{"id":"https://openalex.org/W2068207274","doi":"https://doi.org/10.1093/bioinformatics/btu657","title":"SIST: stress-induced structural transitions in superhelical DNA","display_name":"SIST: stress-induced structural transitions in superhelical DNA","publication_year":2014,"publication_date":"2014-10-04","ids":{"openalex":"https://openalex.org/W2068207274","doi":"https://doi.org/10.1093/bioinformatics/btu657","mag":"2068207274","pmid":"https://pubmed.ncbi.nlm.nih.gov/25282644"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu657","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu657","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/421/49013153/bioinformatics_31_3_421.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/421/49013153/bioinformatics_31_3_421.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008520002","display_name":"Dina Zhabinskaya","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":"Dina Zhabinskaya","raw_affiliation_strings":["1 UC Davis Genome Center and 2 Department of Mathematics, University of California, Davis, CA 95616, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UC Davis Genome Center and 2 Department of Mathematics, University of California, Davis, CA 95616, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041036395","display_name":"Sally Madden","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":false,"raw_author_name":"Sally Madden","raw_affiliation_strings":["1 UC Davis Genome Center and 2 Department of Mathematics, University of California, Davis, CA 95616, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UC Davis Genome Center and 2 Department of Mathematics, University of California, Davis, CA 95616, 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":true,"raw_author_name":"Craig J. Benham","raw_affiliation_strings":["1 UC Davis Genome Center and 2 Department of Mathematics, University of California, Davis, CA 95616, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 UC Davis Genome Center and 2 Department of Mathematics, University of California, Davis, CA 95616, USA","institution_ids":["https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5008520002","https://openalex.org/A5025935554"],"corresponding_institution_ids":["https://openalex.org/I84218800"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.996,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.75315369,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"31","issue":"3","first_page":"421","last_page":"422"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10123","display_name":"DNA Repair Mechanisms","score":0.40059998631477356,"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/T10123","display_name":"DNA Repair Mechanisms","score":0.40059998631477356,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.3393999934196472,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.11060000211000443,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/dna","display_name":"DNA","score":0.5621190071105957},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49280813336372375},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4772596061229706},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44161421060562134},{"id":"https://openalex.org/keywords/stress","display_name":"Stress (linguistics)","score":0.427126944065094},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3023206889629364},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.0782971978187561}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5621190071105957},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49280813336372375},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4772596061229706},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44161421060562134},{"id":"https://openalex.org/C21036866","wikidata":"https://www.wikidata.org/wiki/Q181767","display_name":"Stress (linguistics)","level":2,"score":0.427126944065094},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3023206889629364},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0782971978187561},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004278","descriptor_name":"DNA, Superhelical","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004278","descriptor_name":"DNA, Superhelical","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004278","descriptor_name":"DNA, Superhelical","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","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":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btu657","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu657","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/421/49013153/bioinformatics_31_3_421.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25282644","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25282644","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu657","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu657","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/421/49013153/bioinformatics_31_3_421.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4909705564","display_name":"Stress-Induced DNA Duplex Destabilization in Eukaryotic Genomes","funder_award_id":"0850214","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2068207274.pdf","grobid_xml":"https://content.openalex.org/works/W2068207274.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1968363360","https://openalex.org/W1991098988","https://openalex.org/W2019700487","https://openalex.org/W2036666081","https://openalex.org/W2040175663","https://openalex.org/W2056940122","https://openalex.org/W2077850630"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2117258802","https://openalex.org/W4234157524"],"abstract_inverted_index":{"SUMMARY:":[0],"Supercoiling":[1],"imposes":[2],"stress":[3],"on":[4,61],"a":[5,40,62,128],"DNA":[6,52,94],"molecule":[7],"that":[8,43,66],"can":[9],"drive":[10],"susceptible":[11],"sequences":[12],"into":[13],"alternative":[14],"non-B":[15],"form":[16],"structures.":[17],"This":[18],"phenomenon":[19],"occurs":[20],"frequently":[21],"in":[22,28,48,57,77],"vivo":[23],"and":[24,36,105,136],"has":[25,111],"been":[26],"implicated":[27],"biological":[29],"processes,":[30],"such":[31],"as":[32],"replication,":[33],"transcription,":[34],"recombination":[35],"translocation.":[37],"SIST":[38,58,97,109],"is":[39],"software":[41],"package":[42,135],"analyzes":[44,92,120],"sequence-dependent":[45],"structural":[46],"transitions":[47,104,126],"kilobase":[49],"length":[50],"superhelical":[51,129],"molecules.":[53],"The":[54,108,134],"numerical":[55],"algorithms":[56,100],"are":[59,81,139],"based":[60],"statistical":[63],"mechanical":[64],"model":[65],"calculates":[67],"the":[68,78,84,116,121],"equilibrium":[69],"probability":[70],"of":[71,83],"transition":[72],"for":[73],"each":[74],"base":[75],"pair":[76],"domain.":[79,130],"They":[80],"extensions":[82],"original":[85],"stress-induced":[86],"duplex":[87],"destabilization":[88],"(SIDD)":[89],"method,":[90],"which":[91,119],"stress-driven":[93],"strand":[95],"separation.":[96],"also":[98],"includes":[99],"to":[101,114],"analyze":[102],"B-Z":[103],"cruciform":[106],"extrusion.":[107],"pipeline":[110],"an":[112],"option":[113],"use":[115],"DZCBtrans":[117],"algorithm,":[118],"competition":[122],"among":[123],"these":[124],"three":[125],"within":[127],"AVAILABILITY":[131],"AND":[132],"IMPLEMENTATION:":[133],"additional":[137],"documentation":[138],"freely":[140],"available":[141],"at":[142],"https://bitbucket.org/benhamlab/sist_codes.":[143],"CONTACT:":[144],"dzhabinskaya@ucdavis.edu.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}