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For: Zhang P, He D, Xu Y, Hou J, Pan BF, Wang Y, Liu T, Davis CM, Ehli EA, Tan L, Zhou F, Hu J, Yu Y, Chen X, Nguyen TM, Rosen JM, Hawke DH, Ji Z, Chen Y. Genome-wide identification and differential analysis of translational initiation. Nat Commun 2017;8:1749. [PMID: 29170441 PMCID: PMC5701008 DOI: 10.1038/s41467-017-01981-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 10/31/2017] [Indexed: 01/28/2023]  Open
Number Cited by Other Article(s)
51
Fedorova AD, Kiniry SJ, Andreev DE, Mudge JM, Baranov PV. Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals. Nat Commun 2022;13:7910. [PMID: 36564405 PMCID: PMC9789052 DOI: 10.1038/s41467-022-35595-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]  Open
52
Yang Y, Wang H, Zhang Y, Chen L, Chen G, Bao Z, Yang Y, Xie Z, Zhao Q. An Optimized Proteomics Approach Reveals Novel Alternative Proteins in Mouse Liver Development. Mol Cell Proteomics 2022;22:100480. [PMID: 36494044 PMCID: PMC9823216 DOI: 10.1016/j.mcpro.2022.100480] [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: 06/21/2022] [Revised: 11/15/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]  Open
53
Ansari SA, Dantoft W, Ruiz-Orera J, Syed AP, Blachut S, van Heesch S, Hübner N, Uhlenhaut NH. Integrative analysis of macrophage ribo-Seq and RNA-Seq data define glucocorticoid receptor regulated inflammatory response genes into distinct regulatory classes. Comput Struct Biotechnol J 2022;20:5622-5638. [PMID: 36284713 PMCID: PMC9582734 DOI: 10.1016/j.csbj.2022.09.042] [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: 07/15/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]  Open
54
Duffy EE, Finander B, Choi G, Carter AC, Pritisanac I, Alam A, Luria V, Karger A, Phu W, Sherman MA, Assad EG, Pajarillo N, Khitun A, Crouch EE, Ganesh S, Chen J, Berger B, Sestan N, O'Donnell-Luria A, Huang EJ, Griffith EC, Forman-Kay JD, Moses AM, Kalish BT, Greenberg ME. Developmental dynamics of RNA translation in the human brain. Nat Neurosci 2022;25:1353-1365. [PMID: 36171426 PMCID: PMC10198132 DOI: 10.1038/s41593-022-01164-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 08/12/2022] [Indexed: 01/27/2023]
55
Chothani SP, Adami E, Widjaja AA, Langley SR, Viswanathan S, Pua CJ, Zhihao NT, Harmston N, D'Agostino G, Whiffin N, Mao W, Ouyang JF, Lim WW, Lim S, Lee CQE, Grubman A, Chen J, Kovalik JP, Tryggvason K, Polo JM, Ho L, Cook SA, Rackham OJL, Schafer S. A high-resolution map of human RNA translation. Mol Cell 2022;82:2885-2899.e8. [PMID: 35841888 DOI: 10.1016/j.molcel.2022.06.023] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 03/10/2022] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
56
Puray-Chavez M, Lee N, Tenneti K, Wang Y, Vuong HR, Liu Y, Horani A, Huang T, Gunsten SP, Case JB, Yang W, Diamond MS, Brody SL, Dougherty J, Kutluay SB. The Translational Landscape of SARS-CoV-2-infected Cells Reveals Suppression of Innate Immune Genes. mBio 2022;13:e0081522. [PMID: 35604092 PMCID: PMC9239271 DOI: 10.1128/mbio.00815-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 12/13/2022]  Open
57
Arango D, Sturgill D, Yang R, Kanai T, Bauer P, Roy J, Wang Z, Hosogane M, Schiffers S, Oberdoerffer S. Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. Mol Cell 2022;82:2797-2814.e11. [PMID: 35679869 PMCID: PMC9361928 DOI: 10.1016/j.molcel.2022.05.016] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 12/14/2022]
58
Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development. Nat Cell Biol 2022;24:968-980. [PMID: 35697785 DOI: 10.1038/s41556-022-00928-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/27/2022] [Indexed: 12/12/2022]
59
Sotta N, Chiba Y, Aoyama H, Takamatsu S, Suzuki T, Miwa K, Yamashita Y, Naito S, Fujiwara T. Translational Landscape of a C4 Plant, Sorghum bicolor, Under Normal and Sulfur-Deficient Conditions. PLANT & CELL PHYSIOLOGY 2022;63:592-604. [PMID: 35166349 DOI: 10.1093/pcp/pcac023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
60
Zhang Z, Li Y, Yuan W, Wang Z, Wan C. Proteomic-driven identification of short open reading frame-encoded peptides. Proteomics 2022;22:e2100312. [PMID: 35384297 DOI: 10.1002/pmic.202100312] [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] [Received: 02/25/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/10/2022]
61
Gelhausen R, Müller T, Svensson SL, Alkhnbashi OS, Sharma CM, Eggenhofer F, Backofen R. RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. Brief Bioinform 2022;23:bbab549. [PMID: 35037022 PMCID: PMC8921622 DOI: 10.1093/bib/bbab549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022]  Open
62
Luan Y, Tang N, Yang J, Liu S, Cheng C, Wang Y, Chen C, Guo YN, Wang H, Zhao W, Zhao Q, Li W, Xiang M, Ju R, Xie Z. Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells. Nucleic Acids Res 2022;50:6601-6617. [PMID: 35137207 PMCID: PMC9262593 DOI: 10.1093/nar/gkac053] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 01/13/2022] [Accepted: 02/03/2022] [Indexed: 01/05/2023]  Open
63
van 't Spijker HM, Stackpole EE, Almeida S, Katsara O, Liu B, Shen K, Schneider RJ, Gao FB, Richter JD. Ribosome profiling reveals novel regulation of C9ORF72 GGGGCC repeat-containing RNA translation. RNA (NEW YORK, N.Y.) 2022;28:123-138. [PMID: 34848561 PMCID: PMC8906550 DOI: 10.1261/rna.078963.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
64
Kress WJ, Soltis DE, Kersey PJ, Wegrzyn JL, Leebens-Mack JH, Gostel MR, Liu X, Soltis PS. Green plant genomes: What we know in an era of rapidly expanding opportunities. Proc Natl Acad Sci U S A 2022;119:e2115640118. [PMID: 35042803 PMCID: PMC8795535 DOI: 10.1073/pnas.2115640118] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
65
Xie M, Yang L, Chen G, Wang Y, Xie Z, Wang H. RiboChat: a chat-style web interface for analysis and annotation of ribosome profiling data. Brief Bioinform 2022;23:6511203. [DOI: 10.1093/bib/bbab559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/13/2022]  Open
66
Chen X, Zhang Y, Wang F, Zhou X, Fu Q, Yang X, Lin J, Jin X. A Novel Assessment Model Based on Molecular Subtypes of Hypoxia-Related LncRNAs for Prognosis of Bladder Cancer. Front Cell Dev Biol 2021;9:718991. [PMID: 34869309 PMCID: PMC8634255 DOI: 10.3389/fcell.2021.718991] [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: 06/01/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022]  Open
67
Chen L, Yang Y, Zhang Y, Li K, Cai H, Wang H, Zhao Q. The Small Open Reading Frame-Encoded Peptides: Advances in Methodologies and Functional Studies. Chembiochem 2021;23:e202100534. [PMID: 34862721 DOI: 10.1002/cbic.202100534] [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: 10/06/2021] [Revised: 11/15/2021] [Indexed: 11/07/2022]
68
Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021;57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [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] [Indexed: 01/28/2023]
69
Puray-Chavez M, Lee N, Tenneti K, Wang Y, Vuong HR, Liu Y, Horani A, Huang T, Gunsten SP, Case JB, Yang W, Diamond MS, Brody SL, Dougherty J, Kutluay SB. The translational landscape of SARS-CoV-2 and infected cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.11.03.367516. [PMID: 33173862 PMCID: PMC7654850 DOI: 10.1101/2020.11.03.367516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
70
Chen K, Chen C, Li H, Yang J, Xiang M, Wang H, Xie Z. Widespread translational control regulates retinal development in mouse. Nucleic Acids Res 2021;49:9648-9664. [PMID: 34469513 PMCID: PMC8464051 DOI: 10.1093/nar/gkab749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022]  Open
71
Li Y, Zhou H, Chen X, Zheng Y, Kang Q, Hao D, Zhang L, Song T, Luo H, Hao Y, Chen R, Zhang P, He S. SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. GENOMICS PROTEOMICS & BIOINFORMATICS 2021;19:602-610. [PMID: 34536568 PMCID: PMC9039559 DOI: 10.1016/j.gpb.2021.09.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/30/2022]
72
Zaheed O, Kiniry SJ, Baranov PV, Dean K. Exploring Evidence of Non-coding RNA Translation With Trips-Viz and GWIPS-Viz Browsers. Front Cell Dev Biol 2021;9:703374. [PMID: 34490252 PMCID: PMC8416628 DOI: 10.3389/fcell.2021.703374] [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: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022]  Open
73
He T, Yuan C, Zhao C. Long intragenic non-coding RNA p53-induced transcript (LINC-PINT) as a novel prognosis indicator and therapeutic target in cancer. Biomed Pharmacother 2021;143:112127. [PMID: 34474342 DOI: 10.1016/j.biopha.2021.112127] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/15/2021] [Accepted: 08/24/2021] [Indexed: 12/18/2022]  Open
74
Chen L, Zhang Y, Yang Y, Yang Y, Li H, Dong X, Wang H, Xie Z, Zhao Q. An Integrated Approach for Discovering Noncanonical MHC-I Peptides Encoded by Small Open Reading Frames. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021;32:2346-2357. [PMID: 34260243 DOI: 10.1021/jasms.1c00076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
75
Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments. Nat Commun 2021;12:5094. [PMID: 34429433 PMCID: PMC8384890 DOI: 10.1038/s41467-021-25411-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 08/10/2021] [Indexed: 12/26/2022]  Open
76
Sun M, Wang Y, Zheng C, Wei Y, Hou J, Zhang P, He W, Lv X, Ding Y, Liang H, Hon CC, Chen X, Xu H, Chen Y. Systematic functional interrogation of human pseudogenes using CRISPRi. Genome Biol 2021;22:240. [PMID: 34425866 PMCID: PMC8381491 DOI: 10.1186/s13059-021-02464-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 08/06/2021] [Indexed: 12/13/2022]  Open
77
Ichihara K, Matsumoto A, Nishida H, Kito Y, Shimizu H, Shichino Y, Iwasaki S, Imami K, Ishihama Y, Nakayama KI. Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons. Nucleic Acids Res 2021;49:7298-7317. [PMID: 34226921 PMCID: PMC8287933 DOI: 10.1093/nar/gkab549] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 02/05/2023]  Open
78
Gelhausen R, Svensson SL, Froschauer K, Heyl F, Hadjeras L, Sharma CM, Eggenhofer F, Backofen R. HRIBO: high-throughput analysis of bacterial ribosome profiling data. Bioinformatics 2021;37:2061-2063. [PMID: 33175953 PMCID: PMC8337001 DOI: 10.1093/bioinformatics/btaa959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/25/2020] [Accepted: 11/03/2020] [Indexed: 11/13/2022]  Open
79
Wang H, Wang Y, Yang J, Zhao Q, Tang N, Chen C, Li H, Cheng C, Xie M, Yang Y, Xie Z. Tissue- and stage-specific landscape of the mouse translatome. Nucleic Acids Res 2021;49:6165-6180. [PMID: 34107020 PMCID: PMC8216458 DOI: 10.1093/nar/gkab482] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 04/27/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022]  Open
80
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. Nat Methods 2021;18:507-519. [PMID: 33963355 PMCID: PMC8148648 DOI: 10.1038/s41592-021-01128-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/26/2021] [Indexed: 02/03/2023]
81
Xu C, Zhang J. Mammalian Alternative Translation Initiation Is Mostly Nonadaptive. Mol Biol Evol 2021;37:2015-2028. [PMID: 32145028 DOI: 10.1093/molbev/msaa063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
82
Pan Y, Kadash-Edmondson KE, Wang R, Phillips J, Liu S, Ribas A, Aplenc R, Witte ON, Xing Y. RNA Dysregulation: An Expanding Source of Cancer Immunotherapy Targets. Trends Pharmacol Sci 2021;42:268-282. [PMID: 33711255 PMCID: PMC8761020 DOI: 10.1016/j.tips.2021.01.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/18/2021] [Accepted: 01/25/2021] [Indexed: 12/14/2022]
83
Tian T, Li S, Lang P, Zhao D, Zeng J. Full-length ribosome density prediction by a multi-input and multi-output model. PLoS Comput Biol 2021;17:e1008842. [PMID: 33770074 PMCID: PMC8026034 DOI: 10.1371/journal.pcbi.1008842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 04/07/2021] [Accepted: 03/01/2021] [Indexed: 11/29/2022]  Open
84
Schlesinger D, Elsässer SJ. Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins. FEBS J 2021;289:53-74. [PMID: 33595896 DOI: 10.1111/febs.15769] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/17/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023]
85
Gerashchenko MV, Peterfi Z, Yim SH, Gladyshev VN. Translation elongation rate varies among organs and decreases with age. Nucleic Acids Res 2021;49:e9. [PMID: 33264395 PMCID: PMC7826258 DOI: 10.1093/nar/gkaa1103] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/21/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022]  Open
86
Goel N, Singh S, Aseri TC. Global sequence features based translation initiation site prediction in human genomic sequences. Heliyon 2020;6:e04825. [PMID: 32964155 PMCID: PMC7490824 DOI: 10.1016/j.heliyon.2020.e04825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/25/2020] [Accepted: 08/26/2020] [Indexed: 11/26/2022]  Open
87
Li F, Xing X, Xiao Z, Xu G, Yang X. RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data. BMC Bioinformatics 2020;21:340. [PMID: 32738892 PMCID: PMC7430821 DOI: 10.1186/s12859-020-03670-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/20/2020] [Indexed: 02/08/2023]  Open
88
Kiniry SJ, Michel AM, Baranov PV. Computational methods for ribosome profiling data analysis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020;11:e1577. [PMID: 31760685 DOI: 10.1002/wrna.1577] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/12/2019] [Accepted: 10/16/2019] [Indexed: 12/15/2022]
89
Das Sharma S, Metz JB, Li H, Hobson BD, Hornstein N, Sulzer D, Tang G, Sims PA. Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice. Cell Rep 2020;26:3313-3322.e5. [PMID: 30893603 DOI: 10.1016/j.celrep.2019.02.086] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/27/2018] [Accepted: 02/21/2019] [Indexed: 12/18/2022]  Open
90
Legrand C, Tuorto F. RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data. Nucleic Acids Res 2020;48:e7. [PMID: 31777932 PMCID: PMC6954398 DOI: 10.1093/nar/gkz1074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/15/2019] [Accepted: 11/04/2019] [Indexed: 12/18/2022]  Open
91
Jodoin R, Carrier JC, Rivard N, Bisaillon M, Perreault JP. G-quadruplex located in the 5'UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance. Nucleic Acids Res 2019;47:10247-10266. [PMID: 31504805 PMCID: PMC6821271 DOI: 10.1093/nar/gkz777] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 08/27/2019] [Accepted: 08/31/2019] [Indexed: 12/19/2022]  Open
92
Monteuuis G, Miścicka A, Świrski M, Zenad L, Niemitalo O, Wrobel L, Alam J, Chacinska A, Kastaniotis AJ, Kufel J. Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins. Nucleic Acids Res 2019;47:5777-5791. [PMID: 31216041 PMCID: PMC6582344 DOI: 10.1093/nar/gkz301] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/15/2022]  Open
93
Verbruggen S, Menschaert G. mQC: A post-mapping data exploration tool for ribosome profiling. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2019;181:104806. [PMID: 30401579 DOI: 10.1016/j.cmpb.2018.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 10/05/2018] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
94
uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames. PLoS One 2019;14:e0222459. [PMID: 31513641 PMCID: PMC6742470 DOI: 10.1371/journal.pone.0222459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/29/2019] [Indexed: 12/17/2022]  Open
95
Xu Z, Hu L, Shi B, Geng S, Xu L, Wang D, Lu ZJ. Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events. Nucleic Acids Res 2019;46:e109. [PMID: 29945224 PMCID: PMC6182183 DOI: 10.1093/nar/gky533] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023]  Open
96
Halpin JC, Jangi R, Street TO. Multimapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone. Proteins 2019;88:57-68. [PMID: 31254414 DOI: 10.1002/prot.25766] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/17/2019] [Accepted: 06/25/2019] [Indexed: 11/11/2022]
97
Onder Y, Laothamatas I, Berto S, Sewart K, Kilaru G, Bordieanu B, Stubblefield JJ, Konopka G, Mishra P, Green CB. The Circadian Protein Nocturnin Regulates Metabolic Adaptation in Brown Adipose Tissue. iScience 2019;19:83-92. [PMID: 31357170 PMCID: PMC6664146 DOI: 10.1016/j.isci.2019.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/20/2019] [Accepted: 07/11/2019] [Indexed: 01/19/2023]  Open
98
Akichika S, Hirano S, Shichino Y, Suzuki T, Nishimasu H, Ishitani R, Sugita A, Hirose Y, Iwasaki S, Nureki O, Suzuki T. Cap-specific terminal N 6-methylation of RNA by an RNA polymerase II-associated methyltransferase. Science 2018;363:science.aav0080. [PMID: 30467178 DOI: 10.1126/science.aav0080] [Citation(s) in RCA: 265] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 11/14/2018] [Indexed: 12/14/2022]
99
Ji Z. RibORF: Identifying Genome-Wide Translated Open Reading Frames Using Ribosome Profiling. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2018;124:e67. [PMID: 30178897 PMCID: PMC6168376 DOI: 10.1002/cpmb.67] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Lauria F, Tebaldi T, Bernabò P, Groen EJN, Gillingwater TH, Viero G. riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data. PLoS Comput Biol 2018;14:e1006169. [PMID: 30102689 PMCID: PMC6112680 DOI: 10.1371/journal.pcbi.1006169] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 08/28/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022]  Open
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