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Items: 16

1.

Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling.

Gerresheim GK, Bathke J, Michel AM, Andreev DE, Shalamova LA, Rossbach O, Hu P, Glebe D, Fricke M, Marz M, Goesmann A, Kiniry SJ, Baranov PV, Shatsky IN, Niepmann M.

Int J Mol Sci. 2019 Mar 15;20(6). pii: E1321. doi: 10.3390/ijms20061321.

2.

Trips-Viz: a transcriptome browser for exploring Ribo-Seq data.

Kiniry SJ, O'Connor PBF, Michel AM, Baranov PV.

Nucleic Acids Res. 2019 Jan 8;47(D1):D847-D852. doi: 10.1093/nar/gky842.

3.

PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data.

Kumari R, Michel AM, Baranov PV.

RNA. 2018 Oct;24(10):1297-1304. doi: 10.1261/rna.065235.117. Epub 2018 Jul 26.

PMID:
30049792
4.

TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response.

Andreev DE, Arnold M, Kiniry SJ, Loughran G, Michel AM, Rachinskii D, Baranov PV.

Elife. 2018 Jun 22;7. pii: e32563. doi: 10.7554/eLife.32563.

5.

The GWIPS-viz Browser.

Kiniry SJ, Michel AM, Baranov PV.

Curr Protoc Bioinformatics. 2018 Jun;62(1):e50. doi: 10.1002/cpbi.50. Epub 2018 May 16.

PMID:
29927076
6.

AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation.

Yordanova MM, Loughran G, Zhdanov AV, Mariotti M, Kiniry SJ, O'Connor PBF, Andreev DE, Tzani I, Saffert P, Michel AM, Gladyshev VN, Papkovsky DB, Atkins JF, Baranov PV.

Nature. 2018 Jan 18;553(7688):356-360. doi: 10.1038/nature25174. Epub 2018 Jan 3.

PMID:
29310120
7.

GWIPS-viz: 2018 update.

Michel AM, Kiniry SJ, O'Connor PBF, Mullan JP, Baranov PV.

Nucleic Acids Res. 2018 Jan 4;46(D1):D823-D830. doi: 10.1093/nar/gkx790.

8.

Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity.

Ivanov IP, Wei J, Caster SZ, Smith KM, Michel AM, Zhang Y, Firth AE, Freitag M, Dunlap JC, Bell-Pedersen D, Atkins JF, Sachs MS.

MBio. 2017 Jun 27;8(3). pii: e00844-17. doi: 10.1128/mBio.00844-17.

9.

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.

10.

Illuminating translation with ribosome profiling spectra.

Baranov PV, Michel AM.

Nat Methods. 2016 Feb;13(2):123-4. doi: 10.1038/nmeth.3738. No abstract available.

PMID:
26820545
11.

GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms.

Michel AM, Ahern AM, Donohue CA, Baranov PV.

Proteomics. 2015 Jul;15(14):2410-6. doi: 10.1002/pmic.201400603. Epub 2015 Apr 23.

12.
13.

GWIPS-viz: development of a ribo-seq genome browser.

Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM, Mullan JP, Donohue CA, Higgins DG, Baranov PV.

Nucleic Acids Res. 2014 Jan;42(Database issue):D859-64. doi: 10.1093/nar/gkt1035. Epub 2013 Oct 31.

14.

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):.

15.

Observation of dually decoded regions of the human genome using ribosome profiling data.

Michel AM, Choudhury KR, Firth AE, Ingolia NT, Atkins JF, Baranov PV.

Genome Res. 2012 Nov;22(11):2219-29. doi: 10.1101/gr.133249.111. Epub 2012 May 16.

16.

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences.

Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV.

Nucleic Acids Res. 2011 May;39(10):4220-34. doi: 10.1093/nar/gkr007. Epub 2011 Jan 25.

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