{"id":"https://openalex.org/W1534177438","doi":"https://doi.org/10.1109/csb.2003.1227372","title":"The approximate algorithm for analysis of the strand separation transition in superhelical DNA using nearest neighbor energetics","display_name":"The approximate algorithm for analysis of the strand separation transition in superhelical DNA using nearest neighbor energetics","publication_year":2004,"publication_date":"2004-03-30","ids":{"openalex":"https://openalex.org/W1534177438","doi":"https://doi.org/10.1109/csb.2003.1227372","mag":"1534177438"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2003.1227372","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227372","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110615138","display_name":"C. Bi","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"C. Bi","raw_affiliation_strings":["UC Davis Genome Center, University of California, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"UC Davis Genome Center, University of California, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025935554","display_name":"Craig J. Benham","orcid":"https://orcid.org/0009-0005-4610-2402"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C.J. Benham","raw_affiliation_strings":["UC Davis Genome Center, University of California, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"UC Davis Genome Center, University of California, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5110615138"],"corresponding_institution_ids":["https://openalex.org/I84218800"],"apc_list":null,"apc_paid":null,"fwci":0.2339,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.50986121,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"460","last_page":"461"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9997000098228455,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9997000098228455,"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/T10123","display_name":"DNA Repair Mechanisms","score":0.9976999759674072,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973000288009644,"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/energetics","display_name":"Energetics","score":0.6310670971870422},{"id":"https://openalex.org/keywords/k-nearest-neighbors-algorithm","display_name":"k-nearest neighbors algorithm","score":0.609189510345459},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.5105858445167542},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4581941068172455},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.4501837491989136},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.44416284561157227},{"id":"https://openalex.org/keywords/relaxation","display_name":"Relaxation (psychology)","score":0.4389820098876953},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4190472364425659},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.35387182235717773},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3416895866394043},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2964131534099579},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.27193713188171387},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14417815208435059},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1135266125202179}],"concepts":[{"id":"https://openalex.org/C97514900","wikidata":"https://www.wikidata.org/wiki/Q719597","display_name":"Energetics","level":2,"score":0.6310670971870422},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.609189510345459},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.5105858445167542},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4581941068172455},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4501837491989136},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.44416284561157227},{"id":"https://openalex.org/C2776029896","wikidata":"https://www.wikidata.org/wiki/Q3935810","display_name":"Relaxation (psychology)","level":2,"score":0.4389820098876953},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4190472364425659},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.35387182235717773},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3416895866394043},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2964131534099579},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.27193713188171387},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14417815208435059},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1135266125202179},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/csb.2003.1227372","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227372","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8500000238418579}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W104862819","https://openalex.org/W1968184258","https://openalex.org/W1968363360","https://openalex.org/W1981289453","https://openalex.org/W1993748356","https://openalex.org/W2009095852","https://openalex.org/W2037478998","https://openalex.org/W2046910065","https://openalex.org/W2064601562","https://openalex.org/W2070484449","https://openalex.org/W2074662966","https://openalex.org/W2214602901"],"related_works":["https://openalex.org/W1996263103","https://openalex.org/W2396392055","https://openalex.org/W2068036173","https://openalex.org/W1963514225","https://openalex.org/W2008118406","https://openalex.org/W2090753126","https://openalex.org/W1502749126","https://openalex.org/W2034653027","https://openalex.org/W2389264407","https://openalex.org/W1984441743"],"abstract_inverted_index":{"We":[0,29,96,117],"present":[1],"a":[2,42,66,119,140],"computational":[3,150],"method":[4],"to":[5,13,34,111,152],"analyze":[6,35],"the":[7,22,36,72,77,86,90,106,125,145,153],"propensity":[8],"of":[9,24,41,44,52,75,92,101,155],"superhelically":[10],"stressed":[11,46],"DNA":[12,47,113],"undergo":[14],"strand":[15,53],"separation":[16],"events,":[17],"as":[18],"is":[19,69,129,160],"required":[20],"for":[21],"initiation":[23],"both":[25],"transcription":[26],"and":[27,85,148],"replication.":[28],"build":[30],"in":[31,82,123,162],"silico":[32],"models":[33],"statistical":[37,120],"mechanical":[38,121],"equilibrium":[39,127],"distribution":[40,128],"population":[43],"identical,":[45],"molecules":[48],"among":[49],"its":[50],"states":[51,133],"separation.":[54],"In":[55],"this":[56,94,156],"phenomenon,":[57],"which":[58,124],"we":[59],"call":[60],"stress":[61,93],"induced":[62],"duplex":[63],"destabilization":[64],"(SIDD),":[65],"state":[67],"energy":[68,73,87,103],"determined":[70],"by":[71],"cost":[74],"opening":[76],"specific":[78],"separated":[79],"base":[80,114],"pairs":[81],"that":[83],"state,":[84],"relief":[88],"from":[89,131],"relaxation":[91],"affords.":[95],"use":[97],"experimentally":[98],"measured":[99],"values":[100],"all":[102,132],"parameters,":[104],"including":[105],"nearest":[107],"neighbor":[108],"energetics":[109],"known":[110],"govern":[112],"pair":[115],"stability.":[116],"perform":[118],"analysis":[122,154],"approximate":[126],"calculated":[130],"whose":[134],"free":[135],"energies":[136],"do":[137],"not":[138],"exceed":[139],"user-defined":[141],"threshold.":[142],"This":[143],"provides":[144],"most":[146],"general":[147],"efficient":[149],"approach":[151],"phenomenon.":[157],"The":[158],"algorithm":[159],"implemented":[161],"C++.":[163]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
