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Items: 1 to 20 of 136

1.

Bayesian prediction of RNA translation from ribosome profiling.

Malone B, Atanassov I, Aeschimann F, Li X, Großhans H, Dieterich C.

Nucleic Acids Res. 2017 Apr 7;45(6):2960-2972. doi: 10.1093/nar/gkw1350.

2.

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration.

Crappé J, Ndah E, Koch A, Steyaert S, Gawron D, De Keulenaer S, De Meester E, De Meyer T, Van Criekinge W, Van Damme P, Menschaert G.

Nucleic Acids Res. 2015 Mar 11;43(5):e29. doi: 10.1093/nar/gku1283. Epub 2014 Dec 15.

3.

Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale.

Michel AM, Baranov PV.

Wiley Interdiscip Rev RNA. 2013 Sep-Oct;4(5):473-90. doi: 10.1002/wrna.1172. Epub 2013 May 20. Review. Erratum in: Wiley Interdiscip Rev RNA. 2017 Sep;8(5):.

4.

RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.

Michel AM, Mullan JP, Velayudhan V, O'Connor PB, Donohue CA, Baranov PV.

RNA Biol. 2016;13(3):316-9. doi: 10.1080/15476286.2016.1141862. Epub 2016 Jan 29.

5.

Detecting actively translated open reading frames in ribosome profiling data.

Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U.

Nat Methods. 2016 Feb;13(2):165-70. doi: 10.1038/nmeth.3688. Epub 2015 Dec 14.

PMID:
26657557
6.

The extent of ribosome queuing in budding yeast.

Diament A, Feldman A, Schochet E, Kupiec M, Arava Y, Tuller T.

PLoS Comput Biol. 2018 Jan 29;14(1):e1005951. doi: 10.1371/journal.pcbi.1005951. eCollection 2018 Jan.

7.

Identification of Small Novel Coding Sequences, a Proteogenomics Endeavor.

Olexiouk V, Menschaert G.

Adv Exp Med Biol. 2016;926:49-64. Review.

PMID:
27686805
8.

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes.

Ingolia NT, Lareau LF, Weissman JS.

Cell. 2011 Nov 11;147(4):789-802. doi: 10.1016/j.cell.2011.10.002. Epub 2011 Nov 3.

9.

Ribosomal profiling adds new coding sequences to the proteome.

Mumtaz MA, Couso JP.

Biochem Soc Trans. 2015 Dec;43(6):1271-6. doi: 10.1042/BST20150170. Review.

PMID:
26614672
10.

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density.

O'Connor PB, Andreev DE, Baranov PV.

Nat Commun. 2016 Oct 4;7:12915. doi: 10.1038/ncomms12915.

11.

Studying Selenoprotein mRNA Translation Using RNA-Seq and Ribosome Profiling.

Dalley BK, Baird L, Howard MT.

Methods Mol Biol. 2018;1661:103-123. doi: 10.1007/978-1-4939-7258-6_8.

PMID:
28917040
12.

Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling.

Spealman P, Wang H, May G, Kingsford C, McManus CJ.

Methods Mol Biol. 2016;1358:71-97. doi: 10.1007/978-1-4939-3067-8_5.

PMID:
26463378
13.

Ribosome profiling: a tool for quantitative evaluation of dynamics in mRNA translation.

Juntawong P, Hummel M, Bazin J, Bailey-Serres J.

Methods Mol Biol. 2015;1284:139-73. doi: 10.1007/978-1-4939-2444-8_7.

PMID:
25757771
14.

Ribosome Footprint Profiling of Translation throughout the Genome.

Ingolia NT.

Cell. 2016 Mar 24;165(1):22-33. doi: 10.1016/j.cell.2016.02.066.

15.

sORFs.org: a repository of small ORFs identified by ribosome profiling.

Olexiouk V, Crappé J, Verbruggen S, Verhegen K, Martens L, Menschaert G.

Nucleic Acids Res. 2016 Jan 4;44(D1):D324-9. doi: 10.1093/nar/gkv1175. Epub 2015 Nov 2.

16.

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data.

Lauria F, Tebaldi T, Bernabò P, Groen EJN, Gillingwater TH, Viero G.

PLoS Comput Biol. 2018 Aug 13;14(8):e1006169. doi: 10.1371/journal.pcbi.1006169. eCollection 2018 Aug.

17.

Simple and inexpensive ribosome profiling analysis of mRNA translation.

Reid DW, Shenolikar S, Nicchitta CV.

Methods. 2015 Dec;91:69-74. doi: 10.1016/j.ymeth.2015.07.003. Epub 2015 Jul 8.

18.

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.

Menschaert G, Van Criekinge W, Notelaers T, Koch A, Crappé J, Gevaert K, Van Damme P.

Mol Cell Proteomics. 2013 Jul;12(7):1780-90. doi: 10.1074/mcp.M113.027540. Epub 2013 Feb 21.

19.

Deciphering poxvirus gene expression by RNA sequencing and ribosome profiling.

Yang Z, Cao S, Martens CA, Porcella SF, Xie Z, Ma M, Shen B, Moss B.

J Virol. 2015 Jul;89(13):6874-86. doi: 10.1128/JVI.00528-15. Epub 2015 Apr 22.

20.

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