{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/90895"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/90895","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Bioinformatics analyses of non-coding genomic elements","abstract":"\"Mammalian genomes consist primarily of non-coding sequences (Kellis et al. 2014). Originally castigated as \"\"junk DNA\"\", many non-coding regions have now been characterized as having functional roles, or have been determined to be the causal agent for diseases. Additionally, sequences that are non-functional can be used as neutral markers for population genetics. Determining the role of non-coding sequences or finding sequences usable as neutral markers is computationally and biologically non-trivial. However, recent advances in molecular biology, in particular the reduced cost of next-generation sequencing (NGS), have enabled new experiments that involve these sequences. I will discuss studies using bioinformatics that leveraged these advances to characterize three types of non-coding sequences: endogenous retroviruses, microsatellite markers and transcription factor binding sites. I conducted the bioinformatics design, coding and analyses, working with collaborators who verified findings in the laboratory. The only retrovirus known to be currently transitioning from exogenous to endogenous form is the koala retrovirus (KoRV), making koalas (Phascolarctos cinereus) ideal for examining the early stages of retroviral endogenization. In the first study, I developed a bioinformatics routine to identify distinct retroviral integrants from NGS reads of KoRV retrovirus flanks isolated using koala genomic DNA. In the second study, I developed computationally efficient, user-friendly software that would identify polymorphic microsatellite loci using NGS reads, then design oligonucleotide primers appropriate for amplifying those loci. We developed this software to enable studies to improve understanding of population structure, estimate population size and estimate genetic diversity in genetically depauperate wildlife species. In the third study, I developed a bioinformatics pipeline to characterize gene expression changes during development in the fetal limb tissue of several mammalian species, to better understand the mechanistic differences across evolutionary lineages. We compared development in four species of mammals. The house mouse was used since it is a well-characterized model organism with five digits. The domestic pig was used since it is a well-studied agricultural animal and a model for digit reduction. A species of bat was used since bats undergo wing development. Finally, a species of opossum was used as an outgroup to the three eutherian species.\"","abstract_html":""Mammalian genomes consist primarily of non-coding sequences (Kellis et al. 2014). Originally castigated as ""junk DNA"", many non-coding regions have now been characterized as having functional roles, or have been determined to be the causal agent for diseases. Additionally, sequences that are non-functional can be used as neutral markers for population genetics. Determining the role of non-coding sequences or finding sequences usable as neutral markers is computationally and biologically non-trivial. However, recent advances in molecular biology, in particular the reduced cost of next-generation sequencing (NGS), have enabled new experiments that involve these sequences. I will discuss studies using bioinformatics that leveraged these advances to characterize three types of non-coding sequences: endogenous retroviruses, microsatellite markers and transcription factor binding sites. I conducted the bioinformatics design, coding and analyses, working with collaborators who verified findings in the laboratory. The only retrovirus known to be currently transitioning from exogenous to endogenous form is the koala retrovirus (KoRV), making koalas (Phascolarctos cinereus) ideal for examining the early stages of retroviral endogenization. In the first study, I developed a bioinformatics routine to identify distinct retroviral integrants from NGS reads of KoRV retrovirus flanks isolated using koala genomic DNA. In the second study, I developed computationally efficient, user-friendly software that would identify polymorphic microsatellite loci using NGS reads, then design oligonucleotide primers appropriate for amplifying those loci. We developed this software to enable studies to improve understanding of population structure, estimate population size and estimate genetic diversity in genetically depauperate wildlife species. In the third study, I developed a bioinformatics pipeline to characterize gene expression changes during development in the fetal limb tissue of several mammalian species, to better understand the mechanistic differences across evolutionary lineages. We compared development in four species of mammals. The house mouse was used since it is a well-characterized model organism with five digits. The domestic pig was used since it is a well-studied agricultural animal and a model for digit reduction. A species of bat was used since bats undergo wing development. Finally, a species of opossum was used as an outgroup to the three eutherian species."","abstract_has_math":false,"creators":["Zhao, Kai"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Animal Sciences","degree_department":null,"school":null,"contributors":["Roca, Alfred L.","Cardoso, Felipe C.","Loor, Juan J.","Sinha, Saurabh"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-07-07T21:14:41Z","date_published":"2016-07-07T21:14:41Z","updated_at":"2026-07-22T22:26:34Z","subjects":["transcription factors","hox genes","endogenous retroviruses","koala","sumatran rhinoceros","Phascolarctos cinereus","koala retrovirus","korv"],"languages":["en"],"rights":["Copyright 2016 Kai Zhao"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/90895","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Roca, Alfred L.","Cardoso, Felipe C.","Loor, Juan J.","Sinha, Saurabh"]},{"key":"dc:creator","label":"Author","values":["Zhao, Kai"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2016-07-07T21:14:41Z","2018-07-08T09:15:23Z","2016-04-15","2016-05"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Animal Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["transcription factors","hox genes","endogenous retroviruses","koala","sumatran rhinoceros","Phascolarctos cinereus","koala retrovirus","korv"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2016 Kai Zhao"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/90895"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["\"Mammalian genomes consist primarily of non-coding sequences (Kellis et al. 2014). Originally castigated as \"\"junk DNA\"\", many non-coding regions have now been characterized as having functional roles, or have been determined to be the causal agent for diseases. Additionally, sequences that are non-functional can be used as neutral markers for population genetics. Determining the role of non-coding sequences or finding sequences usable as neutral markers is computationally and biologically non-trivial. However, recent advances in molecular biology, in particular the reduced cost of next-generation sequencing (NGS), have enabled new experiments that involve these sequences. I will discuss studies using bioinformatics that leveraged these advances to characterize three types of non-coding sequences: endogenous retroviruses, microsatellite markers and transcription factor binding sites. I conducted the bioinformatics design, coding and analyses, working with collaborators who verified findings in the laboratory. The only retrovirus known to be currently transitioning from exogenous to endogenous form is the koala retrovirus (KoRV), making koalas (Phascolarctos cinereus) ideal for examining the early stages of retroviral endogenization. In the first study, I developed a bioinformatics routine to identify distinct retroviral integrants from NGS reads of KoRV retrovirus flanks isolated using koala genomic DNA. In the second study, I developed computationally efficient, user-friendly software that would identify polymorphic microsatellite loci using NGS reads, then design oligonucleotide primers appropriate for amplifying those loci. We developed this software to enable studies to improve understanding of population structure, estimate population size and estimate genetic diversity in genetically depauperate wildlife species. In the third study, I developed a bioinformatics pipeline to characterize gene expression changes during development in the fetal limb tissue of several mammalian species, to better understand the mechanistic differences across evolutionary lineages. We compared development in four species of mammals. The house mouse was used since it is a well-characterized model organism with five digits. The domestic pig was used since it is a well-studied agricultural animal and a model for digit reduction. A species of bat was used since bats undergo wing development. Finally, a species of opossum was used as an outgroup to the three eutherian species.\"","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-05-01","The student, Kai Zhao, accepted the attached license on 2016-04-13 at 16:26.","The student, Kai Zhao, submitted this Dissertation for approval on 2016-04-13 at 16:37.","This Dissertation was approved for publication on 2016-04-15 at 08:13.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9211 on 2016-07-07 at 14:16:40","Made available in DSpace on 2016-07-07T21:14:41Z (GMT). No. of bitstreams: 3 ZHAO-DISSERTATION-2016.pdf: 2247656 bytes, checksum: 30daef0d3c41884b383500f38d651072 (MD5) LICENSE.txt: 4205 bytes, checksum: c2cd4b73b8d68ead2a5bcb54af6c557c (MD5) PROQUEST_LICENSE.txt: 4551 bytes, checksum: ca00a57bf5891e20f293755778579a91 (MD5) Previous issue date: 2016-04-15","Embargo set by: Seth Robbins for item 93249 Lift date: 2018-07-07T21:14:52Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 93249 Lift date: 2018-07-07T21:18:16Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 93249 on 2018-07-08T09:15:23Z."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Bioinformatics analyses of non-coding genomic elements"]}]}],"canonical_facts":{"dc:contributor":["Roca, Alfred L.","Cardoso, Felipe C.","Loor, Juan J.","Sinha, Saurabh"],"dc:creator":["Zhao, Kai"],"dc:date":["2016-07-07T21:14:41Z","2018-07-08T09:15:23Z","2016-04-15","2016-05"],"dc:description":["\"Mammalian genomes consist primarily of non-coding sequences (Kellis et al. 2014). Originally castigated as \"\"junk DNA\"\", many non-coding regions have now been characterized as having functional roles, or have been determined to be the causal agent for diseases. Additionally, sequences that are non-functional can be used as neutral markers for population genetics. Determining the role of non-coding sequences or finding sequences usable as neutral markers is computationally and biologically non-trivial. However, recent advances in molecular biology, in particular the reduced cost of next-generation sequencing (NGS), have enabled new experiments that involve these sequences. I will discuss studies using bioinformatics that leveraged these advances to characterize three types of non-coding sequences: endogenous retroviruses, microsatellite markers and transcription factor binding sites. I conducted the bioinformatics design, coding and analyses, working with collaborators who verified findings in the laboratory. The only retrovirus known to be currently transitioning from exogenous to endogenous form is the koala retrovirus (KoRV), making koalas (Phascolarctos cinereus) ideal for examining the early stages of retroviral endogenization. In the first study, I developed a bioinformatics routine to identify distinct retroviral integrants from NGS reads of KoRV retrovirus flanks isolated using koala genomic DNA. In the second study, I developed computationally efficient, user-friendly software that would identify polymorphic microsatellite loci using NGS reads, then design oligonucleotide primers appropriate for amplifying those loci. We developed this software to enable studies to improve understanding of population structure, estimate population size and estimate genetic diversity in genetically depauperate wildlife species. In the third study, I developed a bioinformatics pipeline to characterize gene expression changes during development in the fetal limb tissue of several mammalian species, to better understand the mechanistic differences across evolutionary lineages. We compared development in four species of mammals. The house mouse was used since it is a well-characterized model organism with five digits. The domestic pig was used since it is a well-studied agricultural animal and a model for digit reduction. A species of bat was used since bats undergo wing development. Finally, a species of opossum was used as an outgroup to the three eutherian species.\"","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-05-01","The student, Kai Zhao, accepted the attached license on 2016-04-13 at 16:26.","The student, Kai Zhao, submitted this Dissertation for approval on 2016-04-13 at 16:37.","This Dissertation was approved for publication on 2016-04-15 at 08:13.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9211 on 2016-07-07 at 14:16:40","Made available in DSpace on 2016-07-07T21:14:41Z (GMT). No. of bitstreams: 3 ZHAO-DISSERTATION-2016.pdf: 2247656 bytes, checksum: 30daef0d3c41884b383500f38d651072 (MD5) LICENSE.txt: 4205 bytes, checksum: c2cd4b73b8d68ead2a5bcb54af6c557c (MD5) PROQUEST_LICENSE.txt: 4551 bytes, checksum: ca00a57bf5891e20f293755778579a91 (MD5) Previous issue date: 2016-04-15","Embargo set by: Seth Robbins for item 93249 Lift date: 2018-07-07T21:14:52Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 93249 Lift date: 2018-07-07T21:18:16Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 93249 on 2018-07-08T09:15:23Z."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/90895"],"dc:language":["en"],"dc:rights":["Copyright 2016 Kai Zhao"],"dc:subject":["transcription factors","hox genes","endogenous retroviruses","koala","sumatran rhinoceros","Phascolarctos cinereus","koala retrovirus","korv"],"dc:title":["Bioinformatics analyses of non-coding genomic elements"],"dc:type":["text"],"thesis:degree_discipline":["Animal Sciences"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:26:34Z"}