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For: Dinger ME, Pang KC, Mercer TR, Mattick JS. Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol 2008;4:e1000176. [PMID: 19043537 PMCID: PMC2518207 DOI: 10.1371/journal.pcbi.1000176] [Citation(s) in RCA: 406] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
Number Cited by Other Article(s)
1
Sun D, Zhou X, Su Y, Gao B, Liu P, Lv J. Multi-omics analysis reveals an endogenous competitive regulatory mechanism for resistance to Vibrio parahaemolyticus in the swimming crab, Portunus trituberculatus. FISH & SHELLFISH IMMUNOLOGY 2025;163:110403. [PMID: 40347995 DOI: 10.1016/j.fsi.2025.110403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Revised: 04/27/2025] [Accepted: 05/08/2025] [Indexed: 05/14/2025]
2
Ye F, Chen X, Li Y, Ju A, Sheng Y, Duan L, Zhang J, Zhang Z, Al-Rasheid KAS, Stover NA, Gao S. Comprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling. Nucleic Acids Res 2025;53:gkae1177. [PMID: 39657783 PMCID: PMC11754650 DOI: 10.1093/nar/gkae1177] [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: 02/18/2024] [Revised: 10/29/2024] [Accepted: 11/12/2024] [Indexed: 12/12/2024]  Open
3
Santucci K, Cheng Y, Xu SM, Janitz M. Enhancing novel isoform discovery: leveraging nanopore long-read sequencing and machine learning approaches. Brief Funct Genomics 2024;23:683-694. [PMID: 39158328 DOI: 10.1093/bfgp/elae031] [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] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/20/2024]  Open
4
Naidu P, Holford M. Microscopic marvels: Decoding the role of micropeptides in innate immunity. Immunology 2024;173:605-621. [PMID: 39188052 DOI: 10.1111/imm.13850] [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: 03/11/2024] [Accepted: 07/30/2024] [Indexed: 08/28/2024]  Open
5
Ismail M, Fadul MM, Taha R, Siddig O, Elhafiz M, Yousef BA, Jiang Z, Zhang L, Sun L. Dynamic role of exosomal long non-coding RNA in liver diseases: pathogenesis and diagnostic aspects. Hepatol Int 2024;18:1715-1730. [PMID: 39306594 DOI: 10.1007/s12072-024-10722-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 08/15/2024] [Indexed: 12/11/2024]
6
Chanut-Delalande H, Zanet J. Small ORFs, Big Insights: Drosophila as a Model to Unraveling Microprotein Functions. Cells 2024;13:1645. [PMID: 39404408 PMCID: PMC11475943 DOI: 10.3390/cells13191645] [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: 09/13/2024] [Revised: 09/27/2024] [Accepted: 10/02/2024] [Indexed: 10/19/2024]  Open
7
Nath P, Bhuyan K, Bhattacharyya DK, Barah P. ETENLNC: An end to end lncRNA identification and analysis framework to facilitate construction of known and novel lncRNA regulatory networks. Comput Biol Chem 2024;112:108140. [PMID: 38996755 DOI: 10.1016/j.compbiolchem.2024.108140] [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: 08/31/2023] [Revised: 04/22/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024]
8
Chen WC, Chen WX, Tan YY, Xu YJ, Luo Y, Qian SY, Xu WY, Huang MC, Guo YH, Zhou ZG, Zhang Q, Lu JX, Xie SJ. LncRNA 4930581F22Rik promotes myogenic differentiation by regulating the ERK/MAPK signaling pathway. Heliyon 2024;10:e30640. [PMID: 38774102 PMCID: PMC11107111 DOI: 10.1016/j.heliyon.2024.e30640] [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: 01/11/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/24/2024]  Open
9
Duffy EE, Assad EG, Kalish BT, Greenberg ME. Small but mighty: the rise of microprotein biology in neuroscience. Front Mol Neurosci 2024;17:1386219. [PMID: 38807924 PMCID: PMC11130481 DOI: 10.3389/fnmol.2024.1386219] [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: 02/14/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024]  Open
10
Singh AK. Rules and impacts of nonsense-mediated mRNA decay in the degradation of long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024;15:e1853. [PMID: 38741356 DOI: 10.1002/wrna.1853] [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: 12/30/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
11
Song J, Wang Y, Zhu Z, Wang W, Yang H, Shan Z. Negative Regulation of LINC01013 by METTL3 and YTHDF2 Enhances the Osteogenic Differentiation of Senescent Pre-Osteoblast Cells Induced by Hydrogen Peroxide. Adv Biol (Weinh) 2024;8:e2300642. [PMID: 38548669 DOI: 10.1002/adbi.202300642] [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: 11/26/2023] [Revised: 02/19/2024] [Indexed: 05/15/2024]
12
Pan W, Liu C, Ren T, Chen X, Liang C, Wang J, Yang J. Exploration of lncRNA/circRNA-miRNA-mRNA network in patients with chronic atrophic gastritis in Tibetan plateau areas based on DNBSEQ-G99 RNA sequencing. Sci Rep 2024;14:9212. [PMID: 38649401 PMCID: PMC11035649 DOI: 10.1038/s41598-024-59836-4] [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: 10/27/2023] [Accepted: 04/16/2024] [Indexed: 04/25/2024]  Open
13
Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. Cell Syst 2024;15:388-408.e4. [PMID: 38636458 PMCID: PMC11075746 DOI: 10.1016/j.cels.2024.03.005] [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: 06/23/2023] [Revised: 01/21/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
14
Miravet-Verde S, Mazzolini R, Segura-Morales C, Broto A, Lluch-Senar M, Serrano L. ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs. Nat Commun 2024;15:2091. [PMID: 38453908 PMCID: PMC10920889 DOI: 10.1038/s41467-024-46112-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/14/2024] [Indexed: 03/09/2024]  Open
15
Zhang R, Liu W, Zhang Z. miR-306-5p is involved in chitin metabolism in Aedes albopictus pupae via linc8338-miR-306-5p-XM_019678125.2 axis. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024;200:105811. [PMID: 38582583 DOI: 10.1016/j.pestbp.2024.105811] [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: 09/13/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 04/08/2024]
16
Yadav V, Jena MK, Parashar G, Parashar NC, Joshi H, Ramniwas S, Tuli HS. Emerging role of microRNAs as regulators of protein kinase C substrate MARCKS and MARCKSL1 in cancer. Exp Cell Res 2024;434:113891. [PMID: 38104645 DOI: 10.1016/j.yexcr.2023.113891] [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: 09/24/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
17
Fuchs S, Engelmann S. Small proteins in bacteria - Big challenges in prediction and identification. Proteomics 2023;23:e2200421. [PMID: 37609810 DOI: 10.1002/pmic.202200421] [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: 05/31/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023]
18
Mohsen JJ, Martel AA, Slavoff SA. Microproteins-Discovery, structure, and function. Proteomics 2023;23:e2100211. [PMID: 37603371 PMCID: PMC10841188 DOI: 10.1002/pmic.202100211] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
19
Dimonaco NJ, Clare A, Kenobi K, Aubrey W, Creevey CJ. StORF-Reporter: finding genes between genes. Nucleic Acids Res 2023;51:11504-11517. [PMID: 37897345 PMCID: PMC10682499 DOI: 10.1093/nar/gkad814] [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: 08/23/2022] [Revised: 09/04/2023] [Accepted: 09/27/2023] [Indexed: 10/30/2023]  Open
20
Ghaedrahmati F, Nasrolahi A, Najafi S, Mighani M, Anbiyaee O, Haybar H, Assareh AR, Kempisty B, Dzięgiel P, Azizidoost S, Farzaneh M. Circular RNAs-mediated angiogenesis in human cancers. Clin Transl Oncol 2023;25:3101-3121. [PMID: 37039938 DOI: 10.1007/s12094-023-03178-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/16/2023] [Indexed: 04/12/2023]
21
Sutanto K, Turcotte M. Assessing Global-Local Secondary Structure Fingerprints to Classify RNA Sequences With Deep Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:2736-2747. [PMID: 34633933 DOI: 10.1109/tcbb.2021.3118358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
22
Mattick JS. A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs. Bioessays 2023;45:e2300080. [PMID: 37318305 DOI: 10.1002/bies.202300080] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023]
23
Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548938. [PMID: 37503254 PMCID: PMC10369987 DOI: 10.1101/2023.07.13.548938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
24
Liu D, Lu X, Huang W, Zhuang W. Long non-coding RNAs in non-small cell lung cancer: implications for EGFR-TKI resistance. Front Genet 2023;14:1222059. [PMID: 37456663 PMCID: PMC10349551 DOI: 10.3389/fgene.2023.1222059] [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: 05/13/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023]  Open
25
Leblanc S, Brunet MA, Jacques JF, Lekehal AM, Duclos A, Tremblay A, Bruggeman-Gascon A, Samandi S, Brunelle M, Cohen AA, Scott MS, Roucou X. Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:515-534. [PMID: 36183975 PMCID: PMC10787177 DOI: 10.1016/j.gpb.2022.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/10/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
26
Wozniak M, Czyz M. lncRNAs-EZH2 interaction as promising therapeutic target in cutaneous melanoma. Front Mol Biosci 2023;10:1170026. [PMID: 37325482 PMCID: PMC10265524 DOI: 10.3389/fmolb.2023.1170026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]  Open
27
Hui P, Ni F, Zheng L, Jia L, Wang Z. Identification of immunotherapy-related lncRNA signature for predicting prognosis, immunotherapy responses and drug candidates in bladder cancer. BMC Cancer 2023;23:355. [PMID: 37072750 PMCID: PMC10111848 DOI: 10.1186/s12885-023-10828-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/08/2023] [Indexed: 04/20/2023]  Open
28
Zhang Z, Tian T, Pan N, Wang Y, Peng M, Zhao X, Pan Z, Wan C. Microprotein Dysregulation in the Serum of Patients with Atrial Fibrillation. J Proteome Res 2023;22:1172-1180. [PMID: 36924315 DOI: 10.1021/acs.jproteome.2c00622] [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: 03/18/2023]
29
Fedoreyeva LI. Molecular Mechanisms of Regulation of Root Development by Plant Peptides. PLANTS (BASEL, SWITZERLAND) 2023;12:1320. [PMID: 36987008 PMCID: PMC10053774 DOI: 10.3390/plants12061320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/14/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
30
Mattick JS. RNA out of the mist. Trends Genet 2023;39:187-207. [PMID: 36528415 DOI: 10.1016/j.tig.2022.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
31
Chen K, Zhu X, Wang J, Hao L, Liu Z, Liu Y. ncDENSE: a novel computational method based on a deep learning framework for non-coding RNAs family prediction. BMC Bioinformatics 2023;24:68. [PMID: 36849908 PMCID: PMC9972773 DOI: 10.1186/s12859-023-05191-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/16/2023] [Indexed: 03/01/2023]  Open
32
Hadjeras L, Bartel J, Maier LK, Maaß S, Vogel V, Svensson SL, Eggenhofer F, Gelhausen R, Müller T, Alkhnbashi OS, Backofen R, Becher D, Sharma CM, Marchfelder A. Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry. MICROLIFE 2023;4:uqad001. [PMID: 37223747 PMCID: PMC10117724 DOI: 10.1093/femsml/uqad001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/29/2022] [Accepted: 01/13/2023] [Indexed: 05/25/2023]
33
Activity-Dependent Non-Coding RNA MAPK Interactome of the Human Epileptic Brain. Noncoding RNA 2023;9:ncrna9010003. [PMID: 36649033 PMCID: PMC9844323 DOI: 10.3390/ncrna9010003] [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: 10/01/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023]  Open
34
Lindemann A, Brandes F, Borrmann M, Meidert AS, Kirchner B, Steinlein OK, Schelling G, Pfaffl MW, Reithmair M. Anesthetic‑specific lncRNA and mRNA profile changes in blood during colorectal cancer resection: A prospective, matched‑case pilot study. Oncol Rep 2022;49:28. [PMID: 36562401 PMCID: PMC9813548 DOI: 10.3892/or.2022.8465] [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: 07/22/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022]  Open
35
Li S, Zhang J, Zhang L, Fang X, Luo J, An H, Zhang X. Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.). FRONTIERS IN PLANT SCIENCE 2022;13:1078085. [PMID: 36582646 PMCID: PMC9792668 DOI: 10.3389/fpls.2022.1078085] [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: 10/24/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
36
Kim JY, Lee J, Kang MH, Trang TTM, Lee J, Lee H, Jeong H, Lim PO. Dynamic landscape of long noncoding RNAs during leaf aging in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022;13:1068163. [PMID: 36531391 PMCID: PMC9753222 DOI: 10.3389/fpls.2022.1068163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
37
Wu S, Ren K, Zhao J, Li J, Jia B, Wu X, Dou Y, Fei X, Huan Y, He X, Wang T, Lv W, Wang L, Wang Y, Zhao J, Fei Z, Li S. LncRNA GAS5 represses stemness and malignancy of gliomas via elevating the SPACA6-miR-125a/let-7e Axis. Front Oncol 2022;12:803652. [PMID: 36106122 PMCID: PMC9465381 DOI: 10.3389/fonc.2022.803652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 08/03/2022] [Indexed: 11/13/2022]  Open
38
Kara G, Arun B, Calin GA, Ozpolat B. miRacle of microRNA-Driven Cancer Nanotherapeutics. Cancers (Basel) 2022;14:3818. [PMID: 35954481 PMCID: PMC9367393 DOI: 10.3390/cancers14153818] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/28/2022] [Accepted: 08/04/2022] [Indexed: 12/23/2022]  Open
39
Dey SS, Sharma PK, Munshi AD, Jaiswal S, Behera TK, Kumari K, G. B, Iquebal MA, Bhattacharya RC, Rai A, Kumar D. Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2022;13:884476. [PMID: 35991462 PMCID: PMC9383263 DOI: 10.3389/fpls.2022.884476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
40
Samsing F, Wynne JW, Valenzuela-Muñoz V, Valenzuela-Miranda D, Gallardo-Escárate C, Alexandre PA. Competing endogenous RNA-networks reveal key regulatory microRNAs involved in the response of Atlantic salmon to a novel orthomyxovirus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022;132:104396. [PMID: 35304180 DOI: 10.1016/j.dci.2022.104396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
41
Wang D, Gao Y, Sun S, Li L, Wang K. Expression Profiles and Characteristics of Apple lncRNAs in Roots, Phloem, Leaves, Flowers, and Fruit. Int J Mol Sci 2022;23:ijms23115931. [PMID: 35682639 PMCID: PMC9180697 DOI: 10.3390/ijms23115931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 12/29/2022]  Open
42
Ammunét T, Wang N, Khan S, Elo LL. Deep learning tools are top performers in long non-coding RNA prediction. Brief Funct Genomics 2022;21:230-241. [PMID: 35136929 PMCID: PMC9123429 DOI: 10.1093/bfgp/elab045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/08/2021] [Accepted: 12/02/2021] [Indexed: 11/23/2022]  Open
43
Fijalkowski I, Willems P, Jonckheere V, Simoens L, Van Damme P. Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides. MICROLIFE 2022;3:uqac005. [PMID: 37223358 PMCID: PMC10117744 DOI: 10.1093/femsml/uqac005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 04/18/2022] [Accepted: 04/29/2022] [Indexed: 05/25/2023]
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Zhu H, Jiang S, Zhou W, Chi H, Sun J, Shi J, Zhang Z, Chang L, Yu L, Zhang L, Lyu Z, Xu P, Zhang Y. Ac-LysargiNase efficiently helps genome reannotation of Mycolicibacterium smegmatis MC2 155. J Proteomics 2022;264:104622. [DOI: 10.1016/j.jprot.2022.104622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
45
Peng T, Liu X, Tian F, Xu H, Yang F, Chen X, Gao X, Lv Y, Li J, Pan Y, Shang Q. Functional investigation of lncRNAs and target cytochrome P450 genes related to spirotetramat resistance in Aphis gossypii Glover. PEST MANAGEMENT SCIENCE 2022;78:1982-1991. [PMID: 35092151 DOI: 10.1002/ps.6818] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/07/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
46
The Genome-Wide Identification of Long Non-Coding RNAs Involved in Floral Thermogenesis in Nelumbo nucifera Gaertn. Int J Mol Sci 2022;23:ijms23094901. [PMID: 35563291 PMCID: PMC9102460 DOI: 10.3390/ijms23094901] [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: 03/26/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023]  Open
47
Characterization of Oligopeptides in Solanum lycopersicum Xylem Exudates. Life (Basel) 2022;12:life12040592. [PMID: 35455083 PMCID: PMC9028419 DOI: 10.3390/life12040592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 11/29/2022]  Open
48
Ashrafizadeh M, Paskeh MDA, Mirzaei S, Gholami MH, Zarrabi A, Hashemi F, Hushmandi K, Hashemi M, Nabavi N, Crea F, Ren J, Klionsky DJ, Kumar AP, Wang Y. Targeting autophagy in prostate cancer: preclinical and clinical evidence for therapeutic response. J Exp Clin Cancer Res 2022;41:105. [PMID: 35317831 PMCID: PMC8939209 DOI: 10.1186/s13046-022-02293-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/16/2022] [Indexed: 02/08/2023]  Open
49
Leong AZX, Lee PY, Mohtar MA, Syafruddin SE, Pung YF, Low TY. Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures. J Biomed Sci 2022;29:19. [PMID: 35300685 PMCID: PMC8928697 DOI: 10.1186/s12929-022-00802-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/09/2022] [Indexed: 12/17/2022]  Open
50
Li B, Zhang Z, Wan C. Identification of Microproteins in Hep3B Cells at Different Cell Cycle Stages. J Proteome Res 2022;21:1052-1060. [PMID: 35199523 DOI: 10.1021/acs.jproteome.1c00926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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