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For: Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. Cell 2018;174:1309-1324.e18. [PMID: 30078704 PMCID: PMC6158300 DOI: 10.1016/j.cell.2018.06.052] [Citation(s) in RCA: 490] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/08/2018] [Accepted: 06/27/2018] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
51
Wang X, Lian Q, Dong H, Xu S, Su Y, Wu X. Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzae014. [PMID: 39049508 PMCID: PMC11423854 DOI: 10.1093/gpbjnl/qzae014] [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: 05/01/2022] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/27/2024]
52
Shwab EK, Gingerich DC, Man Z, Gamache J, Garrett ME, Crawford GE, Ashley-Koch AE, Serrano GE, Beach TG, Lutz MW, Chiba-Falek O. Single-nucleus multi-omics of Parkinson's disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks. Acta Neuropathol Commun 2024;12:111. [PMID: 38956662 PMCID: PMC11218415 DOI: 10.1186/s40478-024-01803-1] [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: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024]  Open
53
Sun K, Liu X, Lan X. A single-cell atlas of chromatin accessibility in mouse organogenesis. Nat Cell Biol 2024;26:1200-1211. [PMID: 38977846 DOI: 10.1038/s41556-024-01435-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/29/2024] [Indexed: 07/10/2024]
54
Bilous M, Hérault L, Gabriel AA, Teleman M, Gfeller D. Building and analyzing metacells in single-cell genomics data. Mol Syst Biol 2024;20:744-766. [PMID: 38811801 PMCID: PMC11220014 DOI: 10.1038/s44320-024-00045-6] [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] [Received: 02/04/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024]  Open
55
Kim GD, Shin SI, Jung SW, An H, Choi SY, Eun M, Jun CD, Lee S, Park J. Cell Type- and Age-Specific Expression of lncRNAs across Kidney Cell Types. J Am Soc Nephrol 2024;35:870-885. [PMID: 38621182 PMCID: PMC11230714 DOI: 10.1681/asn.0000000000000354] [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: 12/06/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024]  Open
56
Ma Y, Guo S, Chen Y, Peng Y, Su X, Jiang H, Lin X, Zhang J. Single-nucleus chromatin landscape dataset of mouse brain development and aging. Sci Data 2024;11:616. [PMID: 38866804 PMCID: PMC11169343 DOI: 10.1038/s41597-024-03382-1] [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: 02/26/2024] [Accepted: 05/15/2024] [Indexed: 06/14/2024]  Open
57
Takeuchi F, Kato N. Ploidy inference from single-cell data: application to human and mouse cell atlases. Genetics 2024;227:iyae061. [PMID: 38651869 PMCID: PMC11151930 DOI: 10.1093/genetics/iyae061] [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: 03/18/2024] [Revised: 03/18/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]  Open
58
De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nat Biotechnol 2024;42:916-926. [PMID: 37537502 PMCID: PMC11180611 DOI: 10.1038/s41587-023-01881-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/22/2023] [Indexed: 08/05/2023]
59
Kotliar M, Kartashov A, Barski A. Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly Approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582604. [PMID: 38464095 PMCID: PMC10925325 DOI: 10.1101/2024.02.28.582604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
60
Mendieta JP, Tu X, Jiang D, Yan H, Zhang X, Marand AP, Zhong S, Schmitz RJ. Investigating the cis-Regulatory Basis of C3 and C4 Photosynthesis in Grasses at Single-Cell Resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574340. [PMID: 38405933 PMCID: PMC10888913 DOI: 10.1101/2024.01.05.574340] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
61
Singh R, Wu AP, Mudide A, Berger B. Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors. Cell Syst 2024;15:462-474.e5. [PMID: 38754366 DOI: 10.1016/j.cels.2024.04.005] [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: 04/14/2023] [Revised: 08/25/2023] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
62
Chen S, Liang B, Xu J. Unveiling heterogeneity in MSCs: exploring marker-based strategies for defining MSC subpopulations. J Transl Med 2024;22:459. [PMID: 38750573 PMCID: PMC11094970 DOI: 10.1186/s12967-024-05294-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/11/2024] [Indexed: 05/19/2024]  Open
63
Suen HC, Ou F, Miu KK, Wang Z, Chan WY, Liao J. The single-cell chromatin landscape in gonadal cell lineage specification. BMC Genomics 2024;25:464. [PMID: 38741085 DOI: 10.1186/s12864-024-10376-1] [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: 10/31/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024]  Open
64
Shu C, Street K, Breton CV, Bastain TM, Wilson ML. A review of single-cell transcriptomics and epigenomics studies in maternal and child health. Epigenomics 2024;16:775-793. [PMID: 38709139 PMCID: PMC11318716 DOI: 10.1080/17501911.2024.2343276] [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: 12/18/2023] [Accepted: 04/11/2024] [Indexed: 05/07/2024]  Open
65
Cui X, Chen X, Li Z, Gao Z, Chen S, Jiang R. Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity. NATURE COMPUTATIONAL SCIENCE 2024;4:346-359. [PMID: 38730185 DOI: 10.1038/s43588-024-00625-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/05/2024] [Indexed: 05/12/2024]
66
Hu P, Rychik J, Zhao J, Bai H, Bauer A, Yu W, Rand EB, Dodds KM, Goldberg DJ, Tan K, Wilkins BJ, Pei L. Single-cell multiomics guided mechanistic understanding of Fontan-associated liver disease. Sci Transl Med 2024;16:eadk6213. [PMID: 38657025 PMCID: PMC11103255 DOI: 10.1126/scitranslmed.adk6213] [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: 08/31/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
67
Chen K, Han Y, Wang Y, Zhou D, Wu F, Cai W, Zheng S, Xiao Q, Zhang H, Li W. scMoresDB: A comprehensive database of single-cell multi-omics data for human respiratory system. iScience 2024;27:109567. [PMID: 38617561 PMCID: PMC11015448 DOI: 10.1016/j.isci.2024.109567] [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: 09/07/2023] [Revised: 11/26/2023] [Accepted: 03/22/2024] [Indexed: 04/16/2024]  Open
68
Gao Z, Jiang R, Chen S. OpenAnnotateApi: Python and R packages to efficiently annotate and analyze chromatin accessibility of genomic regions. BIOINFORMATICS ADVANCES 2024;4:vbae055. [PMID: 38645715 PMCID: PMC11031356 DOI: 10.1093/bioadv/vbae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
69
Zhang X, Marand AP, Yan H, Schmitz RJ. scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. Genome Biol 2024;25:90. [PMID: 38589969 PMCID: PMC11003106 DOI: 10.1186/s13059-024-03235-5] [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: 09/28/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024]  Open
70
Fang X, Zhang Y, Miao R, Zhang Y, Yin R, Guan H, Huang X, Tian J. Single-cell sequencing: A promising approach for uncovering the characteristic of pancreatic islet cells in type 2 diabetes. Biomed Pharmacother 2024;173:116292. [PMID: 38394848 DOI: 10.1016/j.biopha.2024.116292] [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: 12/07/2023] [Revised: 02/03/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]  Open
71
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]
72
Zeng Y, Luo M, Shangguan N, Shi P, Feng J, Xu J, Chen K, Lu Y, Yu W, Yang Y. Deciphering cell types by integrating scATAC-seq data with genome sequences. NATURE COMPUTATIONAL SCIENCE 2024;4:285-298. [PMID: 38600256 DOI: 10.1038/s43588-024-00622-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
73
Malekpour SA, Haghverdi L, Sadeghi M. Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms. Brief Bioinform 2024;25:bbae180. [PMID: 38653489 PMCID: PMC11036345 DOI: 10.1093/bib/bbae180] [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: 09/19/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024]  Open
74
Zhang W, Cui Y, Liu B, Loza M, Park SJ, Nakai K. HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data. Brief Bioinform 2024;25:bbae152. [PMID: 38581422 PMCID: PMC10998639 DOI: 10.1093/bib/bbae152] [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: 12/19/2023] [Revised: 02/19/2024] [Accepted: 03/10/2024] [Indexed: 04/08/2024]  Open
75
Caldwell BA, Wu Y, Wang J, Li L. Altered DNA methylation underlies monocyte dysregulation and immune exhaustion memory in sepsis. Cell Rep 2024;43:113894. [PMID: 38442017 PMCID: PMC11654472 DOI: 10.1016/j.celrep.2024.113894] [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: 09/14/2023] [Revised: 01/12/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024]  Open
76
Zhang G, Fu Y, Yang L, Ye F, Zhang P, Zhang S, Ma L, Li J, Wu H, Han X, Wang J, Guo G. Construction of single-cell cross-species chromatin accessibility landscapes with combinatorial-hybridization-based ATAC-seq. Dev Cell 2024;59:793-811.e8. [PMID: 38330939 DOI: 10.1016/j.devcel.2024.01.015] [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: 06/01/2023] [Revised: 11/03/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
77
Miao Z, Wang J, Park K, Kuang D, Kim J. PACS allows comprehensive dissection of multiple factors governing chromatin accessibility from snATAC-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.30.551108. [PMID: 37577623 PMCID: PMC10418058 DOI: 10.1101/2023.07.30.551108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
78
Zhang H, Mulqueen RM, Iannuzo N, Farrera DO, Polverino F, Galligan JJ, Ledford JG, Adey AC, Cusanovich DA. txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility. Genome Biol 2024;25:78. [PMID: 38519979 PMCID: PMC10958877 DOI: 10.1186/s13059-023-03150-1] [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: 05/12/2023] [Accepted: 12/20/2023] [Indexed: 03/25/2024]  Open
79
Goshisht MK. Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges. ACS OMEGA 2024;9:9921-9945. [PMID: 38463314 PMCID: PMC10918679 DOI: 10.1021/acsomega.3c05913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
80
Tang S, Cui X, Wang R, Li S, Li S, Huang X, Chen S. scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data. Nat Commun 2024;15:1629. [PMID: 38388573 PMCID: PMC10884038 DOI: 10.1038/s41467-024-46045-w] [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: 09/21/2023] [Accepted: 02/12/2024] [Indexed: 02/24/2024]  Open
81
Zhang X, Marand AP, Yan H, Schmitz RJ. Massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.17.558155. [PMID: 37786710 PMCID: PMC10541611 DOI: 10.1101/2023.09.17.558155] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
82
Li K, Wang B, Hu H. Research progress of SWI/SNF complex in breast cancer. Epigenetics Chromatin 2024;17:4. [PMID: 38365747 PMCID: PMC10873968 DOI: 10.1186/s13072-024-00531-z] [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: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 02/18/2024]  Open
83
Chew V, Chuang CH, Hsu C. Translational research on drug development and biomarker discovery for hepatocellular carcinoma. J Biomed Sci 2024;31:22. [PMID: 38368324 PMCID: PMC10874078 DOI: 10.1186/s12929-024-01011-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: 09/03/2023] [Accepted: 02/10/2024] [Indexed: 02/19/2024]  Open
84
Sun H, Qu H, Duan K, Du W. scMGCN: A Multi-View Graph Convolutional Network for Cell Type Identification in scRNA-seq Data. Int J Mol Sci 2024;25:2234. [PMID: 38396909 PMCID: PMC10889820 DOI: 10.3390/ijms25042234] [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: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]  Open
85
Abadie K, Clark EC, Valanparambil RM, Ukogu O, Yang W, Daza RM, Ng KKH, Fathima J, Wang AL, Lee J, Nasti TH, Bhandoola A, Nourmohammad A, Ahmed R, Shendure J, Cao J, Kueh HY. Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision. Immunity 2024;57:271-286.e13. [PMID: 38301652 PMCID: PMC10922671 DOI: 10.1016/j.immuni.2023.12.006] [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: 03/09/2023] [Revised: 10/09/2023] [Accepted: 12/07/2023] [Indexed: 02/03/2024]
86
Taskiran II, Spanier KI, Dickmänken H, Kempynck N, Pančíková A, Ekşi EC, Hulselmans G, Ismail JN, Theunis K, Vandepoel R, Christiaens V, Mauduit D, Aerts S. Cell-type-directed design of synthetic enhancers. Nature 2024;626:212-220. [PMID: 38086419 PMCID: PMC10830415 DOI: 10.1038/s41586-023-06936-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/05/2023] [Indexed: 01/19/2024]
87
Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [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: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
88
Mihai IS, Chafle S, Henriksson J. Representing and extracting knowledge from single-cell data. Biophys Rev 2024;16:29-56. [PMID: 38495441 PMCID: PMC10937862 DOI: 10.1007/s12551-023-01091-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/28/2023] [Indexed: 03/19/2024]  Open
89
Moore JR, Nemera MT, D’Souza RD, Hamagami N, Clemens AW, Beard DC, Urman A, Mendoza VR, Gabel HW. Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577861. [PMID: 38352532 PMCID: PMC10862856 DOI: 10.1101/2024.01.30.577861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
90
Yan Y, Liu H, Abedini A, Sheng X, Palmer M, Li H, Susztak K. Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development. Nat Commun 2024;15:873. [PMID: 38287030 PMCID: PMC10824731 DOI: 10.1038/s41467-024-45295-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024]  Open
91
Yan F, Suzuki A, Iwaya C, Pei G, Chen X, Yoshioka H, Yu M, Simon LM, Iwata J, Zhao Z. Single-cell multiomics decodes regulatory programs for mouse secondary palate development. Nat Commun 2024;15:821. [PMID: 38280850 PMCID: PMC10821874 DOI: 10.1038/s41467-024-45199-x] [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: 02/23/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024]  Open
92
Lu C, Wei Y, Abbas M, Agula H, Wang E, Meng Z, Zhang R. Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects. Int J Mol Sci 2024;25:1479. [PMID: 38338756 PMCID: PMC10855595 DOI: 10.3390/ijms25031479] [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: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]  Open
93
Duan Z, Xu S, Sai Srinivasan S, Hwang A, Lee CY, Yue F, Gerstein M, Luan Y, Girgenti M, Zhang J. scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Brief Bioinform 2024;25:bbae096. [PMID: 38493342 PMCID: PMC10944576 DOI: 10.1093/bib/bbae096] [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: 11/06/2023] [Revised: 02/01/2024] [Accepted: 02/20/2024] [Indexed: 03/18/2024]  Open
94
Guo ZH, Wang YB, Wang S, Zhang Q, Huang DS. scCorrector: a robust method for integrating multi-study single-cell data. Brief Bioinform 2024;25:bbad525. [PMID: 38271483 PMCID: PMC10810333 DOI: 10.1093/bib/bbad525] [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: 09/15/2023] [Revised: 11/12/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024]  Open
95
Kim SS, Truong B, Jagadeesh K, Dey KK, Shen AZ, Raychaudhuri S, Kellis M, Price AL. Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nat Commun 2024;15:563. [PMID: 38233398 PMCID: PMC10794712 DOI: 10.1038/s41467-024-44742-0] [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: 04/30/2022] [Accepted: 01/02/2024] [Indexed: 01/19/2024]  Open
96
Kousnetsov R, Bourque J, Surnov A, Fallahee I, Hawiger D. Single-cell sequencing analysis within biologically relevant dimensions. Cell Syst 2024;15:83-103.e11. [PMID: 38198894 DOI: 10.1016/j.cels.2023.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/23/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
97
Xiong H, Wang Q, Li CC, He A. Single-cell joint profiling of multiple epigenetic proteins and gene transcription. SCIENCE ADVANCES 2024;10:eadi3664. [PMID: 38170774 PMCID: PMC10796078 DOI: 10.1126/sciadv.adi3664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
98
Qian FC, Zhou LW, Zhu YB, Li YY, Yu ZM, Feng CC, Fang QL, Zhao Y, Cai FH, Wang QY, Tang HF, Li CQ. scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species. Nucleic Acids Res 2024;52:D285-D292. [PMID: 37897340 PMCID: PMC10767920 DOI: 10.1093/nar/gkad924] [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: 08/15/2023] [Revised: 09/14/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023]  Open
99
Abedini A, Sánchez-Navaro A, Wu J, Klötzer KA, Ma Z, Poudel B, Doke T, Balzer MS, Frederick J, Cernecka H, Liu H, Liang X, Vitale S, Kolkhof P, Susztak K. Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists. J Clin Invest 2024;134:e157165. [PMID: 37906287 PMCID: PMC10760974 DOI: 10.1172/jci157165] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/23/2023] [Indexed: 11/02/2023]  Open
100
Lee AS, Ayers LJ, Kosicki M, Chan WM, Fozo LN, Pratt BM, Collins TE, Zhao B, Rose MF, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Tenney AP, Lee C, Laricchia KM, Barry BJ, Bradford VR, Lek M, MacArthur DG, Lee EA, Talkowski ME, Brand H, Pennacchio LA, Engle EC. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.22.23300468. [PMID: 38234731 PMCID: PMC10793524 DOI: 10.1101/2023.12.22.23300468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
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