{"id":{"repo_id":"cork","oai_identifier":"oai:cora.ucc.ie:10468/5431"},"canonical_url":"https://search.dev.ndltd.org/etd/cork/oai:cora.ucc.ie:10468/5431","repository":{"repo_id":"cork","name":"University College Cork","base_url":"https://cora.ucc.ie/server/oai/request"},"display":{"title":"A study of mRNA translation with computational analysis of ribosome profiling datasets","abstract":"Ribosome profiling is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a “snapshot” of ribosome positions at the transcriptome wide level. The approach was developed in 2009 and was a significant advancement towards the better understanding of the regulation of protein synthesis. I this thesis I describe my analysis of ribosome profiling data. In Chapter 1, I present a review of the recent developments of understanding obtained with ribosome profiling as well as discussing the implications of artifacts on the interpretation of its data. Chapters 2 and 3 details using ribosome profiling to examine the translational response to eIF2 repression and to the deprivation of oxygen and glucose respectively. Chapter 4 details how the interaction of the Shine Dalgarno with the ribosome rRNA alters the length of the mRNA protected fragments. In Chapter 5, I present analysis at identifying the relative impact of mRNA features on local ribosome profiling read density.","abstract_html":"Ribosome profiling is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a “snapshot” of ribosome positions at the transcriptome wide level. The approach was developed in 2009 and was a significant advancement towards the better understanding of the regulation of protein synthesis. I this thesis I describe my analysis of ribosome profiling data. In Chapter 1, I present a review of the recent developments of understanding obtained with ribosome profiling as well as discussing the implications of artifacts on the interpretation of its data. Chapters 2 and 3 details using ribosome profiling to examine the translational response to eIF2 repression and to the deprivation of oxygen and glucose respectively. Chapter 4 details how the interaction of the Shine Dalgarno with the ribosome rRNA alters the length of the mRNA protected fragments. In Chapter 5, I present analysis at identifying the relative impact of mRNA features on local ribosome profiling read density.","abstract_has_math":false,"creators":["O'Connor, Patrick"],"institution":"University College Cork","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Baranov, Pavel V."],"committee_chairs":[],"committee_members":[],"year":2017,"date_issued":"2017","date_published":"2017","updated_at":"2026-07-24T01:48:07Z","subjects":["Translation","Ribosome profiling"],"languages":["en"],"rights":["© 2017, Patrick O'Connor."],"rights_urls":["http://creativecommons.org/licenses/by-nc-nd/3.0/"],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/10468/5431","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Baranov, Pavel V."]},{"key":"dc:creator","label":"Author","values":["O'Connor, Patrick"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2018-02-09T12:07:46Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2018-02-09T12:07:46Z"]},{"key":"dc:date.issued","label":"Date","values":["2017"]},{"key":"dc:publisher","label":"Institution","values":["University College Cork"]},{"key":"dc:type","label":"Dc Type","values":["Doctoral thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["PhD (Science)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Translation","Ribosome profiling"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["© 2017, Patrick O'Connor."]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://creativecommons.org/licenses/by-nc-nd/3.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/10468/5431"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Ribosome profiling is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a “snapshot” of ribosome positions at the transcriptome wide level. The approach was developed in 2009 and was a significant advancement towards the better understanding of the regulation of protein synthesis. I this thesis I describe my analysis of ribosome profiling data. In Chapter 1, I present a review of the recent developments of understanding obtained with ribosome profiling as well as discussing the implications of artifacts on the interpretation of its data. Chapters 2 and 3 details using ribosome profiling to examine the translational response to eIF2 repression and to the deprivation of oxygen and glucose respectively. Chapter 4 details how the interaction of the Shine Dalgarno with the ribosome rRNA alters the length of the mRNA protected fragments. 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I this thesis I describe my analysis of ribosome profiling data. In Chapter 1, I present a review of the recent developments of understanding obtained with ribosome profiling as well as discussing the implications of artifacts on the interpretation of its data. Chapters 2 and 3 details using ribosome profiling to examine the translational response to eIF2 repression and to the deprivation of oxygen and glucose respectively. Chapter 4 details how the interaction of the Shine Dalgarno with the ribosome rRNA alters the length of the mRNA protected fragments. 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