{"id":"https://openalex.org/W30238657","doi":null,"title":"Discovering meaning from biological sequences: focus on predicting misannotated proteins, binding patterns, and g4-quadruplex secondary structures","display_name":"Discovering meaning from biological sequences: focus on predicting misannotated proteins, binding patterns, and g4-quadruplex secondary structures","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W30238657","mag":"30238657"},"language":"en","primary_location":{"id":"pmh:oai:lib.dr.iastate.edu:etd-4540","doi":null,"is_oa":true,"landing_page_url":"https://lib.dr.iastate.edu/etd/13533","pdf_url":"https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=4540&context=etd","source":{"id":"https://openalex.org/S4377196104","display_name":"Iowa State University Digital Repository (Iowa State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I173911158","host_organization_name":"Iowa State University","host_organization_lineage":["https://openalex.org/I173911158"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Graduate Theses and Dissertations","raw_type":"text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=4540&context=etd","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004737962","display_name":"Vasant Honavar","orcid":"https://orcid.org/0000-0001-5399-3489","observed_orcids":["https://orcid.org/0000-0001-5399-3489"]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vasant Honavar","raw_affiliation_strings":["Iowa State University"],"raw_orcid":"https://orcid.org/0000-0001-5399-3489","affiliations":[{"raw_affiliation_string":"Iowa State University","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074103258","display_name":"Drena L Dobbs","orcid":"https://orcid.org/0000-0003-4404-9554","observed_orcids":["https://orcid.org/0000-0003-4404-9554"]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Drena Dobbs","raw_affiliation_strings":["Iowa State University"],"raw_orcid":"https://orcid.org/0000-0003-4404-9554","affiliations":[{"raw_affiliation_string":"Iowa State University","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045214155","display_name":"Carson M. Andorf","orcid":"https://orcid.org/0000-0003-2380-6704","observed_orcids":["https://orcid.org/0000-0003-2380-6704"]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carson M. Andorf","raw_affiliation_strings":["Iowa State University"],"raw_orcid":"https://orcid.org/0000-0003-2380-6704","affiliations":[{"raw_affiliation_string":"Iowa State University","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I173911158"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00203831,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.8730000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.8730000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.046300001442432404,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.02669999934732914,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"protein function prediction","score":0.7519999742507935},{"id":"https://openalex.org/keywords/protein-binding-sites","display_name":"protein binding sites","score":0.4819999933242798},{"id":"https://openalex.org/keywords/maize-genome","display_name":"maize genome","score":0.9340000152587891},{"id":"https://openalex.org/keywords/gene-expression-regulation","display_name":"gene expression regulation","score":0.9179999828338623},{"id":"https://openalex.org/keywords/hypoxia-response","display_name":"hypoxia response","score":0.9259999990463257},{"id":"https://openalex.org/keywords/carbohydrate-metabolism","display_name":"carbohydrate metabolism","score":0.7680000066757202},{"id":"https://openalex.org/keywords/two-stage-classification","display_name":"two-stage classification","score":0.6650000214576721},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"support vector machine","score":0.6959999799728394},{"id":"https://openalex.org/keywords/decision-tree","display_name":"decision tree","score":0.9210000038146973}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.7751789093017578},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.6351519227027893},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6287540197372437},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.5869379043579102},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5349292755126953},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49357306957244873},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4853774309158325},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4502694606781006},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4432866871356964},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.41321998834609985},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.41115081310272217},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35540711879730225},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34165114164352417},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.2755270302295685},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21092039346694946},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2061423659324646},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:lib.dr.iastate.edu:etd-4540","doi":null,"is_oa":true,"landing_page_url":"https://lib.dr.iastate.edu/etd/13533","pdf_url":"https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=4540&context=etd","source":{"id":"https://openalex.org/S4377196104","display_name":"Iowa State University Digital Repository (Iowa State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I173911158","host_organization_name":"Iowa State University","host_organization_lineage":["https://openalex.org/I173911158"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Graduate Theses and Dissertations","raw_type":"text"},{"id":"mag:30238657","doi":null,"is_oa":false,"landing_page_url":"https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=4540&context=etd","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:lib.dr.iastate.edu:etd-4540","doi":null,"is_oa":true,"landing_page_url":"https://lib.dr.iastate.edu/etd/13533","pdf_url":"https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=4540&context=etd","source":{"id":"https://openalex.org/S4377196104","display_name":"Iowa State University Digital Repository (Iowa State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I173911158","host_organization_name":"Iowa State University","host_organization_lineage":["https://openalex.org/I173911158"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Graduate Theses and Dissertations","raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1563226350","display_name":"ITR:  Algorithms and Software for Knowledge Acquisition  from Heterogeneous Distributed Data","funder_award_id":"0219699","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4725533717","display_name":null,"funder_award_id":"07-03580","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G6234298745","display_name":"Chromatin Structure and Genome Response in Maize","funder_award_id":"1025954","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7789932320","display_name":"UniformMu:    A Transposon Resource for Functional Genomics of Maize","funder_award_id":"1116561","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8955459229","display_name":"IGERT: Computational Molecular Biology Training Group","funder_award_id":"9972653","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G9000197013","display_name":null,"funder_award_id":"GM066387","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320311090","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"},{"id":"https://openalex.org/F4320332605","display_name":"Agricultural Research Service","ror":"https://ror.org/02d2m2044"},{"id":"https://openalex.org/F4320332688","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771"},{"id":"https://openalex.org/F4320337368","display_name":"Division of Graduate Education","ror":"https://ror.org/00whkrf32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W30238657.pdf","grobid_xml":"https://content.openalex.org/works/W30238657.grobid-xml"},"referenced_works_count":221,"referenced_works":["https://openalex.org/W19269568","https://openalex.org/W26001942","https://openalex.org/W193142705","https://openalex.org/W277606711","https://openalex.org/W648987057","https://openalex.org/W1491553314","https://openalex.org/W1498183065","https://openalex.org/W1527927437","https://openalex.org/W1538463803","https://openalex.org/W1543932334","https://openalex.org/W1544089433","https://openalex.org/W1550249922","https://openalex.org/W1570448133","https://openalex.org/W1575249057","https://openalex.org/W1700503930","https://openalex.org/W1721320694","https://openalex.org/W1816488618","https://openalex.org/W1848383448","https://openalex.org/W1870496269","https://openalex.org/W1963867239","https://openalex.org/W1964335041","https://openalex.org/W1964578544","https://openalex.org/W1969051510","https://openalex.org/W1970173121","https://openalex.org/W1970772422","https://openalex.org/W1973626596","https://openalex.org/W1975138006","https://openalex.org/W1977224551","https://openalex.org/W1977855826","https://openalex.org/W1980800453","https://openalex.org/W1984476827","https://openalex.org/W1985307298","https://openalex.org/W1985858836","https://openalex.org/W1985904552","https://openalex.org/W1987560617","https://openalex.org/W1990635146","https://openalex.org/W1994716877","https://openalex.org/W1995005227","https://openalex.org/W1995089961","https://openalex.org/W1996351562","https://openalex.org/W1998940503","https://openalex.org/W1999828721","https://openalex.org/W2000136433","https://openalex.org/W2000929500","https://openalex.org/W2002159909","https://openalex.org/W2003172836","https://openalex.org/W2003402631","https://openalex.org/W2005077027","https://openalex.org/W2007634776","https://openalex.org/W2008668132","https://openalex.org/W2009287131","https://openalex.org/W2009758767","https://openalex.org/W2010000445","https://openalex.org/W2010999047","https://openalex.org/W2011025549","https://openalex.org/W2012686113","https://openalex.org/W2012852001","https://openalex.org/W2013447902","https://openalex.org/W2013502943","https://openalex.org/W2014761306","https://openalex.org/W2015625843","https://openalex.org/W2015802360","https://openalex.org/W2015881490","https://openalex.org/W2016491299","https://openalex.org/W2019470386","https://openalex.org/W2020652742","https://openalex.org/W2021191052","https://openalex.org/W2021309719","https://openalex.org/W2022196194","https://openalex.org/W2022657456","https://openalex.org/W2023994926","https://openalex.org/W2024572834","https://openalex.org/W2025131366","https://openalex.org/W2025334731","https://openalex.org/W2027420997","https://openalex.org/W2027696068","https://openalex.org/W2028820256","https://openalex.org/W2032968787","https://openalex.org/W2032984763","https://openalex.org/W2033366093","https://openalex.org/W2036661917","https://openalex.org/W2037796399","https://openalex.org/W2038873127","https://openalex.org/W2039465881","https://openalex.org/W2039856444","https://openalex.org/W2041084399","https://openalex.org/W2041204140","https://openalex.org/W2044723896","https://openalex.org/W2045284889","https://openalex.org/W2046043517","https://openalex.org/W2047544230","https://openalex.org/W2049275721","https://openalex.org/W2050640439","https://openalex.org/W2050913592","https://openalex.org/W2053423550","https://openalex.org/W2055043387","https://openalex.org/W2055257835","https://openalex.org/W2056192318","https://openalex.org/W2057119643","https://openalex.org/W2059980912","https://openalex.org/W2060797027","https://openalex.org/W2062475405","https://openalex.org/W2063961010","https://openalex.org/W2064802889","https://openalex.org/W2065042047","https://openalex.org/W2065304353","https://openalex.org/W2066192175","https://openalex.org/W2069389043","https://openalex.org/W2070517644","https://openalex.org/W2070575931","https://openalex.org/W2071712505","https://openalex.org/W2073583385","https://openalex.org/W2076789164","https://openalex.org/W2080398714","https://openalex.org/W2080661557","https://openalex.org/W2082380079","https://openalex.org/W2085277871","https://openalex.org/W2086438164","https://openalex.org/W2087548537","https://openalex.org/W2087574732","https://openalex.org/W2090411726","https://openalex.org/W2091254099","https://openalex.org/W2093916754","https://openalex.org/W2094174735","https://openalex.org/W2094392347","https://openalex.org/W2094931538","https://openalex.org/W2096253801","https://openalex.org/W2097521277","https://openalex.org/W2101641832","https://openalex.org/W2102814386","https://openalex.org/W2103105682","https://openalex.org/W2103860090","https://openalex.org/W2104087716","https://openalex.org/W2104437738","https://openalex.org/W2104776061","https://openalex.org/W2106006432","https://openalex.org/W2107040871","https://openalex.org/W2107286926","https://openalex.org/W2108594680","https://openalex.org/W2111286354","https://openalex.org/W2111973517","https://openalex.org/W2113410382","https://openalex.org/W2114358087","https://openalex.org/W2114875557","https://openalex.org/W2116156409","https://openalex.org/W2117529527","https://openalex.org/W2119449687","https://openalex.org/W2119782490","https://openalex.org/W2121218617","https://openalex.org/W2122846880","https://openalex.org/W2123151657","https://openalex.org/W2123724498","https://openalex.org/W2124145810","https://openalex.org/W2124320575","https://openalex.org/W2124331814","https://openalex.org/W2124675284","https://openalex.org/W2124833836","https://openalex.org/W2125013516","https://openalex.org/W2127464112","https://openalex.org/W2129013431","https://openalex.org/W2129229605","https://openalex.org/W2129448726","https://openalex.org/W2130479394","https://openalex.org/W2130652515","https://openalex.org/W2130790725","https://openalex.org/W2133191750","https://openalex.org/W2134206588","https://openalex.org/W2134789671","https://openalex.org/W2135921450","https://openalex.org/W2136224545","https://openalex.org/W2136280642","https://openalex.org/W2136930152","https://openalex.org/W2137186746","https://openalex.org/W2137424160","https://openalex.org/W2137820697","https://openalex.org/W2140336988","https://openalex.org/W2140883620","https://openalex.org/W2141356165","https://openalex.org/W2141624700","https://openalex.org/W2141881946","https://openalex.org/W2141885858","https://openalex.org/W2143583668","https://openalex.org/W2145957695","https://openalex.org/W2147643191","https://openalex.org/W2148319892","https://openalex.org/W2148603752","https://openalex.org/W2150066952","https://openalex.org/W2152030946","https://openalex.org/W2152285853","https://openalex.org/W2153495256","https://openalex.org/W2153499430","https://openalex.org/W2154599673","https://openalex.org/W2155019453","https://openalex.org/W2155030096","https://openalex.org/W2156056868","https://openalex.org/W2156575897","https://openalex.org/W2157894204","https://openalex.org/W2158714788","https://openalex.org/W2159148537","https://openalex.org/W2160979370","https://openalex.org/W2161257366","https://openalex.org/W2162017027","https://openalex.org/W2162883202","https://openalex.org/W2164686527","https://openalex.org/W2165495989","https://openalex.org/W2165604073","https://openalex.org/W2165801360","https://openalex.org/W2167318540","https://openalex.org/W2167785155","https://openalex.org/W2167867998","https://openalex.org/W2168158291","https://openalex.org/W2168264491","https://openalex.org/W2168272116","https://openalex.org/W2168486353","https://openalex.org/W2169745877","https://openalex.org/W2171830519","https://openalex.org/W2312695517","https://openalex.org/W2317195393","https://openalex.org/W2333089562","https://openalex.org/W2334054197","https://openalex.org/W2915190566"],"related_works":["https://openalex.org/W6990484973","https://openalex.org/W41109829","https://openalex.org/W4214633024","https://openalex.org/W2961480866","https://openalex.org/W4323809934","https://openalex.org/W7096113691","https://openalex.org/W1973626596","https://openalex.org/W7098152087","https://openalex.org/W7097208936","https://openalex.org/W295615070"],"abstract_inverted_index":{"Proteins":[0],"are":[1,43,101],"the":[2,61,77,94,172,215,221,317],"principal":[3],"catalytic":[4],"agents,":[5],"structural":[6],"elements,":[7],"signal":[8],"transmitters,":[9],"transporters,":[10],"and":[11,25,39,49,74,116,134,170,177,220,271,279,321,333],"molecular":[12],"machines":[13,129],"in":[14,23,46,52,93,161,243,250,267,292,299,325],"cells.":[15],"Experimental":[16],"determination":[17],"of":[18,57,80,90,159,217,223,257,269,296],"protein":[19,36,41,193,204,330],"function":[20],"is":[21,85,205],"expensive":[22,144],"time":[24],"resources":[26],"compared":[27],"to":[28,69,237,245,301,303,319],"computational":[29,234],"methods.":[30,106],"Hence,":[31],"assigning":[32],"proteins":[33,160,169,173,212],"function,":[34],"predicting":[35],"binding":[37,78,218,225,331],"patterns,":[38,332],"understanding":[40,329],"regulation":[42,252,295],"important":[44],"problems":[45],"functional":[47],"genomics":[48],"key":[50],"challenges":[51],"bioinformatics.":[53],"This":[54],"dissertation":[55],"comprises":[56],"three":[58,314],"studies.":[59],"In":[60],"first":[62,98,108],"two":[63,99],"papers,":[64],"we":[65,183,230],"apply":[66],"machine-learning":[67,111],"methods":[68],"(1)":[70,148],"identify":[71,238],"misannotated":[72,153,168,327],"sequences":[73,92,154],"(2)":[75],"predict":[76,320],"patterns":[79],"proteins.":[81],"The":[82,97,107,282],"third":[83],"paper":[84],"(3)":[86],"a":[87,122,156,162,185,192,202,206,233,261,288,335],"genome-wide":[88,235],"analysis":[89],"G4-quadruplex":[91,240],"maize":[95,244,283],"genome.":[96],"papers":[100],"based":[102,213],"on":[103,214],"two-stage":[104],"classification":[105,137],"stage":[109],"uses":[110],"approaches":[112],"that":[113,136,312],"combine":[114],"composition-based":[115],"sequence-based":[117],"features.":[118],"We":[119,166,310],"use":[120],"either":[121],"decision":[123],"trees":[124],"(HDTree)":[125],"or":[126,140],"support":[127],"vector":[128],"(SVM)":[130],"as":[131],"second-stage":[132],"classifiers":[133],"show":[135,171],"performance":[138],"reaches":[139],"outperforms":[141],"more":[142],"computationally":[143],"approaches.":[145],"For":[146,180,227],"study":[147,181,228],"our":[149,313],"method":[150],"identified":[151,167],"potential":[152,248],"within":[155],"well-characterized":[157],"set":[158],"popular":[163],"bioinformatics":[164],"database.":[165],"have":[174,316],"contradicting":[175],"AmiGO":[176],"UniProt":[178],"annotations.":[179],"(2),":[182],"developed":[184],"three-phase":[186],"approach:":[187],"Phase":[188,198,208],"I":[189],"classifies":[190,210],"whether":[191,201],"binds":[194],"with":[195,274],"another":[196],"protein.":[197],"II":[199],"determines":[200],"protein-binding":[203],"hub.":[207],"III":[209],"hub":[211],"number":[216,222],"sites":[219],"concurrent":[224],"partners.":[226],"(3),":[229],"carried":[231],"out":[232],"screen":[236],"non-telomeric":[239],"(G4Q)":[241],"elements":[242,285],"explore":[246],"their":[247,265],"role":[249,291],"gene":[251,297,340],"for":[253,264,307,339],"flowering":[254],"plants.":[255],"Analysis":[256],"G4Q-containing":[258],"genes":[259,268],"uncovered":[260],"striking":[262],"tendency":[263],"enrichment":[266],"networks":[270],"pathways":[272],"associated":[273],"electron":[275],"transport,":[276],"sugar":[277],"degradation,":[278],"hypoxia":[280,302],"responsiveness.":[281],"G4Q":[284],"may":[286],"play":[287],"previously":[289],"unrecognized":[290],"coordinating":[293],"global":[294],"expression":[298],"response":[300],"control":[304],"carbohydrate":[305],"metabolism":[306],"anaerobic":[308],"metabolism.":[309],"demonstrated":[311],"studies":[315],"ability":[318],"provide":[322],"new":[323,337],"insights":[324],"classifying":[326],"proteins,":[328],"identifying":[334],"potentially":[336],"model":[338],"regulation.":[341]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
