{"id":"https://openalex.org/W2032268510","doi":"https://doi.org/10.1109/tcbb.2015.2396057","title":"Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability","display_name":"Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability","publication_year":2015,"publication_date":"2015-01-23","ids":{"openalex":"https://openalex.org/W2032268510","doi":"https://doi.org/10.1109/tcbb.2015.2396057","mag":"2032268510","pmid":"https://pubmed.ncbi.nlm.nih.gov/26451825"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2015.2396057","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2396057","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5018788438","display_name":"Jan Zrimec","orcid":"https://orcid.org/0000-0002-7099-961X"},"institutions":[{"id":"https://openalex.org/I4210135816","display_name":"Institute of Metagenomics and Microbial Technologies (Slovenia)","ror":"https://ror.org/03xe8sk89","country_code":"SI","type":"company","lineage":["https://openalex.org/I4210135816"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Jan Zrimec","raw_affiliation_strings":["Institute for Metagenomics and Microbial Technologies, Ljubljana, Slovenia",", Institute for Metagenomics and Microbial Technologies, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Metagenomics and Microbial Technologies, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210135816"]},{"raw_affiliation_string":", Institute for Metagenomics and Microbial Technologies, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210135816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011434869","display_name":"Ale\u0161 Lapanje","orcid":"https://orcid.org/0000-0002-2603-0844"},"institutions":[{"id":"https://openalex.org/I4210135816","display_name":"Institute of Metagenomics and Microbial Technologies (Slovenia)","ror":"https://ror.org/03xe8sk89","country_code":"SI","type":"company","lineage":["https://openalex.org/I4210135816"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Ales Lapanje","raw_affiliation_strings":["Institute for Metagenomics and Microbial Technologies, Ljubljana, Slovenia",", Institute for Metagenomics and Microbial Technologies, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Metagenomics and Microbial Technologies, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210135816"]},{"raw_affiliation_string":", Institute for Metagenomics and Microbial Technologies, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210135816"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210135816"],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":0.4128,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.62693874,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"5","first_page":"1137","last_page":"1145"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9976000189781189,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9950000047683716,"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/duplex","display_name":"Duplex (building)","score":0.8421421051025391},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.6777475476264954},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.37966787815093994},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27007341384887695},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18927571177482605}],"concepts":[{"id":"https://openalex.org/C99611785","wikidata":"https://www.wikidata.org/wiki/Q6453233","display_name":"Duplex (building)","level":3,"score":0.8421421051025391},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6777475476264954},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.37966787815093994},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27007341384887695},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18927571177482605}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009691","descriptor_name":"Nucleic Acid Denaturation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009691","descriptor_name":"Nucleic Acid Denaturation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009691","descriptor_name":"Nucleic Acid Denaturation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044366","descriptor_name":"Transition Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044366","descriptor_name":"Transition Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044366","descriptor_name":"Transition Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2015.2396057","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2396057","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26451825","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26451825","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1662921478","display_name":null,"funder_award_id":"FP7/2007\u20132011","funder_id":"https://openalex.org/F4320333065","funder_display_name":"Seventh Framework Programme"},{"id":"https://openalex.org/G5764745514","display_name":"Coastal Sea Research","funder_award_id":"P1-0237","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G63770550","display_name":null,"funder_award_id":"FP7/2007 - 2013","funder_id":"https://openalex.org/F4320333065","funder_display_name":"Seventh Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"},{"id":"https://openalex.org/F4320333065","display_name":"Seventh Framework Programme","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W1570448133","https://openalex.org/W1608292591","https://openalex.org/W1825157170","https://openalex.org/W1964855214","https://openalex.org/W1966103562","https://openalex.org/W1968729097","https://openalex.org/W1969670694","https://openalex.org/W1979853470","https://openalex.org/W1982845482","https://openalex.org/W1988980407","https://openalex.org/W1990923586","https://openalex.org/W1994142222","https://openalex.org/W1999515447","https://openalex.org/W2001394772","https://openalex.org/W2006700468","https://openalex.org/W2011246544","https://openalex.org/W2012226733","https://openalex.org/W2014717496","https://openalex.org/W2017407107","https://openalex.org/W2021356303","https://openalex.org/W2021525650","https://openalex.org/W2029987289","https://openalex.org/W2030092313","https://openalex.org/W2031547464","https://openalex.org/W2038532304","https://openalex.org/W2039665773","https://openalex.org/W2039922463","https://openalex.org/W2043016308","https://openalex.org/W2053742705","https://openalex.org/W2054115419","https://openalex.org/W2069611162","https://openalex.org/W2074662966","https://openalex.org/W2074981222","https://openalex.org/W2077069790","https://openalex.org/W2083321361","https://openalex.org/W2092175013","https://openalex.org/W2093768536","https://openalex.org/W2095364377","https://openalex.org/W2105039093","https://openalex.org/W2105122253","https://openalex.org/W2106130068","https://openalex.org/W2107578440","https://openalex.org/W2111400482","https://openalex.org/W2111441093","https://openalex.org/W2112279048","https://openalex.org/W2112333437","https://openalex.org/W2115016070","https://openalex.org/W2115655830","https://openalex.org/W2121365413","https://openalex.org/W2127646692","https://openalex.org/W2132688829","https://openalex.org/W2134977238","https://openalex.org/W2135754005","https://openalex.org/W2138283130","https://openalex.org/W2138834599","https://openalex.org/W2139576948","https://openalex.org/W2140633690","https://openalex.org/W2142784993","https://openalex.org/W2145186783","https://openalex.org/W2145754372","https://openalex.org/W2148699366","https://openalex.org/W2154118981","https://openalex.org/W2155684957","https://openalex.org/W2155844132","https://openalex.org/W2171526214","https://openalex.org/W2966207845","https://openalex.org/W3102090129","https://openalex.org/W3125541931","https://openalex.org/W4241480733"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W2139106479","https://openalex.org/W2740027808"],"abstract_inverted_index":{"DNA":[0,15,20,32,69],"melting":[1],"bubbles":[2],"are":[3],"the":[4,47,60,87,145,162],"basis":[5],"of":[6,43,57,91,126,137,148,155,160],"many":[7],"DNA-protein":[8],"interactions,":[9],"such":[10],"as":[11,110,112,133,135],"those":[12],"in":[13,120,130],"regulatory":[14,68],"regions":[16,70,132,139],"driving":[17],"gene":[18,25],"expression,":[19],"replication":[21],"and":[22,35,74],"bacterial":[23],"horizontal":[24],"transfer.":[26],"Bubble":[27],"formation":[28],"is":[29,52,83,113,119,151],"affected":[30],"by":[31,96],"duplex":[33,38,44,89,101,128],"stability":[34,45],"thermally":[36],"induced":[37],"destabilization":[39,92,131,142],"(TIDD).":[40],"Although":[41],"prediction":[42,56,146],"with":[46,59,71,115],"nearest":[48],"neighbor":[49],"(NN)":[50],"method":[51],"much":[53],"faster":[54],"than":[55,158],"TIDD":[58,66,82,108,118,170],"Peyrard-Bishop-Dauxois":[61],"(PBD)":[62],"model,":[63],"PBD":[64,80],"predicted":[65,81,114,173],"defines":[67],"higher":[72],"accuracy":[73],"detail.":[75],"Here,":[76],"we":[77],"considered":[78],"that":[79,99,159],"inherently":[84],"related":[85],"to":[86,106,123,141],"intrinsic":[88],"stabilities":[90,102,129],"regions.":[93],"We":[94],"show":[95],"regression":[97],"modeling":[98],"NN":[100,127],"can":[103,171],"be":[104,172],"used":[105],"predict":[107],"almost":[109],"accurately":[111],"PBD.":[116],"Predicted":[117],"fact":[121],"ascribed":[122],"non-linear":[124],"transformation":[125],"well":[134],"effects":[136],"neighboring":[138],"relative":[140],"size.":[143],"Since":[144],"time":[147],"our":[149,175],"models":[150,163],"over":[152],"six":[153],"orders":[154],"magnitude":[156],"shorter":[157],"PBD,":[161],"present":[164],"an":[165],"accessible":[166],"tool":[167],"for":[168],"researchers.":[169],"on":[174],"webserver":[176],"at":[177],"http://tidd.immt.eu.":[178]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
