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For: Loher P, Karathanasis N, Londin E, F. Bray P, Pliatsika V, Telonis AG, Rigoutsos I. IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets. Bioinformatics 2021;37:1828-1838. [PMID: 33471076 PMCID: PMC8317110 DOI: 10.1093/bioinformatics/btab016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/30/2020] [Accepted: 01/10/2021] [Indexed: 01/21/2023]  Open
Number Cited by Other Article(s)
1
Nersisyan S, Loher P, Nazeraj I, Shao Z, Fullard JF, Voloudakis G, Girdhar K, Roussos P, Rigoutsos I. Comprehensive profiling of small RNAs and their changes and linkages to mRNAs in schizophrenia and bipolar disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.24.630254. [PMID: 39763727 PMCID: PMC11703252 DOI: 10.1101/2024.12.24.630254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
2
Calin GA, Hubé F, Ladomery MR, Delihas N, Ferracin M, Poliseno L, Agnelli L, Alahari SK, Yu AM, Zhong XB. The 2024 Nobel Prize in Physiology or Medicine: microRNA Takes Center Stage. Noncoding RNA 2024;10:62. [PMID: 39728607 PMCID: PMC11679529 DOI: 10.3390/ncrna10060062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Accepted: 12/03/2024] [Indexed: 12/28/2024]  Open
3
Vivek AT, Arya A, Swain SP, Kumar S. athisomiRDB: A comprehensive database of Arabidopsis isomiRs. Database (Oxford) 2024;2024:baae115. [PMID: 39514415 PMCID: PMC11544919 DOI: 10.1093/database/baae115] [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: 02/10/2024] [Revised: 09/04/2024] [Accepted: 10/17/2024] [Indexed: 11/16/2024]
4
Cherlin T, Jing Y, Shah S, Kennedy A, Telonis AG, Pliatsika V, Wilson H, Thompson L, Vlantis PI, Loher P, Leiby B, Rigoutsos I. The subcellular distribution of miRNA isoforms, tRNA-derived fragments, and rRNA-derived fragments depends on nucleotide sequence and cell type. BMC Biol 2024;22:205. [PMID: 39267057 PMCID: PMC11397057 DOI: 10.1186/s12915-024-01970-6] [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: 12/07/2022] [Accepted: 08/01/2024] [Indexed: 09/14/2024]  Open
5
Maltseva D, Kirillov I, Zhiyanov A, Averinskaya D, Suvorov R, Gubani D, Kudriaeva A, Belogurov A, Tonevitsky A. Incautious design of shRNAs for stable overexpression of miRNAs could result in generation of undesired isomiRs. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024;1867:195046. [PMID: 38876159 DOI: 10.1016/j.bbagrm.2024.195046] [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: 11/17/2023] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
6
Wagner V, Meese E, Keller A. The intricacies of isomiRs: from classification to clinical relevance. Trends Genet 2024;40:784-796. [PMID: 38862304 DOI: 10.1016/j.tig.2024.05.007] [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: 03/22/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/13/2024]
7
Pliatsika V, Cherlin T, Loher P, Vlantis P, Nagarkar P, Nersisyan S, Rigoutsos I. MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs). Nucleic Acids Res 2024;52:D229-D238. [PMID: 37843123 PMCID: PMC10767805 DOI: 10.1093/nar/gkad833] [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: 08/13/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]  Open
8
Akins RB, Ostberg K, Cherlin T, Tsiouplis NJ, Loher P, Rigoutsos I. The Typical tRNA Co-Expresses Multiple 5' tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease. Noncoding RNA 2023;9:69. [PMID: 37987365 PMCID: PMC10660753 DOI: 10.3390/ncrna9060069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]  Open
9
Nersisyan S, Montenont E, Loher P, Middleton EA, Campbell R, Bray P, Rigoutsos I. Characterization of all small RNAs in and comparisons across cultured megakaryocytes and platelets of healthy individuals and COVID-19 patients. J Thromb Haemost 2023;21:3252-3267. [PMID: 37558133 DOI: 10.1016/j.jtha.2023.07.028] [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: 05/25/2023] [Revised: 07/03/2023] [Accepted: 07/24/2023] [Indexed: 08/11/2023]
10
Nersisyan S, Zhiyanov A, Engibaryan N, Maltseva D, Tonevitsky A. A novel approach for a joint analysis of isomiR and mRNA expression data reveals features of isomiR targeting in breast cancer. Front Genet 2022;13:1070528. [PMID: 36531236 PMCID: PMC9751988 DOI: 10.3389/fgene.2022.1070528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/21/2022] [Indexed: 07/31/2023]  Open
11
Distefano R, Tomasello L, Rampioni Vinciguerra GL, Gasparini P, Xiang Y, Bagnoli M, Marceca GP, Fadda P, Laganà A, Acunzo M, Ma Q, Nigita G, Croce CM. Pan-Cancer Analysis of Canonical and Modified miRNAs Enhances the Resolution of the Functional miRNAome in Cancer. Cancer Res 2022;82:3687-3700. [PMID: 36040379 PMCID: PMC9574374 DOI: 10.1158/0008-5472.can-22-0240] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/24/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
12
Giannella A, Riccetti S, Sinigaglia A, Piubelli C, Razzaboni E, Di Battista P, Agostini M, Dal Molin E, Manganelli R, Gobbi F, Ceolotto G, Barzon L. Circulating microRNA signatures associated with disease severity and outcome in COVID-19 patients. Front Immunol 2022;13:968991. [PMID: 36032130 PMCID: PMC9403711 DOI: 10.3389/fimmu.2022.968991] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/20/2022] [Indexed: 12/14/2022]  Open
13
Epigenomic Modifications in Modern and Ancient Genomes. Genes (Basel) 2022;13:genes13020178. [PMID: 35205223 PMCID: PMC8872240 DOI: 10.3390/genes13020178] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/26/2022]  Open
14
MicroRNA Isoforms Contribution to Melanoma Pathogenesis. Noncoding RNA 2021;7:ncrna7040063. [PMID: 34698264 PMCID: PMC8544706 DOI: 10.3390/ncrna7040063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022]  Open
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