnol 2024;42:960-974. [PMID: 37640946 PMCID: PMC11525041 DOI: 10.1038/s41587-023-01909-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
17
Tang X, Zhang Y, Zhang H, Zhang N, Dai Z, Cheng Q, Li Y. Single-Cell Sequencing: High-Resolution Analysis of Cellular Heterogeneity in Autoimmune Diseases. Clin Rev Allergy Immunol 2024;66:376-400. [PMID: 39186216 DOI: 10.1007/s12016-024-09001-6] [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] [Accepted: 07/20/2024] [Indexed: 08/27/2024]
18
Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024;908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [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: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
19
Yabo YA, Heiland DH. Understanding glioblastoma at the single-cell level: Recent advances and future challenges. PLoS Biol 2024;22:e3002640. [PMID: 38814900 PMCID: PMC11139343 DOI: 10.1371/journal.pbio.3002640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]  Open
20
Duhan L, Kumari D, Naime M, Parmar VS, Chhillar AK, Dangi M, Pasrija R. Single-cell transcriptomics: background, technologies, applications, and challenges. Mol Biol Rep 2024;51:600. [PMID: 38689046 DOI: 10.1007/s11033-024-09553-y] [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: 02/09/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
21
Yang C, Jin Y, Yin Y. Integration of single-cell transcriptome and chromatin accessibility and its application on tumor investigation. LIFE MEDICINE 2024;3:lnae015. [PMID: 39872661 PMCID: PMC11749461 DOI: 10.1093/lifemedi/lnae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/25/2024] [Indexed: 01/30/2025]
22
Lim J, Park C, Kim M, Kim H, Kim J, Lee DS. Advances in single-cell omics and multiomics for high-resolution molecular profiling. Exp Mol Med 2024;56:515-526. [PMID: 38443594 PMCID: PMC10984936 DOI: 10.1038/s12276-024-01186-2] [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: 08/30/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 03/07/2024]  Open
23
Crespo-García E, Bueno-Costa A, Esteller M. Single-cell analysis of the epitranscriptome: RNA modifications under the microscope. RNA Biol 2024;21:1-8. [PMID: 38368619 PMCID: PMC10877985 DOI: 10.1080/15476286.2024.2315385] [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] [Revised: 01/19/2024] [Accepted: 02/02/2024] [Indexed: 02/20/2024]  Open
24
Tang W, Wen H, Liu R, Ding J, Jin W, Xie Y, Liu H, Tang J. Single-Cell Multimodal Prediction via Transformers. ARXIV 2023:arXiv:2303.00233v3. [PMID: 37645040 PMCID: PMC10462176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
25
Hu Y, Shen F, Yang X, Han T, Long Z, Wen J, Huang J, Shen J, Guo Q. Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity. Clin Epigenetics 2023;15:161. [PMID: 37821906 PMCID: PMC10568863 DOI: 10.1186/s13148-023-01574-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]  Open
26
Huang Y, Li L, An G, Yang X, Cui M, Song X, Lin J, Zhang X, Yao Z, Wan C, Zhou C, Zhao J, Song K, Ren S, Xia X, Fu X, Lan Y, Hu X, Wang W, Wang M, Zheng Y, Miao K, Bai X, Hutchins AP, Chang G, Gao S, Zhao XY. Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination. Nat Cell Biol 2023;25:1520-1534. [PMID: 37723297 DOI: 10.1038/s41556-023-01232-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 08/15/2023] [Indexed: 09/20/2023]
27
Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
28
Baysoy A, Bai Z, Satija R, Fan R. The technological landscape and applications of single-cell multi-omics. Nat Rev Mol Cell Biol 2023;24:695-713. [PMID: 37280296 PMCID: PMC10242609 DOI: 10.1038/s41580-023-00615-w] [Citation(s) in RCA: 363] [Impact Index Per Article: 181.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/08/2023]
29
Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol 2023;20:597-614. [PMID: 37258747 PMCID: PMC10527367 DOI: 10.1038/s41575-023-00784-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2023] [Indexed: 06/02/2023]
30
Vandereyken K, Sifrim A, Thienpont B, Voet T. Methods and applications for single-cell and spatial multi-omics. Nat Rev Genet 2023;24:494-515. [PMID: 36864178 PMCID: PMC9979144 DOI: 10.1038/s41576-023-00580-2] [Citation(s) in RCA: 461] [Impact Index Per Article: 230.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 03/04/2023]
31
Thakur S, Haider S, Natrajan R. Implications of tumour heterogeneity on cancer evolution and therapy resistance: lessons from breast cancer. J Pathol 2023;260:621-636. [PMID: 37587096 DOI: 10.1002/path.6158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 08/18/2023]
32
Zhang J, Sheng H, Hu C, Li F, Cai B, Ma Y, Wang Y, Ma Y. Effects of DNA Methylation on Gene Expression and Phenotypic Traits in Cattle: A Review. Int J Mol Sci 2023;24:11882. [PMID: 37569258 PMCID: PMC10419045 DOI: 10.3390/ijms241511882] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023]  Open
33
Xie B, Gao D, Zhou B, Chen S, Wang L. New discoveries in the field of metabolism by applying single-cell and spatial omics. J Pharm Anal 2023;13:711-725. [PMID: 37577385 PMCID: PMC10422156 DOI: 10.1016/j.jpha.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 08/15/2023]  Open
34
Piwecka M, Rajewsky N, Rybak-Wolf A. Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease. Nat Rev Neurol 2023;19:346-362. [PMID: 37198436 PMCID: PMC10191412 DOI: 10.1038/s41582-023-00809-y] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 05/19/2023]
35
Liu F, Wang Y, Gu H, Wang X. Technologies and applications of single-cell DNA methylation sequencing. Theranostics 2023;13:2439-2454. [PMID: 37215576 PMCID: PMC10196823 DOI: 10.7150/thno.82582] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/09/2023] [Indexed: 05/24/2023]  Open
36
Simultaneous Measurement of DNA Methylation and Nucleosome Occupancy in Single Cells Using scNOMe-Seq. Methods Mol Biol 2023;2611:231-247. [PMID: 36807071 DOI: 10.1007/978-1-0716-2899-7_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
37
Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq. Methods Mol Biol 2023;2611:187-230. [PMID: 36807070 DOI: 10.1007/978-1-0716-2899-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
38
Iqbal W, Zhou W. Computational Methods for Single-cell DNA Methylome Analysis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:48-66. [PMID: 35718270 PMCID: PMC10372927 DOI: 10.1016/j.gpb.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022]
39
Guo L, Kong D, Liu J, Zhan L, Luo L, Zheng W, Zheng Q, Chen C, Sun S. Breast cancer heterogeneity and its implication in personalized precision therapy. Exp Hematol Oncol 2023;12:3. [PMID: 36624542 PMCID: PMC9830930 DOI: 10.1186/s40164-022-00363-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023]  Open
40
Kong S, Li R, Tian Y, Zhang Y, Lu Y, Ou Q, Gao P, Li K, Zhang Y. Single-cell omics: A new direction for functional genetic research in human diseases and animal models. Front Genet 2023;13:1100016. [PMID: 36685871 PMCID: PMC9846559 DOI: 10.3389/fgene.2022.1100016] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023]  Open
41
Preissl S, Gaulton KJ, Ren B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet 2023;24:21-43. [PMID: 35840754 PMCID: PMC9771884 DOI: 10.1038/s41576-022-00509-1] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
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Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing. Nat Commun 2022;13:7939. [PMID: 36566265 PMCID: PMC9789962 DOI: 10.1038/s41467-022-35650-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/15/2022] [Indexed: 12/25/2022]  Open
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Wei A, Wu H. Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. Development 2022;149:dev182683. [PMID: 36519514 PMCID: PMC10108609 DOI: 10.1242/dev.182683] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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O'Neill H, Lee H, Gupta I, Rodger EJ, Chatterjee A. Single-Cell DNA Methylation Analysis in Cancer. Cancers (Basel) 2022;14:6171. [PMID: 36551655 PMCID: PMC9777108 DOI: 10.3390/cancers14246171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]  Open
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022;13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022]  Open
46
Petrova V, Song R, DEEP Consortium, Nordström KJV, Walter J, Wong JJL, Armstrong N, Rasko JEJ, Schmitz U. Increased chromatin accessibility facilitates intron retention in specific cell differentiation states. Nucleic Acids Res 2022;50:11563-11579. [PMID: 36354002 PMCID: PMC9723627 DOI: 10.1093/nar/gkac994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022]  Open
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Mukherjee P, Park SH, Pathak N, Patino CA, Bao G, Espinosa HD. Integrating Micro and Nano Technologies for Cell Engineering and Analysis: Toward the Next Generation of Cell Therapy Workflows. ACS NANO 2022;16:15653-15680. [PMID: 36154011 DOI: 10.1021/acsnano.2c05494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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Morgan DM, Shreffler WG, Love JC. Revealing the heterogeneity of CD4+ T cells through single-cell transcriptomics. J Allergy Clin Immunol 2022;150:748-755. [DOI: 10.1016/j.jaci.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/07/2022]
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Battaglia S, Dong K, Wu J, Chen Z, Najm FJ, Zhang Y, Moore MM, Hecht V, Shoresh N, Bernstein BE. Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements. Nat Genet 2022;54:1504-1513. [PMID: 36195755 PMCID: PMC10567064 DOI: 10.1038/s41588-022-01188-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/18/2022] [Indexed: 11/07/2022]
50
A guide to systems-level immunomics. Nat Immunol 2022;23:1412-1423. [PMID: 36138185 DOI: 10.1038/s41590-022-01309-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 08/09/2022] [Indexed: 02/04/2023]
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