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For: Fritsch C, Herrmann A, Nothnagel M, Szafranski K, Huse K, Schumann F, Schreiber S, Platzer M, Krawczak M, Hampe J, Brosch M. Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res 2012;22:2208-18. [PMID: 22879431 PMCID: PMC3483550 DOI: 10.1101/gr.139568.112] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Number Cited by Other Article(s)
101
Chew GL, Pauli A, Schier AF. Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun 2016;7:11663. [PMID: 27216465 PMCID: PMC4890304 DOI: 10.1038/ncomms11663] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 04/18/2016] [Indexed: 02/07/2023]  Open
102
SUMO5, a Novel Poly-SUMO Isoform, Regulates PML Nuclear Bodies. Sci Rep 2016;6:26509. [PMID: 27211601 PMCID: PMC4876461 DOI: 10.1038/srep26509] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/04/2016] [Indexed: 12/23/2022]  Open
103
Towards understanding pre-mRNA splicing mechanisms and the role of SR proteins. Gene 2016;587:107-19. [PMID: 27154819 DOI: 10.1016/j.gene.2016.04.057] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 04/30/2016] [Indexed: 01/04/2023]
104
Atanassov BS, Mohan RD, Lan X, Kuang X, Lu Y, Lin K, McIvor E, Li W, Zhang Y, Florens L, Byrum SD, Mackintosh SG, Calhoun-Davis T, Koutelou E, Wang L, Tang DG, Tackett AJ, Washburn MP, Workman JL, Dent SYR. ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth. Mol Cell 2016;62:558-71. [PMID: 27132940 DOI: 10.1016/j.molcel.2016.03.030] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 02/04/2016] [Accepted: 03/25/2016] [Indexed: 10/21/2022]
105
Nakahigashi K, Takai Y, Kimura M, Abe N, Nakayashiki T, Shiwa Y, Yoshikawa H, Wanner BL, Ishihama Y, Mori H. Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling. DNA Res 2016;23:193-201. [PMID: 27013550 PMCID: PMC4909307 DOI: 10.1093/dnares/dsw008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 02/06/2016] [Indexed: 01/12/2023]  Open
106
Lian X, Guo J, Gu W, Cui Y, Zhong J, Jin J, He QY, Wang T, Zhang G. Genome-Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells. PLoS Genet 2016;12:e1005901. [PMID: 26926465 PMCID: PMC4771717 DOI: 10.1371/journal.pgen.1005901] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/05/2016] [Indexed: 11/18/2022]  Open
107
Selective mRNA translation in erythropoiesis. Biochem Soc Trans 2016;43:343-7. [PMID: 26009174 DOI: 10.1042/bst20150009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
108
Hu Q, Merchante C, Stepanova AN, Alonso JM, Heber S. Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana. IEEE Trans Nanobioscience 2016;15:148-57. [PMID: 26886998 DOI: 10.1109/tnb.2016.2516950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
109
Sheshukova EV, Shindyapina AV, Komarova TV, Dorokhov YL. “Matreshka” genes with alternative reading frames. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
110
Popa A, Lebrigand K, Barbry P, Waldmann R. Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells. BMC Genomics 2016;17:52. [PMID: 26764022 PMCID: PMC4712605 DOI: 10.1186/s12864-016-2384-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/06/2016] [Indexed: 01/02/2023]  Open
111
Liu B, Qian SB. Characterizing inactive ribosomes in translational profiling. ACTA ACUST UNITED AC 2016;4:e1138018. [PMID: 27335722 DOI: 10.1080/21690731.2015.1138018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/20/2015] [Accepted: 12/28/2015] [Indexed: 01/10/2023]
112
Mouilleron H, Delcourt V, Roucou X. Death of a dogma: eukaryotic mRNAs can code for more than one protein. Nucleic Acids Res 2016;44:14-23. [PMID: 26578573 PMCID: PMC4705651 DOI: 10.1093/nar/gkv1218] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/13/2022]  Open
113
Gao X, Wan J, Qian SB. Genome-Wide Profiling of Alternative Translation Initiation Sites. Methods Mol Biol 2016;1358:303-16. [PMID: 26463392 DOI: 10.1007/978-1-4939-3067-8_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
114
Olexiouk V, Menschaert G. Identification of Small Novel Coding Sequences, a Proteogenomics Endeavor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016;926:49-64. [PMID: 27686805 DOI: 10.1007/978-3-319-42316-6_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
115
Bartholomäus A, Del Campo C, Ignatova Z. Mapping the non-standardized biases of ribosome profiling. Biol Chem 2016;397:23-35. [DOI: 10.1515/hsz-2015-0197] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 08/25/2015] [Indexed: 01/30/2023]
116
Detecting actively translated open reading frames in ribosome profiling data. Nat Methods 2015;13:165-70. [PMID: 26657557 DOI: 10.1038/nmeth.3688] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/28/2015] [Indexed: 12/23/2022]
117
Saghatelian A, Couso JP. Discovery and characterization of smORF-encoded bioactive polypeptides. Nat Chem Biol 2015;11:909-16. [PMID: 26575237 PMCID: PMC4956473 DOI: 10.1038/nchembio.1964] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 10/19/2015] [Indexed: 12/13/2022]
118
Tian Y, Yang JE. Emerging landscape of short open reading frame-encoded peptides. Shijie Huaren Xiaohua Zazhi 2015;23:4954-4960. [DOI: 10.11569/wcjd.v23.i31.4954] [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] [Indexed: 02/06/2023]  Open
119
Housman G, Ulitsky I. Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015;1859:31-40. [PMID: 26265145 DOI: 10.1016/j.bbagrm.2015.07.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/18/2015] [Accepted: 07/19/2015] [Indexed: 12/12/2022]
120
Stern-Ginossar N, Ingolia NT. Ribosome Profiling as a Tool to Decipher Viral Complexity. Annu Rev Virol 2015;2:335-49. [PMID: 26958919 DOI: 10.1146/annurev-virology-100114-054854] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
121
Aeschimann F, Xiong J, Arnold A, Dieterich C, Großhans H. Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling. Methods 2015;85:75-89. [PMID: 26102273 DOI: 10.1016/j.ymeth.2015.06.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/10/2015] [Accepted: 06/15/2015] [Indexed: 01/08/2023]  Open
122
Bahrami-Samani E, Vo DT, de Araujo PR, Vogel C, Smith AD, Penalva LOF, Uren PJ. Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. WILEY INTERDISCIPLINARY REVIEWS. RNA 2015;6:291-310. [PMID: 25515586 PMCID: PMC4397117 DOI: 10.1002/wrna.1274] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/24/2014] [Accepted: 10/29/2014] [Indexed: 11/10/2022]
123
Michel AM, Ahern AM, Donohue CA, Baranov PV. GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms. Proteomics 2015;15:2410-6. [PMID: 25736862 PMCID: PMC4832365 DOI: 10.1002/pmic.201400603] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/03/2015] [Accepted: 02/26/2015] [Indexed: 01/08/2023]
124
de Klerk E, Fokkema IFAC, Thiadens KAMH, Goeman JJ, Palmblad M, den Dunnen JT, von Lindern M, 't Hoen PAC. Assessing the translational landscape of myogenic differentiation by ribosome profiling. Nucleic Acids Res 2015;43:4408-28. [PMID: 25873627 PMCID: PMC4482065 DOI: 10.1093/nar/gkv281] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/21/2015] [Indexed: 01/08/2023]  Open
125
Tang S, Lomsadze A, Borodovsky M. Identification of protein coding regions in RNA transcripts. Nucleic Acids Res 2015;43:e78. [PMID: 25870408 PMCID: PMC4499116 DOI: 10.1093/nar/gkv227] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 03/05/2015] [Indexed: 01/08/2023]  Open
126
Smith JE, Baker KE. Nonsense-mediated RNA decay--a switch and dial for regulating gene expression. Bioessays 2015;37:612-23. [PMID: 25820233 DOI: 10.1002/bies.201500007] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
127
de Klerk E, 't Hoen PAC. Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. Trends Genet 2015;31:128-39. [PMID: 25648499 DOI: 10.1016/j.tig.2015.01.001] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/22/2014] [Accepted: 01/05/2015] [Indexed: 12/13/2022]
128
Pauli A, Valen E, Schier AF. Identifying (non-)coding RNAs and small peptides: challenges and opportunities. Bioessays 2015;37:103-12. [PMID: 25345765 PMCID: PMC4433033 DOI: 10.1002/bies.201400103] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
129
Hu Q, Merchante C, Stepanova AN, Alonso JM, Heber S. A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana. BIOINFORMATICS RESEARCH AND APPLICATIONS 2015. [DOI: 10.1007/978-3-319-19048-8_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
130
Quantitative profiling of initiating ribosomes in vivo. Nat Methods 2014;12:147-53. [PMID: 25486063 PMCID: PMC4344187 DOI: 10.1038/nmeth.3208] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/30/2014] [Indexed: 12/29/2022]
131
Michel AM, Andreev DE, Baranov PV. Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning. BMC Bioinformatics 2014;15:380. [PMID: 25413677 PMCID: PMC4245810 DOI: 10.1186/s12859-014-0380-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/05/2014] [Indexed: 11/29/2022]  Open
132
King HA, Gerber AP. Translatome profiling: methods for genome-scale analysis of mRNA translation. Brief Funct Genomics 2014;15:22-31. [PMID: 25380596 DOI: 10.1093/bfgp/elu045] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
133
Gawron D, Gevaert K, Van Damme P. The proteome under translational control. Proteomics 2014;14:2647-62. [PMID: 25263132 DOI: 10.1002/pmic.201400165] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/21/2014] [Accepted: 09/23/2014] [Indexed: 02/02/2023]
134
Tsotakos N, Silveyra P, Lin Z, Thomas N, Vaid M, Floros J. Regulation of translation by upstream translation initiation codons of surfactant protein A1 splice variants. Am J Physiol Lung Cell Mol Physiol 2014;308:L58-75. [PMID: 25326576 DOI: 10.1152/ajplung.00058.2014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
135
Kearse MG, Todd PK. Repeat-associated non-AUG translation and its impact in neurodegenerative disease. Neurotherapeutics 2014;11:721-31. [PMID: 25005000 PMCID: PMC4391382 DOI: 10.1007/s13311-014-0292-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
136
Zupanic A, Meplan C, Grellscheid SN, Mathers JC, Kirkwood TBL, Hesketh JE, Shanley DP. Detecting translational regulation by change point analysis of ribosome profiling data sets. RNA (NEW YORK, N.Y.) 2014;20:1507-1518. [PMID: 25147239 PMCID: PMC4174433 DOI: 10.1261/rna.045286.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/25/2014] [Indexed: 06/03/2023]
137
Aspden JL, Eyre-Walker YC, Phillips RJ, Amin U, Mumtaz MAS, Brocard M, Couso JP. Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq. eLife 2014;3:e03528. [PMID: 25144939 PMCID: PMC4359375 DOI: 10.7554/elife.03528] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/19/2014] [Indexed: 12/11/2022]  Open
138
Zhang J, Lou X, Shen H, Zellmer L, Sun Y, Liu S, Xu N, Liao DJ. Isoforms of wild type proteins often appear as low molecular weight bands on SDS-PAGE. Biotechnol J 2014;9:1044-54. [PMID: 24906056 DOI: 10.1002/biot.201400072] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/03/2014] [Accepted: 06/04/2014] [Indexed: 11/08/2022]
139
Baboo S, Cook PR. "Dark matter" worlds of unstable RNA and protein. Nucleus 2014;5:281-6. [PMID: 25482115 PMCID: PMC4152340 DOI: 10.4161/nucl.29577] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 12/11/2022]  Open
140
Baboo S, Bhushan B, Jiang H, Grovenor CRM, Pierre P, Davis BG, Cook PR. Most human proteins made in both nucleus and cytoplasm turn over within minutes. PLoS One 2014;9:e99346. [PMID: 24911415 PMCID: PMC4050049 DOI: 10.1371/journal.pone.0099346] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 05/13/2014] [Indexed: 12/25/2022]  Open
141
Crappé J, Van Criekinge W, Menschaert G. Little things make big things happen: A summary of micropeptide encoding genes. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
142
Van Damme P, Gawron D, Van Criekinge W, Menschaert G. N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. Mol Cell Proteomics 2014;13:1245-61. [PMID: 24623590 DOI: 10.1074/mcp.m113.036442] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
143
Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 2014;15:193-204. [PMID: 24514441 DOI: 10.1038/nrg3520] [Citation(s) in RCA: 402] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
144
Skarshewski A, Stanton-Cook M, Huber T, Al Mansoori S, Smith R, Beatson SA, Rothnagel JA. uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation. BMC Bioinformatics 2014;15:36. [PMID: 24484385 PMCID: PMC3914846 DOI: 10.1186/1471-2105-15-36] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 01/11/2014] [Indexed: 01/17/2023]  Open
145
Dassi E, Re A, Leo S, Tebaldi T, Pasini L, Peroni D, Quattrone A. AURA 2: Empowering discovery of post-transcriptional networks. ACTA ACUST UNITED AC 2014;2:e27738. [PMID: 26779400 PMCID: PMC4705823 DOI: 10.4161/trla.27738] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/11/2013] [Accepted: 01/05/2014] [Indexed: 12/19/2022]
146
Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 2014;15:205-13. [PMID: 24468696 DOI: 10.1038/nrg3645] [Citation(s) in RCA: 435] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
147
Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. Genome-wide annotation and quantitation of translation by ribosome profiling. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2014;Chapter 4:4.18.1-4.18.19. [PMID: 23821443 DOI: 10.1002/0471142727.mb0418s103] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
148
Arias C, Weisburd B, Stern-Ginossar N, Mercier A, Madrid AS, Bellare P, Holdorf M, Weissman JS, Ganem D. KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features. PLoS Pathog 2014;10:e1003847. [PMID: 24453964 PMCID: PMC3894221 DOI: 10.1371/journal.ppat.1003847] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 10/20/2013] [Indexed: 01/08/2023]  Open
149
von Arnim AG, Jia Q, Vaughn JN. Regulation of plant translation by upstream open reading frames. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014;214:1-12. [PMID: 24268158 DOI: 10.1016/j.plantsci.2013.09.006] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 05/08/2023]
150
Dunn JG, Foo CK, Belletier NG, Gavis ER, Weissman JS. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. eLife 2013;2:e01179. [PMID: 24302569 PMCID: PMC3840789 DOI: 10.7554/elife.01179] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
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