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For: Duan Y, Zhang W, Cheng Y, Shi M, Xia XQ. A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs. RNA 2021;27:80-98. [PMID: 33055239 PMCID: PMC7749630 DOI: 10.1261/rna.074724.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Number Cited by Other Article(s)
1
Zhang A, Pi W, Wang Y, Li Y, Wang J, Liu S, Cui X, Liu H, Yao D, Zhao R. Update on functional analysis of long non-coding RNAs in common crops. FRONTIERS IN PLANT SCIENCE 2024;15:1389154. [PMID: 38872885 PMCID: PMC11169716 DOI: 10.3389/fpls.2024.1389154] [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: 02/21/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024]
2
Huang E, Frydman C, Xiao X. Navigating the landscape of epitranscriptomics and host immunity. Genome Res 2024;34:515-529. [PMID: 38702197 PMCID: PMC11146601 DOI: 10.1101/gr.278412.123] [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: 05/06/2024]
3
Kang J, Chung A, Suresh S, Bonzi LC, Sourisse JM, Ramirez‐Calero S, Romeo D, Petit‐Marty N, Pegueroles C, Schunter C. Long non-coding RNAs mediate fish gene expression in response to ocean acidification. Evol Appl 2024;17:e13655. [PMID: 38357358 PMCID: PMC10866067 DOI: 10.1111/eva.13655] [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: 08/24/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024]  Open
4
Hong L, Yang P, Zhang L, Liu X, Wei X, Xiao W, Yu Z, Zhang J, Peng Y, Wu X, Tang W, Zhi F, Li G, Li A, Lin J, Liu S, Zhang H, Xiang L, Wang J. The VAX2-LINC01189-hnRNPF signaling axis regulates cell invasion and migration in gastric cancer. Cell Death Discov 2023;9:387. [PMID: 37865686 PMCID: PMC10590441 DOI: 10.1038/s41420-023-01688-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/28/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023]  Open
5
Ballarino M, Pepe G, Helmer-Citterich M, Palma A. Exploring the landscape of tools and resources for the analysis of long non-coding RNAs. Comput Struct Biotechnol J 2023;21:4706-4716. [PMID: 37841333 PMCID: PMC10568309 DOI: 10.1016/j.csbj.2023.09.041] [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: 08/12/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023]  Open
6
Hidalgo M, Ramos C, Zolla G. Analysis of lncRNAs in Lupinus mutabilis (Tarwi) and Their Potential Role in Drought Response. Noncoding RNA 2023;9:48. [PMID: 37736894 PMCID: PMC10514842 DOI: 10.3390/ncrna9050048] [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: 07/11/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/23/2023]  Open
7
Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption. Cells 2023;12:cells12050729. [PMID: 36899864 PMCID: PMC10001313 DOI: 10.3390/cells12050729] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023]  Open
8
Transcriptomes of Zebrafish in Early Stages of Multiple Viral Invasions Reveal the Role of Sterols in Innate Immune Switch-On. Int J Mol Sci 2023;24:ijms24054427. [PMID: 36901854 PMCID: PMC10003308 DOI: 10.3390/ijms24054427] [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: 01/06/2023] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023]  Open
9
Chen JW, Shrestha L, Green G, Leier A, Marquez-Lago TT. The hitchhikers' guide to RNA sequencing and functional analysis. Brief Bioinform 2023;24:bbac529. [PMID: 36617463 PMCID: PMC9851315 DOI: 10.1093/bib/bbac529] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 01/10/2023]  Open
10
Profiling the Spatial Expression Pattern and ceRNA Network of lncRNA, miRNA, and mRNA Associated with the Development of Intermuscular Bones in Zebrafish. BIOLOGY 2022;12:biology12010075. [PMID: 36671767 PMCID: PMC9855694 DOI: 10.3390/biology12010075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023]
11
Singh D, Roy J. A large-scale benchmark study of tools for the classification of protein-coding and non-coding RNAs. Nucleic Acids Res 2022;50:12094-12111. [PMID: 36420898 PMCID: PMC9757047 DOI: 10.1093/nar/gkac1092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 10/22/2022] [Accepted: 10/28/2022] [Indexed: 11/27/2022]  Open
12
Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development. Int J Mol Sci 2022;23:ijms231911547. [PMID: 36232849 PMCID: PMC9569805 DOI: 10.3390/ijms231911547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022]  Open
13
Ou X, Zhou X, Li J, Ye J, Liu H, Fang D, Cai Q, Cai S, He Y, Xu J. p53-Induced LINC00893 Regulates RBFOX2 Stability to Suppress Gastric Cancer Progression. Front Cell Dev Biol 2022;9:796451. [PMID: 35127712 PMCID: PMC8807521 DOI: 10.3389/fcell.2021.796451] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/29/2021] [Indexed: 01/07/2023]  Open
14
Ye W, Duan Y, Zhang W, Cheng Y, Shi M, Xia XQ. Comprehensive analysis of hub mRNA, lncRNA and miRNA, and associated ceRNA networks implicated in grass carp (Ctenopharyngodon idella) growth traits. Genomics 2021;113:4004-4014. [PMID: 34614437 DOI: 10.1016/j.ygeno.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/03/2021] [Accepted: 10/01/2021] [Indexed: 01/19/2023]
15
Zheng H, Talukder A, Li X, Hu H. A systematic evaluation of the computational tools for lncRNA identification. Brief Bioinform 2021;22:6343529. [PMID: 34368833 DOI: 10.1093/bib/bbab285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022]  Open
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