P
Patrick B F O'Connor
Researcher at University College Cork
Publications - 20
Citations - 1094
Patrick B F O'Connor is an academic researcher from University College Cork. The author has contributed to research in topics: Ribosome profiling & Gene. The author has an hindex of 11, co-authored 20 publications receiving 862 citations. Previous affiliations of Patrick B F O'Connor include University of California, San Francisco.
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Journal ArticleDOI
Translation of 5' leaders is pervasive in genes resistant to eIF2 repression
Dmitry E. Andreev,Patrick B F O'Connor,Ciara Fahey,Elaine Kenny,Ilya M. Terenin,Sergey E. Dmitriev,Paul Cormican,Derek W. Morris,Ivan N. Shatsky,Pavel V. Baranov +9 more
TL;DR: Phylogenetic analysis suggests that at least two regulatory uORFs in SLC35A4 and MIEF1 encode functional protein products, and site-specific mutagenesis of two identified stress resistant mRNAs demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases.
Journal ArticleDOI
Insights into the mechanisms of eukaryotic translation gained with ribosome profiling.
Dmitry E. Andreev,Patrick B F O'Connor,Gary Loughran,Sergey E. Dmitriev,Pavel V. Baranov,Ivan N. Shatsky +5 more
TL;DR: This review will focus on how recent findings made with RiboSeq have revealed important details of the molecular mechanisms of translation in eukaryotes.
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Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes
Dmitry E. Andreev,Dmitry E. Andreev,Patrick B F O'Connor,Alexander V. Zhdanov,Ruslan I. Dmitriev,Ivan N. Shatsky,Dmitri B. Papkovsky,Pavel V. Baranov +7 more
TL;DR: These findings uncover novel regulatory mechanisms of translational response to OGD in mammalian cells that are different from the classical pathways such as hypoxia inducible factor (HIF) signaling, while also revealing sophisticated organization of protein coding information in certain genes.
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Comparative survey of the relative impact of mRNA features on local ribosome profiling read density.
TL;DR: A simple normalization method, Ribo-seq Unit Step Transformation (RUST), which is robust and outperforms other normalization techniques in the presence of heterogeneous noise and illustrated how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally.
Journal ArticleDOI
RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.
Audrey M. Michel,James P. A. Mullan,Vimalkumar Velayudhan,Patrick B F O'Connor,Claire A. Donohue,Pavel V. Baranov +5 more
TL;DR: RiboGalaxy is presented, a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz, and offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data.