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Items: 12

1.

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

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

Nucleic Acids Res. 2018 Sep 20. doi: 10.1093/nar/gky842. [Epub ahead of print]

PMID:
30239879
2.

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
3.

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.

4.

Itm2a silencing rescues lamin A mediated inhibition of 3T3-L1 adipocyte differentiation.

Davies SJ, Ryan J, O'Connor PBF, Kenny E, Morris D, Baranov PV, O'Connor R, McCarthy TV.

Adipocyte. 2017 Oct 2;6(4):259-276. doi: 10.1080/21623945.2017.1362510. Epub 2017 Sep 5.

5.

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling.

Andreev DE, O'Connor PB, Loughran G, Dmitriev SE, Baranov PV, Shatsky IN.

Nucleic Acids Res. 2017 Jan 25;45(2):513-526. doi: 10.1093/nar/gkw1190. Epub 2016 Dec 6. Review.

6.

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.

7.

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.

8.

The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype.

Dieudonné FX, O'Connor PB, Gubler-Jaquier P, Yasrebi H, Conne B, Nikolaev S, Antonarakis S, Baranov PV, Curran J.

BMC Genomics. 2015 Nov 21;16:986. doi: 10.1186/s12864-015-2179-8.

9.

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes.

Andreev DE, O'Connor PB, Zhdanov AV, Dmitriev RI, Shatsky IN, Papkovsky DB, Baranov PV.

Genome Biol. 2015 May 6;16:90. doi: 10.1186/s13059-015-0651-z.

10.

Translation of 5' leaders is pervasive in genes resistant to eIF2 repression.

Andreev DE, O'Connor PB, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, Cormican P, Morris DW, Shatsky IN, Baranov PV.

Elife. 2015 Jan 26;4:e03971. doi: 10.7554/eLife.03971.

11.

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.

12.

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments.

O'Connor PB, Li GW, Weissman JS, Atkins JF, Baranov PV.

Bioinformatics. 2013 Jun 15;29(12):1488-91. doi: 10.1093/bioinformatics/btt184. Epub 2013 Apr 19.

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