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For: Yin X, Jing Y, Xu H. Mining for missed sORF-encoded peptides. Expert Rev Proteomics 2019;16:257-266. [PMID: 30669886 DOI: 10.1080/14789450.2019.1571919] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Number Cited by Other Article(s)
1
Huang J, Yang P, Pan W, Wu F, Qiu J, Ma Z. The role of polypeptides encoded by ncRNAs in cancer. Gene 2024;928:148817. [PMID: 39098512 DOI: 10.1016/j.gene.2024.148817] [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: 04/12/2024] [Revised: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
2
Huang K, Yu L, Lu D, Zhu Z, Shu M, Ma Z. Long non-coding RNAs in ferroptosis, pyroptosis and necroptosis: from functions to clinical implications in cancer therapy. Front Oncol 2024;14:1437698. [PMID: 39267831 PMCID: PMC11390357 DOI: 10.3389/fonc.2024.1437698] [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: 05/24/2024] [Accepted: 08/12/2024] [Indexed: 09/15/2024]  Open
3
Rodriguez JM, Abascal F, Cerdán-Vélez D, Gómez LM, Vázquez J, Tress ML. Evidence for widespread translation of 5' untranslated regions. Nucleic Acids Res 2024;52:8112-8126. [PMID: 38953162 DOI: 10.1093/nar/gkae571] [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: 02/07/2024] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]  Open
4
Xie X, Sinha S. Quantitative estimates of the regulatory influence of long non-coding RNAs on global gene expression variation using TCGA breast cancer transcriptomic data. PLoS Comput Biol 2024;20:e1012103. [PMID: 38838009 PMCID: PMC11198904 DOI: 10.1371/journal.pcbi.1012103] [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: 01/19/2023] [Revised: 06/25/2024] [Accepted: 04/24/2024] [Indexed: 06/07/2024]  Open
5
Salgado JCS, Alnoch RC, Polizeli MDLTDM, Ward RJ. Microenzymes: Is There Anybody Out There? Protein J 2024;43:393-404. [PMID: 38507106 DOI: 10.1007/s10930-024-10193-1] [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] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
6
Purohit K, Reddy N, Sunna A. Exploring the Potential of Bioactive Peptides: From Natural Sources to Therapeutics. Int J Mol Sci 2024;25:1391. [PMID: 38338676 PMCID: PMC10855437 DOI: 10.3390/ijms25031391] [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: 12/01/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024]  Open
7
Lin CH, Hsieh FC, Wang M, Hsu C, Hsu HW, Yang CC, Yang CY, Wu HY. Identification of subgenomic mRNAs derived from the coronavirus 1a/1b protein gene: Implications for coronavirus transcription. Virology 2024;589:109920. [PMID: 37952466 DOI: 10.1016/j.virol.2023.109920] [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: 08/23/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023]
8
Guo Y, Tian W, Wang D, Yang L, Wang Z, Wu X, Zhi Y, Zhang K, Wang Y, Li Z, Jiang R, Sun G, Li G, Tian Y, Wang H, Kang X, Liu X, Li H. LncHLEF promotes hepatic lipid synthesis through miR-2188-3p/GATA6 axis and encoding peptides and enhances intramuscular fat deposition via exosome. Int J Biol Macromol 2023;253:127061. [PMID: 37751822 DOI: 10.1016/j.ijbiomac.2023.127061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 09/28/2023]
9
Anders J, Stadler PF. RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions. J Integr Bioinform 2023;20:jib-2022-0046. [PMID: 37615674 PMCID: PMC10757073 DOI: 10.1515/jib-2022-0046] [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: 08/25/2022] [Accepted: 02/15/2023] [Indexed: 08/25/2023]  Open
10
Saga Y, Shimoyama Y, Yamada Y, Morikawa N, Kawata T. The cytosolic lncRNA dutA affects STATa signaling and developmental commitment in Dictyostelium. Genes Cells 2023;28:111-128. [PMID: 36504347 DOI: 10.1111/gtc.12997] [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: 11/07/2022] [Revised: 11/27/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
11
Yang JE, Zhong WJ, Li JF, Lin YY, Liu FT, Tian H, Chen YJ, Luo XY, Zhuang SM. LINC00998-encoded micropeptide SMIM30 promotes the G1/S transition of cell cycle by regulating cytosolic calcium level. Mol Oncol 2022;17:901-916. [PMID: 36495128 PMCID: PMC10158777 DOI: 10.1002/1878-0261.13358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/04/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]  Open
12
Zheng X, Guo Y, Zhang R, Chen H, Liu S, Qiu S, Xiang M. The mitochondrial micropeptide Stmp1 promotes retinal cell differentiation. Biochem Biophys Res Commun 2022;636:79-86. [DOI: 10.1016/j.bbrc.2022.10.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
13
Zheng X, Xiang M. Mitochondrion-located peptides and their pleiotropic physiological functions. FEBS J 2022;289:6919-6935. [PMID: 35599630 DOI: 10.1111/febs.16532] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 01/13/2023]
14
Identification of Differentially Expressed Intronic Transcripts in Osteosarcoma. Noncoding RNA 2022;8:ncrna8060073. [PMID: 36412907 PMCID: PMC9680297 DOI: 10.3390/ncrna8060073] [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: 09/22/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/14/2022]  Open
15
Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress. Mol Cell Proteomics 2022;21:100423. [PMID: 36210010 PMCID: PMC9650054 DOI: 10.1016/j.mcpro.2022.100423] [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: 05/12/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/09/2022]  Open
16
Zhao S, Meng J, Kang Q, Luan Y. Identifying LncRNA-Encoded Short Peptides Using Optimized Hybrid Features and Ensemble Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2873-2881. [PMID: 34383651 DOI: 10.1109/tcbb.2021.3104288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
17
Wang T, Yao Y, Hu X, Zhao Y. Message in hand: the application of CRISPRi, RNAi, and LncRNA in adenocarcinoma. Med Oncol 2022;39:148. [PMID: 35834017 DOI: 10.1007/s12032-022-01727-7] [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: 07/12/2021] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
18
Aggarwal S, Raj A, Kumar D, Dash D, Yadav AK. False discovery rate: the Achilles' heel of proteogenomics. Brief Bioinform 2022;23:6582880. [PMID: 35534181 DOI: 10.1093/bib/bbac163] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/14/2022] [Accepted: 04/12/2022] [Indexed: 12/25/2022]  Open
19
Cancer-related micropeptides encoded by ncRNAs: Promising drug targets and prognostic biomarkers. Cancer Lett 2022;547:215723. [DOI: 10.1016/j.canlet.2022.215723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 02/07/2023]
20
Yuanyuan J, Xinqiang Y. Micropeptides Identified from Human Genomes. J Proteome Res 2022;21:865-873. [DOI: 10.1021/acs.jproteome.1c00889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
21
Small open reading frames in plant research: from prediction to functional characterization. 3 Biotech 2022;12:76. [PMID: 35251879 PMCID: PMC8873315 DOI: 10.1007/s13205-022-03147-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 02/11/2022] [Indexed: 11/01/2022]  Open
22
Papadopoulos C, Chevrollier N, Lopes A. Exploring the Peptide Potential of Genomes. Methods Mol Biol 2022;2405:63-82. [PMID: 35298808 DOI: 10.1007/978-1-0716-1855-4_3] [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: 06/14/2023]
23
Zhao D, Wang C, Yan S, Chen R. Advances in the identification of long non-coding RNA binding proteins. Anal Biochem 2021;639:114520. [PMID: 34896376 DOI: 10.1016/j.ab.2021.114520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/04/2021] [Accepted: 12/04/2021] [Indexed: 02/06/2023]
24
Zhao S, Meng J, Luan Y. LncRNA-Encoded Short Peptides Identification Using Feature Subset Recombination and Ensemble Learning. Interdiscip Sci 2021;14:101-112. [PMID: 34304369 DOI: 10.1007/s12539-021-00464-1] [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: 03/24/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 11/28/2022]
25
Wang B, Wang Z, Pan N, Huang J, Wan C. Improved Identification of Small Open Reading Frames Encoded Peptides by Top-Down Proteomic Approaches and De Novo Sequencing. Int J Mol Sci 2021;22:ijms22115476. [PMID: 34067398 PMCID: PMC8197016 DOI: 10.3390/ijms22115476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/20/2022]  Open
26
Yadav A, Sanyal I, Rai SP, Lata C. An overview on miRNA-encoded peptides in plant biology research. Genomics 2021;113:2385-2391. [PMID: 34022345 DOI: 10.1016/j.ygeno.2021.05.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/20/2021] [Accepted: 05/17/2021] [Indexed: 01/25/2023]
27
Hu F, Lu J, Matheson LS, Díaz-Muñoz MD, Saveliev A, Turner M. ORFLine: a bioinformatic pipeline to prioritise small open reading frames identifies candidate secreted small proteins from lymphocytes. Bioinformatics 2021;37:3152-3159. [PMID: 33970232 PMCID: PMC8504629 DOI: 10.1093/bioinformatics/btab339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/25/2021] [Accepted: 04/30/2021] [Indexed: 11/30/2022]  Open
28
Vitorino R, Guedes S, Amado F, Santos M, Akimitsu N. The role of micropeptides in biology. Cell Mol Life Sci 2021;78:3285-3298. [PMID: 33507325 PMCID: PMC11073438 DOI: 10.1007/s00018-020-03740-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022]
29
Yang M, Shang X, Zhou Y, Wang C, Wei G, Tang J, Zhang M, Liu Y, Cao J, Zhang Q. Full-Length Transcriptome Analysis of Plasmodium falciparum by Single-Molecule Long-Read Sequencing. Front Cell Infect Microbiol 2021;11:631545. [PMID: 33708645 PMCID: PMC7942025 DOI: 10.3389/fcimb.2021.631545] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/05/2021] [Indexed: 11/25/2022]  Open
30
Nasir MA, Nawaz S, Huang J. A Mini-review of Computational Approaches to Predict Functions and Findings of Novel Micro Peptides. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200811130522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
31
Xing J, Liu H, Jiang W, Wang L. LncRNA-Encoded Peptide: Functions and Predicting Methods. Front Oncol 2021;10:622294. [PMID: 33520729 PMCID: PMC7842084 DOI: 10.3389/fonc.2020.622294] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]  Open
32
van Tilburg GBA, Murachelli AG, Fish A, van der Heden van Noort GJ, Ovaa H, Sixma TK. K27-Linked Diubiquitin Inhibits UCHL3 via an Unusual Kinetic Trap. Cell Chem Biol 2020;28:191-201.e8. [PMID: 33238157 DOI: 10.1016/j.chembiol.2020.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/25/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023]
33
Murgan SS, Abd Elaziz FJ, Nasr AMA, Elfaki MEE, Khalil EAG. Ovarian Cancer: Tumor-Specific Urinary Micro-Peptides Profiling as Potential Biomarkers for Early Diagnosis. Proteomes 2020;8:proteomes8040032. [PMID: 33137912 PMCID: PMC7709102 DOI: 10.3390/proteomes8040032] [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: 09/08/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022]  Open
34
Wang S, Tian L, Liu H, Li X, Zhang J, Chen X, Jia X, Zheng X, Wu S, Chen Y, Yan J, Wu L. Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline. MOLECULAR PLANT 2020;13:1078-1093. [PMID: 32445888 DOI: 10.1016/j.molp.2020.05.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/04/2020] [Accepted: 05/18/2020] [Indexed: 05/10/2023]
35
Understanding the proteome encoded by "non-coding RNAs": new insights into human genome. SCIENCE CHINA. LIFE SCIENCES 2020;63:986-995. [PMID: 32318910 DOI: 10.1007/s11427-019-1677-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/12/2020] [Indexed: 01/19/2023]
36
Peng J, Zhang H, Niu H, Wu R. Peptidomic analyses: The progress in enrichment and identification of endogenous peptides. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115835] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
37
Yu JF, Qu A, Tang HC, Wang FH, Wang CL, Wang HM, Wang JH, Zhu HQ. A novel numerical model for protein sequences analysis based on spherical coordinates and multiple physicochemical properties of amino acids. Biopolymers 2019;110:e23282. [PMID: 30977898 DOI: 10.1002/bip.23282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 01/25/2023]
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