{"id":{"repo_id":"uwo","oai_identifier":"oai:uwo.scholaris.ca:20.500.14721/36910"},"canonical_url":"https://search.dev.ndltd.org/etd/uwo/oai:uwo.scholaris.ca:20.500.14721/36910","repository":{"repo_id":"uwo","name":"Western University","base_url":"https://uwo.scholaris.ca/server/oai/request"},"display":{"title":"Oligonucleotide Design for Whole Genome Tiling Arrays","abstract":"Oligonucleotides are short, single-stranded fragments of DNA or RNA, designed to readily bind with a unique part in the target sequence. They have many important applications including PCR (polymerase chain reaction) amplification, microarrays, or FISH (fluorescence in situ hybridization) probes. While traditional microarrays are commonly used for measuring gene expression levels by probing for sequences of known and predicted genes, high-density, whole genome tiling arrays probe intensively for sequences that are known to exist in a contiguous region. Current programs for designing oligonucleotides for tiling arrays are not able to produce results that are close to optimal since they allow oligonucleotides that are too similar with non-targets, thus enabling unwanted cross-hybridization. We present a new program, BOND-tile, that produces much better tiling arrays, as shown by extensive comparison with leading programs.","abstract_html":"Oligonucleotides are short, single-stranded fragments of DNA or RNA, designed to readily bind with a unique part in the target sequence. They have many important applications including PCR (polymerase chain reaction) amplification, microarrays, or FISH (fluorescence in situ hybridization) probes. While traditional microarrays are commonly used for measuring gene expression levels by probing for sequences of known and predicted genes, high-density, whole genome tiling arrays probe intensively for sequences that are known to exist in a contiguous region. Current programs for designing oligonucleotides for tiling arrays are not able to produce results that are close to optimal since they allow oligonucleotides that are too similar with non-targets, thus enabling unwanted cross-hybridization. We present a new program, BOND-tile, that produces much better tiling arrays, as shown by extensive comparison with leading programs.","abstract_has_math":false,"creators":["Dong, Qin"],"institution":"The University of Western Ontario","degree_name":"M Sc","degree_level":null,"degree_discipline":"Computer Science","degree_department":null,"school":null,"contributors":[],"advisors":["Lucian Ilie"],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-01-22","date_published":"2014-01-22","updated_at":"2026-07-27T21:56:11Z","subjects":["DNA","oligonucleotide","tiling arrays","microarrays"],"languages":["en_ca"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/20.500.14721/36910","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Lucian Ilie"]},{"key":"dc:creator","label":"Author","values":["Dong, Qin"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2025-07-10T21:27:29Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2025-07-10T21:27:29Z"]},{"key":"dc:date.issued","label":"Date","values":["2014-01-22"]},{"key":"dc:publisher","label":"Institution","values":["The University of Western Ontario"]},{"key":"dc:type","label":"Dc Type","values":["thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Computer Science"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M Sc"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["DNA","oligonucleotide","tiling arrays","microarrays"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en_ca"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/20.500.14721/36910"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The thesis cover page in the PDF document includes references to Western University’s previous institutional repository platform, known as Scholarship@Western, and links to that platform (beginning with ir.lib.uwo.ca). In citing or referring to this thesis, use the DOI or handle from this page instead. Sample citation: Author name, \"Thesis title.\" (Year). Western University Open Repository. https://doi.org/10.71858/123456."]},{"key":"dc:description.abstract","label":"Abstract","values":["Oligonucleotides are short, single-stranded fragments of DNA or RNA, designed to readily bind with a unique part in the target sequence. They have many important applications including PCR (polymerase chain reaction) amplification, microarrays, or FISH (fluorescence in situ hybridization) probes. While traditional microarrays are commonly used for measuring gene expression levels by probing for sequences of known and predicted genes, high-density, whole genome tiling arrays probe intensively for sequences that are known to exist in a contiguous region. Current programs for designing oligonucleotides for tiling arrays are not able to produce results that are close to optimal since they allow oligonucleotides that are too similar with non-targets, thus enabling unwanted cross-hybridization. We present a new program, BOND-tile, that produces much better tiling arrays, as shown by extensive comparison with leading programs."]},{"key":"dc:title","label":"Title","values":["Oligonucleotide Design for Whole Genome Tiling Arrays"]}]}],"canonical_facts":{"dc:contributor.advisor":["Lucian Ilie"],"dc:creator":["Dong, Qin"],"dc:date.accessioned":["2025-07-10T21:27:29Z"],"dc:date.available":["2025-07-10T21:27:29Z"],"dc:date.issued":["2014-01-22"],"dc:description":["The thesis cover page in the PDF document includes references to Western University’s previous institutional repository platform, known as Scholarship@Western, and links to that platform (beginning with ir.lib.uwo.ca). In citing or referring to this thesis, use the DOI or handle from this page instead. Sample citation: Author name, \"Thesis title.\" (Year). Western University Open Repository. https://doi.org/10.71858/123456."],"dc:description.abstract":["Oligonucleotides are short, single-stranded fragments of DNA or RNA, designed to readily bind with a unique part in the target sequence. They have many important applications including PCR (polymerase chain reaction) amplification, microarrays, or FISH (fluorescence in situ hybridization) probes. While traditional microarrays are commonly used for measuring gene expression levels by probing for sequences of known and predicted genes, high-density, whole genome tiling arrays probe intensively for sequences that are known to exist in a contiguous region. Current programs for designing oligonucleotides for tiling arrays are not able to produce results that are close to optimal since they allow oligonucleotides that are too similar with non-targets, thus enabling unwanted cross-hybridization. We present a new program, BOND-tile, that produces much better tiling arrays, as shown by extensive comparison with leading programs."],"dc:identifier.uri":["https://hdl.handle.net/20.500.14721/36910"],"dc:language.iso":["en_ca"],"dc:publisher":["The University of Western Ontario"],"dc:subject":["DNA","oligonucleotide","tiling arrays","microarrays"],"dc:title":["Oligonucleotide Design for Whole Genome Tiling Arrays"],"dc:type":["thesis"],"thesis:degree_discipline":["Computer Science"],"thesis:degree_name":["M Sc"]},"updated_at":"2026-07-27T21:56:11Z"}