{"id":"https://openalex.org/W2787629429","doi":"https://doi.org/10.1142/s0219720018400036","title":"Bacterial promoter prediction: Selection of dynamic and static physical properties of DNA for reliable sequence classification","display_name":"Bacterial promoter prediction: Selection of dynamic and static physical properties of DNA for reliable sequence classification","publication_year":2018,"publication_date":"2018-01-31","ids":{"openalex":"https://openalex.org/W2787629429","doi":"https://doi.org/10.1142/s0219720018400036","mag":"2787629429","pmid":"https://pubmed.ncbi.nlm.nih.gov/29382253"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720018400036","is_oa":true,"landing_page_url":"https://doi.org/10.1142/s0219720018400036","pdf_url":"https://www.worldscientific.com/doi/pdf/10.1142/S0219720018400036","source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://www.worldscientific.com/doi/pdf/10.1142/S0219720018400036","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047430870","display_name":"Artem Andreevich Ryasik","orcid":"https://orcid.org/0000-0003-3035-1293"},"institutions":[{"id":"https://openalex.org/I4210155801","display_name":"Institute of Cell Biophysics","ror":"https://ror.org/05gbnpz65","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210155801"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Artem Ryasik","raw_affiliation_strings":["Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia"],"raw_orcid":"https://orcid.org/0000-0003-3035-1293","affiliations":[{"raw_affiliation_string":"Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia","institution_ids":["https://openalex.org/I4210155801"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031259244","display_name":"\u041c. \u0410. \u041e\u0440\u043b\u043e\u0432","orcid":"https://orcid.org/0000-0001-9954-1664"},"institutions":[{"id":"https://openalex.org/I4210155801","display_name":"Institute of Cell Biophysics","ror":"https://ror.org/05gbnpz65","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210155801"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Mikhail Orlov","raw_affiliation_strings":["Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia","institution_ids":["https://openalex.org/I4210155801"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103831377","display_name":"Evgenia Andreevna Zykova","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155801","display_name":"Institute of Cell Biophysics","ror":"https://ror.org/05gbnpz65","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210155801"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Evgenia Zykova","raw_affiliation_strings":["Department of Applied Research Informatization, State Institute of Information Technologies and Telecommunications (SIIT&amp;T Informika), per. Brusov 21 st.2, Moscow, 125009, Russia","Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Research Informatization, State Institute of Information Technologies and Telecommunications (SIIT&amp;T Informika), per. Brusov 21 st.2, Moscow, 125009, Russia","institution_ids":[]},{"raw_affiliation_string":"Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia","institution_ids":["https://openalex.org/I4210155801"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013397801","display_name":"Timofei Ermak","orcid":null},"institutions":[{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Timofei Ermak","raw_affiliation_strings":["Laboratory of Molecular Genetics Systems, Institute of Cytology and Genetics, pr. Akademika Lavrentyeva 10, Novosibirsk 630090, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Genetics Systems, Institute of Cytology and Genetics, pr. Akademika Lavrentyeva 10, Novosibirsk 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020746275","display_name":"Anatoly Sorokin","orcid":"https://orcid.org/0000-0002-0047-0606"},"institutions":[{"id":"https://openalex.org/I4210155801","display_name":"Institute of Cell Biophysics","ror":"https://ror.org/05gbnpz65","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210155801"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Anatoly Sorokin","raw_affiliation_strings":["Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mechanism of Cell Genome Functioning Laboratory, Institute of Cell Biophysics, ul. Institutskaya 3, Pushchino 142290, Russia","institution_ids":["https://openalex.org/I4210155801"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5047430870"],"corresponding_institution_ids":["https://openalex.org/I4210155801"],"apc_list":null,"apc_paid":null,"fwci":0.6516,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.67474645,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"16","issue":"01","first_page":"1840003","last_page":"1840003"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9995999932289124,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9995999932289124,"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":0.9994000196456909,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9965999722480774,"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/classifier","display_name":"Classifier (UML)","score":0.6988852620124817},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5725260376930237},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5182145237922668},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.507583737373352},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4805753231048584},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42544251680374146},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41781002283096313},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3884134292602539},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.355366051197052},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3424641788005829},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1547553539276123}],"concepts":[{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.6988852620124817},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5725260376930237},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5182145237922668},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.507583737373352},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4805753231048584},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42544251680374146},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41781002283096313},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3884134292602539},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.355366051197052},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3424641788005829},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1547553539276123},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720018400036","is_oa":true,"landing_page_url":"https://doi.org/10.1142/s0219720018400036","pdf_url":"https://www.worldscientific.com/doi/pdf/10.1142/S0219720018400036","source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:29382253","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29382253","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":{"id":"doi:10.1142/s0219720018400036","is_oa":true,"landing_page_url":"https://doi.org/10.1142/s0219720018400036","pdf_url":"https://www.worldscientific.com/doi/pdf/10.1142/S0219720018400036","source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life below water","score":0.7599999904632568,"id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G1027583532","display_name":null,"funder_award_id":"16-37-00303 mol_a","funder_id":"https://openalex.org/F4320321079","funder_display_name":"Russian Foundation for Basic Research"}],"funders":[{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2787629429.pdf","grobid_xml":"https://content.openalex.org/works/W2787629429.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1564164899","https://openalex.org/W1825157170","https://openalex.org/W1838362592","https://openalex.org/W1965118572","https://openalex.org/W1974916610","https://openalex.org/W1996815852","https://openalex.org/W1999220636","https://openalex.org/W2002735806","https://openalex.org/W2010008055","https://openalex.org/W2016381774","https://openalex.org/W2027855312","https://openalex.org/W2036251513","https://openalex.org/W2050550887","https://openalex.org/W2055063781","https://openalex.org/W2056422388","https://openalex.org/W2056904039","https://openalex.org/W2058517672","https://openalex.org/W2061799500","https://openalex.org/W2064189258","https://openalex.org/W2066716706","https://openalex.org/W2067218340","https://openalex.org/W2081885582","https://openalex.org/W2091129777","https://openalex.org/W2092855609","https://openalex.org/W2101492309","https://openalex.org/W2101536723","https://openalex.org/W2105089812","https://openalex.org/W2111492198","https://openalex.org/W2113355556","https://openalex.org/W2119780058","https://openalex.org/W2121365413","https://openalex.org/W2132688829","https://openalex.org/W2137573089","https://openalex.org/W2142784993","https://openalex.org/W2146135000","https://openalex.org/W2147783816","https://openalex.org/W2152293875","https://openalex.org/W2157884850","https://openalex.org/W2166516473","https://openalex.org/W2168393276","https://openalex.org/W2313339984","https://openalex.org/W2321703975","https://openalex.org/W2416264703","https://openalex.org/W2468220216","https://openalex.org/W2582743722","https://openalex.org/W2963739921","https://openalex.org/W4245949115"],"related_works":["https://openalex.org/W1969771092","https://openalex.org/W2795723184","https://openalex.org/W2025529750","https://openalex.org/W2891858816","https://openalex.org/W184057646","https://openalex.org/W2042874675","https://openalex.org/W129398428","https://openalex.org/W3212414177","https://openalex.org/W1967718992","https://openalex.org/W2007418658"],"abstract_inverted_index":{"Predicting":[0],"promoter":[1,143,150],"activity":[2],"of":[3,17,28,35,44,70,100,107,125,155],"DNA":[4,18,45,101,108,144],"fragment":[5],"is":[6],"an":[7,32],"important":[8],"task":[9],"for":[10,38,66,122],"computational":[11],"biology.":[12],"Approaches":[13],"using":[14],"physical":[15,36,98],"properties":[16,37,65,99,106],"to":[19,61,120,146],"predict":[20],"bacterial":[21],"promoters":[22],"have":[23,86,131],"recently":[24],"gained":[25],"a":[26,40,55,139],"lot":[27],"attention.":[29],"To":[30,81],"select":[31,62],"adequate":[33],"set":[34],"training":[39],"classifier,":[41],"various":[42],"characteristics":[43],"molecule":[46],"should":[47],"be":[48,147],"taken":[49],"into":[50],"consideration.":[51],"Here,":[52],"we":[53,85,130],"present":[54],"systematic":[56],"approach":[57],"that":[58,91,133],"allows":[59],"us":[60],"less":[63],"correlated":[64],"classification":[67],"by":[68],"means":[69],"both":[71],"correlation":[72],"and":[73,96],"cophenetic":[74],"coefficients":[75],"as":[76,78,138],"well":[77],"concordance":[79],"matrices.":[80],"prove":[82],"this":[83],"concept,":[84],"developed":[87],"the":[88,112,134,153],"first":[89],"classifier":[90,135],"uses":[92],"not":[93],"only":[94],"sequence":[95],"static":[97],"fragment,":[102],"but":[103],"also":[104],"dynamic":[105],"open":[109],"states.":[110],"Therefore,":[111],"best":[113],"performing":[114],"models":[115],"with":[116],"accuracy":[117],"values":[118],"up":[119],"90%":[121],"all":[123],"types":[124],"sequences":[126],"were":[127],"obtained.":[128],"Furthermore,":[129],"demonstrated":[132],"can":[136],"serve":[137],"reliable":[140],"tool":[141],"enabling":[142],"fragments":[145],"distinguished":[148],"from":[149],"islands":[151],"despite":[152],"similarity":[154],"their":[156],"nucleotide":[157],"sequences.":[158]},"counts_by_year":[{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
