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For: Ziegenhain C, Vieth B, Parekh S, Reinius B, Guillaumet-Adkins A, Smets M, Leonhardt H, Heyn H, Hellmann I, Enard W. Comparative Analysis of Single-Cell RNA Sequencing Methods. Mol Cell 2017;65:631-643.e4. [PMID: 28212749 DOI: 10.1016/j.molcel.2017.01.023] [Citation(s) in RCA: 947] [Impact Index Per Article: 118.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/01/2016] [Accepted: 01/17/2017] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
1
Tian Q, Zou Q, Jia L. Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes. NAR Genom Bioinform 2025;7:lqaf056. [PMID: 40371010 PMCID: PMC12076406 DOI: 10.1093/nargab/lqaf056] [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: 12/13/2024] [Revised: 04/23/2025] [Accepted: 05/01/2025] [Indexed: 05/16/2025]  Open
2
Bhuvaragavan S, Sruthi K, Nivetha R, Keerthana CB, Marieshwari BN, Janarthanan S. PacBio-based de novo transcriptomics of the coconut rhinoceros beetle Oryctes rhinoceros identifies physiologically important full-length genes and sheds insights into the molecular relationship (chitin synthase) between Scarabaeidae (Coleoptera) and Hymenoptera. 3 Biotech 2025;15:182. [PMID: 40417658 PMCID: PMC12095764 DOI: 10.1007/s13205-025-04348-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 05/05/2025] [Indexed: 05/27/2025]  Open
3
Yu L, Lin Y, Xu X, Yang P, Yang JYH. Interpretable Differential Abundance Signature (iDAS). SMALL METHODS 2025:e2500572. [PMID: 40420636 DOI: 10.1002/smtd.202500572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2025] [Revised: 04/28/2025] [Indexed: 05/28/2025]
4
da Silva JEH, Bernardino HS, de Oliveira IL, Camata JJ. A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data. Biosystems 2025;253:105464. [PMID: 40409400 DOI: 10.1016/j.biosystems.2025.105464] [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: 03/11/2024] [Revised: 03/20/2025] [Accepted: 04/17/2025] [Indexed: 05/25/2025]
5
Arya A, Tripathi P, Dubey N, Aier I, Kumar Varadwaj P. Navigating single-cell RNA-sequencing: protocols, tools, databases, and applications. Genomics Inform 2025;23:13. [PMID: 40382658 DOI: 10.1186/s44342-025-00044-5] [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: 01/22/2025] [Accepted: 04/07/2025] [Indexed: 05/20/2025]  Open
6
Wang H, Cheng P, Wang J, Lv H, Han J, Hou Z, Xu R, Chen W. Advances in spatial transcriptomics and its application in the musculoskeletal system. Bone Res 2025;13:54. [PMID: 40379648 DOI: 10.1038/s41413-025-00429-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 03/10/2025] [Accepted: 03/17/2025] [Indexed: 05/19/2025]  Open
7
Wu T, Li X, Zheng F, Liu H, Yu Y. Intercellular communication between FAP+ fibroblasts and SPP1+ macrophages in prostate cancer via multi-omics. Front Immunol 2025;16:1560998. [PMID: 40438108 PMCID: PMC12116517 DOI: 10.3389/fimmu.2025.1560998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 04/23/2025] [Indexed: 06/01/2025]  Open
8
Vieitas-Gaspar N, Soares-Cunha C, Rodrigues AJ. From valence encoding to motivated behavior: A focus on the nucleus accumbens circuitry. Neurosci Biobehav Rev 2025;172:106125. [PMID: 40154653 DOI: 10.1016/j.neubiorev.2025.106125] [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: 01/27/2025] [Revised: 03/21/2025] [Accepted: 03/23/2025] [Indexed: 04/01/2025]
9
Theunissen L, Mortier T, Saeys Y, Waegeman W. Evaluation of out-of-distribution detection methods for data shifts in single-cell transcriptomics. Brief Bioinform 2025;26:bbaf239. [PMID: 40439669 PMCID: PMC12121363 DOI: 10.1093/bib/bbaf239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Revised: 04/01/2025] [Accepted: 05/05/2025] [Indexed: 06/02/2025]  Open
10
Li C, Liao J, Chen B, Wang Q. Heterogeneity of the tumor immune cell microenvironment revealed by single-cell sequencing in head and neck cancer. Crit Rev Oncol Hematol 2025;209:104677. [PMID: 40023465 DOI: 10.1016/j.critrevonc.2025.104677] [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: 12/05/2024] [Revised: 02/16/2025] [Accepted: 02/26/2025] [Indexed: 03/04/2025]  Open
11
Yu X, Ren Y, Xia M, Shu Z, Zhu L. Decoupled GNNs based on multi-view contrastive learning for scRNA-seq data clustering. Brief Bioinform 2025;26:bbaf198. [PMID: 40366859 PMCID: PMC12077398 DOI: 10.1093/bib/bbaf198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 03/25/2025] [Accepted: 04/07/2025] [Indexed: 05/16/2025]  Open
12
Tang R, Jiang L, Ji Q, Kang P, Liu Y, Miao P, Xu X, Tang M. Resveratrol targeting MDM2/P53/PUMA axis to inhibit colonocyte apoptosis in DSS-induced ulcerative colitis mice. Front Pharmacol 2025;16:1572906. [PMID: 40371345 PMCID: PMC12075554 DOI: 10.3389/fphar.2025.1572906] [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: 02/07/2025] [Accepted: 04/07/2025] [Indexed: 05/16/2025]  Open
13
Zhang Z, Sun Y, Peng Q, Li T, Zhou P. Integrating Dynamical Systems Modeling with Spatiotemporal scRNA-Seq Data Analysis. ENTROPY (BASEL, SWITZERLAND) 2025;27:453. [PMID: 40422408 DOI: 10.3390/e27050453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2025] [Revised: 04/18/2025] [Accepted: 04/19/2025] [Indexed: 05/28/2025]
14
Cheng J, Zhang T, Cheng Y, Gebeyew K, Tan Z, He Z. Single-Cell RNA Sequencing Outperforms Single-Nucleus RNA Sequencing in Analyzing Pancreatic Cell Diversity and Gene Expression in Goats. Int J Mol Sci 2025;26:3916. [PMID: 40332786 PMCID: PMC12027589 DOI: 10.3390/ijms26083916] [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: 02/08/2025] [Revised: 04/15/2025] [Accepted: 04/19/2025] [Indexed: 05/08/2025]  Open
15
Black GS, Huang X, Qiao Y, Moos P, Sampath D, Stephens DM, Woyach JA, Marth GT. Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia. Genome Res 2025;35:686-697. [PMID: 39965935 PMCID: PMC12047255 DOI: 10.1101/gr.279049.124] [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: 03/15/2024] [Accepted: 01/30/2025] [Indexed: 02/20/2025]
16
Sukys A, Grima R. Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data. Nucleic Acids Res 2025;53:gkaf295. [PMID: 40240003 PMCID: PMC12000877 DOI: 10.1093/nar/gkaf295] [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: 01/24/2024] [Revised: 03/22/2025] [Accepted: 03/28/2025] [Indexed: 04/18/2025]  Open
17
Shao Y, Chen C, Yu X, Yan J, Guo J, Ye G. Comprehensive analysis of scRNA-seq and bulk RNA-seq data via machine learning and bioinformatics reveals the role of lysine metabolism-related genes in gastric carcinogenesis. BMC Cancer 2025;25:644. [PMID: 40205350 PMCID: PMC11984278 DOI: 10.1186/s12885-025-14051-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: 11/02/2024] [Accepted: 03/31/2025] [Indexed: 04/11/2025]  Open
18
Ma M, Luo Q, Chen L, Liu F, Yin L, Guan B. Novel insights into kidney disease: the scRNA-seq and spatial transcriptomics approaches: a literature review. BMC Nephrol 2025;26:181. [PMID: 40200175 DOI: 10.1186/s12882-025-04103-5] [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: 12/25/2024] [Accepted: 03/28/2025] [Indexed: 04/10/2025]  Open
19
Yang H, Sun W, Li J, Zhang X. Epigenetics factors in schizophrenia: future directions for etiologic and therapeutic study approaches. Ann Gen Psychiatry 2025;24:21. [PMID: 40186258 PMCID: PMC11969811 DOI: 10.1186/s12991-025-00557-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 03/14/2025] [Indexed: 04/07/2025]  Open
20
Thomson A, Rehn J, Yeung D, Breen J, White D. Deciphering IGH rearrangement complexity and detection strategies in acute lymphoblastic leukaemia. NPJ Precis Oncol 2025;9:99. [PMID: 40185891 PMCID: PMC11971345 DOI: 10.1038/s41698-025-00887-9] [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: 12/01/2024] [Accepted: 03/19/2025] [Indexed: 04/07/2025]  Open
21
Traversa D, Chiara M. Mapping Cell Identity from scRNA-seq: A primer on computational methods. Comput Struct Biotechnol J 2025;27:1559-1569. [PMID: 40270709 PMCID: PMC12017876 DOI: 10.1016/j.csbj.2025.03.051] [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: 11/15/2024] [Revised: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/25/2025]  Open
22
Saleh RO, Hjazi A, Rab SO, Uthirapathy S, Ganesan S, Shankhyan A, Ravi Kumar M, Sharma GC, Kariem M, Ahmed JK. Single-cell RNA Sequencing Contributes to the Treatment of Acute Myeloid Leukaemia With Hematopoietic Stem Cell Transplantation, Chemotherapy, and Immunotherapy. J Biochem Mol Toxicol 2025;39:e70218. [PMID: 40233268 DOI: 10.1002/jbt.70218] [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: 10/21/2024] [Revised: 01/31/2025] [Accepted: 03/02/2025] [Indexed: 04/17/2025]
23
Llera-Oyola J, Pérez-Moraga R, Parras M, Rosón B. How to view the female reproductive tract through single-cell looking glasses. Am J Obstet Gynecol 2025;232:S21-S43. [PMID: 40253081 DOI: 10.1016/j.ajog.2024.08.040] [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: 08/29/2023] [Revised: 07/04/2024] [Accepted: 08/24/2024] [Indexed: 04/21/2025]
24
Wang F, Zhang Y, Sun M, Li M, Wang Y, Zhang D, Yao S. Single-cell sequencing reveals the same heterogeneity of neutrophils in heatstroke-induced lung and liver injury. Mucosal Immunol 2025:S1933-0219(25)00031-5. [PMID: 40158777 DOI: 10.1016/j.mucimm.2025.03.005] [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: 11/19/2024] [Revised: 02/23/2025] [Accepted: 03/25/2025] [Indexed: 04/02/2025]
25
Yi T, Wu S, Yang Y, Li X, Yang S, Zhang Y, Zhang L, Hu Y, Zhang G, Li J, Yang D. Single-nucleus RNA sequencing reveals dynamic changes in the microenvironment of visceral adipose tissue and metabolic characteristics after cold exposure. Front Endocrinol (Lausanne) 2025;16:1562431. [PMID: 40196457 PMCID: PMC11973077 DOI: 10.3389/fendo.2025.1562431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Accepted: 03/04/2025] [Indexed: 04/09/2025]  Open
26
Nicoll AG, Szavits-Nossan J, Evans MR, Grima R. Transient power-law behaviour following induction distinguishes between competing models of stochastic gene expression. Nat Commun 2025;16:2833. [PMID: 40121209 PMCID: PMC11929856 DOI: 10.1038/s41467-025-58127-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/10/2025] [Indexed: 03/25/2025]  Open
27
Liao X, Li Y, Li S, Wen L, Li X, Yu B. Enhanced Integration of Single-Cell Multi-Omics Data Using Graph Attention Networks. ACS Synth Biol 2025;14:931-942. [PMID: 39888834 DOI: 10.1021/acssynbio.4c00864] [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] [Indexed: 02/02/2025]
28
Hong J, Lu S, Shan G, Yang Y, Li B, Yang D. Application and Progression of Single-Cell RNA Sequencing in Diabetes Mellitus and Diabetes Complications. J Diabetes Res 2025;2025:3248350. [PMID: 40135071 PMCID: PMC11936531 DOI: 10.1155/jdr/3248350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 02/26/2025] [Indexed: 03/27/2025]  Open
29
Wan X, Zou Y, Zhou Q, Tang Q, Zhu G, Jia L, Yu X, Mo H, Yang X, Wang S. Tumor Prognostic Risk Model Related to Monocytes/Macrophages in Hepatocellular Carcinoma Based on Machine Learning and Multi-Omics. Biol Proced Online 2025;27:9. [PMID: 40065214 PMCID: PMC11892220 DOI: 10.1186/s12575-025-00270-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Accepted: 02/13/2025] [Indexed: 03/14/2025]  Open
30
Rajalekshmi R, Agrawal DK. Synergistic potential of stem cells and microfluidics in regenerative medicine. Mol Cell Biochem 2025;480:1481-1493. [PMID: 39285093 PMCID: PMC11842489 DOI: 10.1007/s11010-024-05108-8] [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: 04/12/2024] [Accepted: 08/27/2024] [Indexed: 02/21/2025]
31
Yao Y, Luo Y, Liang X, Zhong L, Wang Y, Hong Z, Song C, Xu Z, Wang J, Zhang M. The role of oxidative stress-mediated fibro-adipogenic progenitor senescence in skeletal muscle regeneration and repair. Stem Cell Res Ther 2025;16:104. [PMID: 40025535 PMCID: PMC11872320 DOI: 10.1186/s13287-025-04242-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 02/18/2025] [Indexed: 03/04/2025]  Open
32
Huang J, Hu Y, Wang S, Liu Y, Sun X, Wang X, Yu H. Single-cell RNA sequencing in autoimmune diseases: New insights and challenges. Pharmacol Ther 2025;267:108807. [PMID: 39894174 DOI: 10.1016/j.pharmthera.2025.108807] [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: 01/02/2025] [Accepted: 01/29/2025] [Indexed: 02/04/2025]
33
Yu B, Zhang J, Han Y, Gao F, Jing P, Zhang P, Jing G, Zhou S, Wang HY. Intratumoral Injection of Cytotoxic Drugs Plus Hapten Elicits Significant Immune Responses in Sentinel Lymph Nodes: Implications for Cancer Immunotherapy. Pancreas 2025;54:e227-e234. [PMID: 39999315 DOI: 10.1097/mpa.0000000000002439] [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] [Indexed: 02/27/2025]
34
Gu XY, Gu SL, Chen ZY, Tong JL, Li XY, Dong H, Zhang CY, Qian WX, Ma XC, Yi CH, Yi YX. Uncovering immune cell heterogeneity in hepatocellular carcinoma by combining single-cell RNA sequencing with T-cell receptor sequencing. World J Hepatol 2025;17:99046. [PMID: 40027555 PMCID: PMC11866147 DOI: 10.4254/wjh.v17.i2.99046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 11/13/2024] [Accepted: 12/31/2024] [Indexed: 02/20/2025]  Open
35
An Q, Duan L, Wang Y, Wang F, Liu X, Liu C, Hu Q. Role of CD4+ T cells in cancer immunity: a single-cell sequencing exploration of tumor microenvironment. J Transl Med 2025;23:179. [PMID: 39953548 PMCID: PMC11829416 DOI: 10.1186/s12967-025-06167-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Accepted: 01/22/2025] [Indexed: 02/17/2025]  Open
36
Fan BL, Chen LH, Chen LL, Guo H. Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects. Int J Mol Sci 2025;26:1466. [PMID: 40003933 PMCID: PMC11855028 DOI: 10.3390/ijms26041466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 01/21/2025] [Accepted: 01/21/2025] [Indexed: 02/27/2025]  Open
37
Zhao MY, Shen ZL, Dai H, Xu WY, Wang LN, Gu Y, Zhao JH, Yu TH, Wang CZ, Xu JF, Chen GJ, Chen DH, Hong WM, Zhang F. Single-cell sequencing elucidates the mechanism of NUSAP1 in glioma and its diagnostic and prognostic significance. Front Immunol 2025;16:1512867. [PMID: 39975552 PMCID: PMC11835852 DOI: 10.3389/fimmu.2025.1512867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 01/17/2025] [Indexed: 02/21/2025]  Open
38
Molla Desta G, Birhanu AG. Advancements in single-cell RNA sequencing and spatial transcriptomics: transforming biomedical research. Acta Biochim Pol 2025;72:13922. [PMID: 39980637 PMCID: PMC11835515 DOI: 10.3389/abp.2025.13922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 01/20/2025] [Indexed: 02/22/2025]
39
Bramon Mora B, Lindsay H, Thiébaut A, Stuart KD, Gottardo R. tagtango: an application to compare single-cell annotations. Bioinformatics 2025;41:btaf012. [PMID: 39798134 PMCID: PMC11814489 DOI: 10.1093/bioinformatics/btaf012] [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: 07/16/2024] [Revised: 12/11/2024] [Accepted: 01/08/2025] [Indexed: 01/15/2025]  Open
40
Ju WS, Kim S, Lee JY, Lee H, No J, Lee S, Oh K. Gene Editing for Enhanced Swine Production: Current Advances and Prospects. Animals (Basel) 2025;15:422. [PMID: 39943192 PMCID: PMC11815767 DOI: 10.3390/ani15030422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2024] [Revised: 01/23/2025] [Accepted: 01/24/2025] [Indexed: 02/16/2025]  Open
41
Rodov A, Baniadam H, Zeiser R, Amit I, Yosef N, Wertheimer T, Ingelfinger F. Towards the Next Generation of Data-Driven Therapeutics Using Spatially Resolved Single-Cell Technologies and Generative AI. Eur J Immunol 2025;55:e202451234. [PMID: 39964048 PMCID: PMC11834372 DOI: 10.1002/eji.202451234] [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: 09/26/2024] [Revised: 01/28/2025] [Accepted: 02/03/2025] [Indexed: 02/21/2025]
42
Yang Y, Zhu L, Zhao J, Zhang B, Wang X, Cheung WW, Zhao C, Zhou P. Single-Cell Analysis of Endothelial Cell Injury in IgA Nephropathy. Immun Inflamm Dis 2025;13:e70149. [PMID: 39945225 PMCID: PMC11822453 DOI: 10.1002/iid3.70149] [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: 06/30/2024] [Revised: 09/25/2024] [Accepted: 01/21/2025] [Indexed: 02/16/2025]  Open
43
Goss K, Horwitz EM. Single-cell multiomics to advance cell therapy. Cytotherapy 2025;27:137-145. [PMID: 39530970 DOI: 10.1016/j.jcyt.2024.10.009] [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: 09/13/2024] [Revised: 10/21/2024] [Accepted: 10/21/2024] [Indexed: 11/16/2024]
44
Khosroabadi Z, Azaryar S, Dianat-Moghadam H, Amoozgar Z, Sharifi M. Single cell RNA sequencing improves the next generation of approaches to AML treatment: challenges and perspectives. Mol Med 2025;31:33. [PMID: 39885388 PMCID: PMC11783831 DOI: 10.1186/s10020-025-01085-w] [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: 10/03/2024] [Accepted: 01/16/2025] [Indexed: 02/01/2025]  Open
45
Maji RK, Leisegang MS, Boon RA, Schulz MH. Revealing microRNA regulation in single cells. Trends Genet 2025:S0168-9525(24)00317-2. [PMID: 39863489 DOI: 10.1016/j.tig.2024.12.009] [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: 11/18/2024] [Revised: 12/22/2024] [Accepted: 12/26/2024] [Indexed: 01/27/2025]
46
Hakala S, Hämäläinen A, Sandelin S, Giannareas N, Närvä E. Detection of Cancer Stem Cells from Patient Samples. Cells 2025;14:148. [PMID: 39851576 PMCID: PMC11764358 DOI: 10.3390/cells14020148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 01/16/2025] [Accepted: 01/17/2025] [Indexed: 01/26/2025]  Open
47
Zhao Q, Li S, Krall L, Li Q, Sun R, Yin Y, Fu J, Zhang X, Wang Y, Yang M. Deciphering cellular complexity: advances and future directions in single-cell protein analysis. Front Bioeng Biotechnol 2025;12:1507460. [PMID: 39877263 PMCID: PMC11772399 DOI: 10.3389/fbioe.2024.1507460] [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: 10/07/2024] [Accepted: 12/19/2024] [Indexed: 01/31/2025]  Open
48
Yang T, Zhang N, Yang N. Single-cell sequencing in diabetic retinopathy: progress and prospects. J Transl Med 2025;23:49. [PMID: 39806376 PMCID: PMC11727737 DOI: 10.1186/s12967-024-06066-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: 10/11/2024] [Accepted: 12/30/2024] [Indexed: 01/16/2025]  Open
49
Cao Z, Wang Y, Grima R. Deterministic patterns in single-cell transcriptomic data. NPJ Syst Biol Appl 2025;11:6. [PMID: 39799124 PMCID: PMC11724867 DOI: 10.1038/s41540-025-00490-5] [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: 11/27/2024] [Accepted: 01/06/2025] [Indexed: 01/15/2025]  Open
50
Tzaban S, Stern O, Zisman E, Eisenberg G, Klein S, Frankenburg S, Lotem M. Alternative splicing of modulatory immune receptors in T lymphocytes: a newly identified and targetable mechanism for anticancer immunotherapy. Front Immunol 2025;15:1490035. [PMID: 39845971 PMCID: PMC11752881 DOI: 10.3389/fimmu.2024.1490035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 11/25/2024] [Indexed: 01/24/2025]  Open
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