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For: Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. Widespread RNA and DNA sequence differences in the human transcriptome. Science 2011;333:53-8. [PMID: 21596952 PMCID: PMC3204392 DOI: 10.1126/science.1207018] [Citation(s) in RCA: 315] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
1
Ibrahim NA, Shalaby IM, Ghobashy MA, Taeleb AA, Elkhawass EA. Filling the void: Morphological and molecular phylogenetic analyses of helminths assemblage from the Egyptian egret Bubulcus ibis. Parasitol Int 2025;104:102972. [PMID: 39307346 DOI: 10.1016/j.parint.2024.102972] [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: 05/05/2024] [Revised: 09/09/2024] [Accepted: 09/17/2024] [Indexed: 09/26/2024]
2
Wu Y, Xie X, Zhu J, Guan L, Li M. Overview and Prospects of DNA Sequence Visualization. Int J Mol Sci 2025;26:477. [PMID: 39859192 PMCID: PMC11764684 DOI: 10.3390/ijms26020477] [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: 11/19/2024] [Revised: 12/30/2024] [Accepted: 01/04/2025] [Indexed: 01/27/2025]  Open
3
Stolc V, Karhanek M, Freund F, Griko Y, Loftus DJ, Ohayon MM. Metabolic stress in space: ROS-induced mutations in mice hint at a new path to cancer. Redox Biol 2024;78:103398. [PMID: 39586121 PMCID: PMC11625351 DOI: 10.1016/j.redox.2024.103398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Accepted: 10/14/2024] [Indexed: 11/27/2024]  Open
4
Li Z, Luo L, Ju X, Huang S, Lei L, Yu Y, Liu J, Zhang P, Chi T, Ma P, Huang C, Huang X, Ding Q, Zhang Y. Viral N protein hijacks deaminase-containing RNA granules to enhance SARS-CoV-2 mutagenesis. EMBO J 2024;43:6444-6468. [PMID: 39567830 PMCID: PMC11649915 DOI: 10.1038/s44318-024-00314-y] [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: 02/18/2024] [Revised: 10/28/2024] [Accepted: 11/06/2024] [Indexed: 11/22/2024]  Open
5
Park DG, Kang W, Shin IJ, Chalita M, Oh HS, Hyun DW, Kim H, Chun J, An YS, Lee EJ, Yoon JH. Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease. Neurobiol Dis 2024;201:106655. [PMID: 39218360 DOI: 10.1016/j.nbd.2024.106655] [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: 06/18/2024] [Revised: 07/31/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]  Open
6
Fu ZC, Gao BQ, Nan F, Ma XK, Yang L. DEMINING: A deep learning model embedded framework to distinguish RNA editing from DNA mutations in RNA sequencing data. Genome Biol 2024;25:258. [PMID: 39380061 PMCID: PMC11463134 DOI: 10.1186/s13059-024-03397-2] [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: 12/15/2023] [Accepted: 09/20/2024] [Indexed: 10/10/2024]  Open
7
Chatterjee P, Ghosal P, Shit S, Biswas A, Mallik S, Allabun S, Othman M, Ali AH, Elshiekh E, Soufiene BO. Ribosomal computing: implementation of the computational method. BMC Bioinformatics 2024;25:321. [PMID: 39358680 PMCID: PMC11448306 DOI: 10.1186/s12859-024-05945-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: 03/30/2024] [Accepted: 09/23/2024] [Indexed: 10/04/2024]  Open
8
Zhao H, Wu Z, Wang Z, Ru J, Wang S, Li Y, Hou S, Zhang Y, Wang X. Genomic Landscape and Regulation of RNA Editing in Pekin Ducks Susceptible to Duck Hepatitis A Virus Genotype 3 Infection. Int J Mol Sci 2024;25:10413. [PMID: 39408741 PMCID: PMC11476845 DOI: 10.3390/ijms251910413] [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: 08/29/2024] [Revised: 09/25/2024] [Accepted: 09/26/2024] [Indexed: 10/20/2024]  Open
9
Leonard AS, Mapel XM, Pausch H. RNA-DNA differences in variant calls from cattle tissues result in erroneous eQTLs. BMC Genomics 2024;25:750. [PMID: 39090567 PMCID: PMC11295900 DOI: 10.1186/s12864-024-10645-z] [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: 05/16/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]  Open
10
Bernal YA, Durán E, Solar I, Sagredo EA, Armisén R. ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer. Int J Mol Sci 2024;25:7424. [PMID: 39000531 PMCID: PMC11242177 DOI: 10.3390/ijms25137424] [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: 05/04/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024]  Open
11
XIONG J, FENG T, YUAN BF. [Advances in mapping analysis of ribonucleic acid modifications through sequencing]. Se Pu 2024;42:632-645. [PMID: 38966972 PMCID: PMC11224946 DOI: 10.3724/sp.j.1123.2023.12025] [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: 12/20/2023] [Indexed: 07/06/2024]  Open
12
Kose C, Lindsey-Boltz LA, Sancar A, Jiang Y. Genome-wide analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans. PLoS Genet 2024;20:e1011365. [PMID: 39028758 PMCID: PMC11290646 DOI: 10.1371/journal.pgen.1011365] [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: 11/16/2023] [Revised: 07/31/2024] [Accepted: 07/08/2024] [Indexed: 07/21/2024]  Open
13
Chen C, Bundschuh R. A-to-I Editing Is Subtype-Specific in Non-Hodgkin Lymphomas. Genes (Basel) 2024;15:864. [PMID: 39062643 PMCID: PMC11276283 DOI: 10.3390/genes15070864] [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: 05/17/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024]  Open
14
Yoon HJ, Kang W, Jo S, Hwang YS, Lee JH, Chung SJ, Park YK. Dietary quality and the gut microbiome in early-stage Parkinson's disease patients. Nutr Neurosci 2024;27:761-769. [PMID: 37711026 DOI: 10.1080/1028415x.2023.2253025] [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: 09/16/2023]
15
Cottrell KA, Ryu S, Pierce JR, Soto Torres L, Bohlin HE, Schab AM, Weber JD. Induction of Viral Mimicry Upon Loss of DHX9 and ADAR1 in Breast Cancer Cells. CANCER RESEARCH COMMUNICATIONS 2024;4:986-1003. [PMID: 38530197 PMCID: PMC10993856 DOI: 10.1158/2767-9764.crc-23-0488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/24/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024]
16
Kose C, Lindsey-Boltz LA, Sancar A, Jiang Y. Genome-wide analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.12.562083. [PMID: 37904932 PMCID: PMC10614815 DOI: 10.1101/2023.10.12.562083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
17
Li J, Li C, Xu W. Liver cancer-specific mutations in functional domains of ADAR2 lead to the elevation of coding and non-coding RNA editing in multiple tumor-related genes. Mol Genet Genomics 2024;299:1. [PMID: 38170228 DOI: 10.1007/s00438-023-02091-5] [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: 08/24/2023] [Accepted: 10/17/2023] [Indexed: 01/05/2024]
18
Liu J, Zhao T, Zheng C, Ma L, Song F, Tian L, Cai W, Li H, Duan Y. An orthology-based methodology as a complementary approach to retrieve evolutionarily conserved A-to-I RNA editing sites. RNA Biol 2024;21:29-45. [PMID: 39256954 PMCID: PMC11404581 DOI: 10.1080/15476286.2024.2397757] [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] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024]  Open
19
GWAK SEUNGHEE, LEE JUHYUN, OH EUNJI, LEE DOHYUN, HAN WONSHIK, KIM JONGMIN, KIM KYONGTAI. Vaccinia-related kinase 2 variants differentially affect breast cancer growth by regulating kinase activity. Oncol Res 2023;32:421-432. [PMID: 38186576 PMCID: PMC10765118 DOI: 10.32604/or.2023.031031] [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: 05/11/2023] [Accepted: 08/03/2023] [Indexed: 01/09/2024]  Open
20
Xu Y, Liu J, Zhao T, Song F, Tian L, Cai W, Li H, Duan Y. Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes. Int J Mol Sci 2023;24:17126. [PMID: 38138955 PMCID: PMC10742984 DOI: 10.3390/ijms242417126] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023]  Open
21
Tan MH. Identification of Bona Fide RNA Editing Sites: History, Challenges, and Opportunities. Acc Chem Res 2023;56:3033-3044. [PMID: 37827987 DOI: 10.1021/acs.accounts.3c00462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
22
Cottrell KA, Ryu S, Torres LS, Schab AM, Weber JD. Induction of viral mimicry upon loss of DHX9 and ADAR1 in breast cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530307. [PMID: 36909617 PMCID: PMC10002699 DOI: 10.1101/2023.02.27.530307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
23
Sun H, Li K, Liu C, Yi C. Regulation and functions of non-m6A mRNA modifications. Nat Rev Mol Cell Biol 2023;24:714-731. [PMID: 37369853 DOI: 10.1038/s41580-023-00622-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
24
Morales DR, Rennie S, Uchida S. Benchmarking RNA Editing Detection Tools. BIOTECH 2023;12:56. [PMID: 37754200 PMCID: PMC10527054 DOI: 10.3390/biotech12030056] [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: 07/13/2023] [Revised: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023]  Open
25
Pecori R, Ren W, Pirmoradian M, Wang X, Liu D, Berglund M, Li W, Tasakis RN, Di Giorgio S, Ye X, Li X, Arnold A, Wüst S, Schneider M, Selvasaravanan KD, Fuell Y, Stafforst T, Amini RM, Sonnevi K, Enblad G, Sander B, Wahlin BE, Wu K, Zhang H, Helm D, Binder M, Papavasiliou FN, Pan-Hammarström Q. ADAR1-mediated RNA editing promotes B cell lymphomagenesis. iScience 2023;26:106864. [PMID: 37255666 PMCID: PMC10225930 DOI: 10.1016/j.isci.2023.106864] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023]  Open
26
Chen R, Li F, Guo X, Bi Y, Li C, Pan S, Coin LJM, Song J. ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. Brief Bioinform 2023;24:bbad170. [PMID: 37150785 PMCID: PMC10565902 DOI: 10.1093/bib/bbad170] [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: 01/31/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/09/2023]  Open
27
Wei L. Retrospect of the Two-Year Debate: What Fuels the Evolution of SARS-CoV-2: RNA Editing or Replication Error? Curr Microbiol 2023;80:151. [PMID: 36976379 PMCID: PMC10044072 DOI: 10.1007/s00284-023-03279-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/19/2023] [Indexed: 03/29/2023]
28
Tyagi S, Kabade PG, Gnanapragasam N, Singh UM, Gurjar AKS, Rai A, Sinha P, Kumar A, Singh VK. Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition. Int J Mol Sci 2023;24:ijms24021098. [PMID: 36674611 PMCID: PMC9861248 DOI: 10.3390/ijms24021098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 01/09/2023]  Open
29
Ruschil C, Gabernet G, Kemmerer CL, Jarboui MA, Klose F, Poli S, Ziemann U, Nahnsen S, Kowarik MC. Cladribine treatment specifically affects peripheral blood memory B cell clones and clonal expansion in multiple sclerosis patients. Front Immunol 2023;14:1133967. [PMID: 36960053 PMCID: PMC10028280 DOI: 10.3389/fimmu.2023.1133967] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/13/2023] [Indexed: 03/09/2023]  Open
30
Guo Y, van der Heijden YF, Maruri F, Jiang L, Morrison R, Sterling TR. RNA editing in Mycobacterium tuberculosis. Microbiol Res 2022;264:127174. [PMID: 36067705 PMCID: PMC11332325 DOI: 10.1016/j.micres.2022.127174] [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: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022]
31
Caldwell RM, Flynn RA. Discovering glycoRNA: Traditional and Non‐Canonical Approaches to Studying RNA Modifications. Isr J Chem 2022. [DOI: 10.1002/ijch.202200059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
32
Fusion Gene Detection and Quantification by Asymmetric Capture Sequencing (aCAP-Seq). J Mol Diagn 2022;24:1113-1127. [PMID: 35963522 DOI: 10.1016/j.jmoldx.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022]  Open
33
Cai H, Liu X, Zheng X. RNA editing detection in SARS-CoV-2 transcriptome should be different from traditional SNV identification. J Appl Genet 2022;63:587-594. [PMID: 35661108 PMCID: PMC9166928 DOI: 10.1007/s13353-022-00706-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 10/31/2022]
34
Pishesha N, Harmand TJ, Ploegh HL. A guide to antigen processing and presentation. Nat Rev Immunol 2022;22:751-764. [PMID: 35418563 DOI: 10.1038/s41577-022-00707-2] [Citation(s) in RCA: 290] [Impact Index Per Article: 96.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
35
Poor evidence for host-dependent regular RNA editing in the transcriptome of SARS-CoV-2. J Appl Genet 2022;63:413-421. [PMID: 35179717 PMCID: PMC8854479 DOI: 10.1007/s13353-022-00687-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/21/2021] [Accepted: 02/13/2022] [Indexed: 12/18/2022]
36
Pan Y, Li M, Huang J, Pan W, Shi T, Guo Q, Yang G, Nie X. Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat. Int J Mol Sci 2022;23:1405. [PMID: 35163325 PMCID: PMC8836135 DOI: 10.3390/ijms23031405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/19/2022]  Open
37
Hwang T, Kim S, Chowdhury T, Yu HJ, Kim KM, Kang H, Won JK, Park SH, Shin JH, Park CK. Genome-wide perturbations of Alu expression and Alu-associated post-transcriptional regulations distinguish oligodendroglioma from other gliomas. Commun Biol 2022;5:62. [PMID: 35042936 PMCID: PMC8766575 DOI: 10.1038/s42003-022-03011-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 12/27/2021] [Indexed: 01/09/2023]  Open
38
Quiver MH, Lachance J. Adaptive eQTLs reveal the evolutionary impacts of pleiotropy and tissue-specificity while contributing to health and disease. HGG ADVANCES 2022;3:100083. [PMID: 35047867 PMCID: PMC8756519 DOI: 10.1016/j.xhgg.2021.100083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/21/2021] [Indexed: 11/24/2022]  Open
39
Akhlaghpour H. An RNA-Based Theory of Natural Universal Computation. J Theor Biol 2021;537:110984. [PMID: 34979104 DOI: 10.1016/j.jtbi.2021.110984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
40
Tao S, Ren Z, Yang Z, Duan S, Wan Z, Huang J, Liu C, Wei G. Effects of Different Molecular Weight Polysaccharides From Dendrobium officinale Kimura & Migo on Human Colorectal Cancer and Transcriptome Analysis of Differentially Expressed Genes. Front Pharmacol 2021;12:704486. [PMID: 34925000 PMCID: PMC8678483 DOI: 10.3389/fphar.2021.704486] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022]  Open
41
Ma Y, Dammer EB, Felsky D, Duong DM, Klein HU, White CC, Zhou M, Logsdon BA, McCabe C, Xu J, Wang M, Wingo TS, Lah JJ, Zhang B, Schneider J, Allen M, Wang X, Ertekin-Taner N, Seyfried NT, Levey AI, Bennett DA, De Jager PL. Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. Nat Commun 2021;12:7035. [PMID: 34857756 PMCID: PMC8640037 DOI: 10.1038/s41467-021-27204-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 11/04/2021] [Indexed: 11/09/2022]  Open
42
Tedjasaputra TR, Hatta M, Massi MN, Natzir R, Bukhari A, Masadah R, Parewangi ML, Prihantono P, Nariswati R, Tedjasaputra V. Prediction of hereditary nonpolyposis colorectal cancer using mRNA MSH2 quantitative and the correlation with nonmodifiable factor. World J Gastrointest Pathophysiol 2021;12:130-142. [DOI: 10.4291/wjgp.v12.i6.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
43
Tedjasaputra TR, Hatta M, Massi MN, Natzir R, Bukhari A, Masadah R, Parewangi ML, Prihantono P, Nariswati R, Tedjasaputra V. Prediction of hereditary nonpolyposis colorectal cancer using mRNA MSH2 quantitative and the correlation with nonmodifiable factor. World J Gastrointest Pathophysiol 2021;12:134-146. [PMID: 34877027 PMCID: PMC8611184 DOI: 10.4291/wjgp.v12.i6.134] [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: 01/27/2021] [Revised: 03/13/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023]  Open
44
Wen J, Rusch M, Brady SW, Shao Y, Edmonson MN, Shaw TI, Powers BB, Tian L, Easton J, Mullighan CG, Gruber T, Ellison D, Zhang J. The landscape of coding RNA editing events in pediatric cancer. BMC Cancer 2021;21:1233. [PMID: 34789196 PMCID: PMC8597231 DOI: 10.1186/s12885-021-08956-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 11/02/2021] [Indexed: 01/09/2023]  Open
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Owens MC, Zhang C, Liu KF. Recent technical advances in the study of nucleic acid modifications. Mol Cell 2021;81:4116-4136. [PMID: 34480848 PMCID: PMC9109655 DOI: 10.1016/j.molcel.2021.07.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 12/30/2022]
46
Tan KT, Ding LW, Wu CS, Tenen DG, Yang H. Repurposing RNA sequencing for discovery of RNA modifications in clinical cohorts. SCIENCE ADVANCES 2021;7:eabd2605. [PMID: 34348892 PMCID: PMC8336963 DOI: 10.1126/sciadv.abd2605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/14/2021] [Indexed: 05/07/2023]
47
Light D, Haas R, Yazbak M, Elfand T, Blau T, Lamm AT. RESIC: A Tool for Comprehensive Adenosine to Inosine RNA Editing Site Identification and Classification. Front Genet 2021;12:686851. [PMID: 34367244 PMCID: PMC8343188 DOI: 10.3389/fgene.2021.686851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/07/2021] [Indexed: 11/25/2022]  Open
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Yévenes M, Núñez-Acuña G, Gallardo-Escárate C, Gajardo G. Adaptive Differences in Gene Expression in Farm-Impacted Seedbeds of the Native Blue Mussel Mytilus chilensis. Front Genet 2021;12:666539. [PMID: 34093658 PMCID: PMC8174845 DOI: 10.3389/fgene.2021.666539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 01/02/2023]  Open
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Torsin LI, Petrescu GED, Sabo AA, Chen B, Brehar FM, Dragomir MP, Calin GA. Editing and Chemical Modifications on Non-Coding RNAs in Cancer: A New Tale with Clinical Significance. Int J Mol Sci 2021;22:ijms22020581. [PMID: 33430133 PMCID: PMC7827606 DOI: 10.3390/ijms22020581] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022]  Open
50
Discovering A-to-I RNA Editing Through Chemical Methodology "ICE-seq". Methods Mol Biol 2021;2181:113-148. [PMID: 32729078 DOI: 10.1007/978-1-0716-0787-9_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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