{"id":"https://openalex.org/W2110444675","doi":"https://doi.org/10.1142/s0219720010004677","title":"SNPS IN THE HIV-1 TATA BOX AND THE AIDS PANDEMIC","display_name":"SNPS IN THE HIV-1 TATA BOX AND THE AIDS PANDEMIC","publication_year":2010,"publication_date":"2010-03-05","ids":{"openalex":"https://openalex.org/W2110444675","doi":"https://doi.org/10.1142/s0219720010004677","mag":"2110444675","pmid":"https://pubmed.ncbi.nlm.nih.gov/20556865"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720010004677","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010004677","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045849494","display_name":"\u0412. \u0412. \u0421\u0443\u0441\u043b\u043e\u0432","orcid":"https://orcid.org/0000-0002-1940-9389"},"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":true,"raw_author_name":"VALENTIN V. SUSLOV","raw_affiliation_strings":["Sector of Evolutionary Bioinformatics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia"],"affiliations":[{"raw_affiliation_string":"Sector of Evolutionary Bioinformatics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037933008","display_name":"\u041f. \u041c. \u041f\u043e\u043d\u043e\u043c\u0430\u0440\u0435\u043d\u043a\u043e","orcid":"https://orcid.org/0000-0003-2715-9612"},"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":"PETR M. PONOMARENKO","raw_affiliation_strings":["Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006578987","display_name":"\u0412. \u041c. \u0415\u0444\u0438\u043c\u043e\u0432","orcid":"https://orcid.org/0000-0003-3035-8049"},"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":"VADIM M. EFIMOV","raw_affiliation_strings":["Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008259802","display_name":"\u041b. \u041a. \u0421\u0430\u0432\u0438\u043d\u043a\u043e\u0432\u0430","orcid":"https://orcid.org/0000-0003-4543-4104"},"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":"LUDMILA K. SAVINKOVA","raw_affiliation_strings":["Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025425343","display_name":"\u041c. \u041f. \u041f\u043e\u043d\u043e\u043c\u0430\u0440\u0435\u043d\u043a\u043e","orcid":"https://orcid.org/0000-0003-1663-318X"},"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":"MIKHAIL P. PONOMARENKO","raw_affiliation_strings":["Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038764591","display_name":"\u041d. \u0410. \u041a\u043e\u043b\u0447\u0430\u043d\u043e\u0432","orcid":"https://orcid.org/0000-0001-6800-8787"},"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":"NIKOLAY A. KOLCHANOV","raw_affiliation_strings":["Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5045849494"],"corresponding_institution_ids":["https://openalex.org/I4210116466"],"apc_list":null,"apc_paid":null,"fwci":0.3159,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.53308015,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"08","issue":"03","first_page":"607","last_page":"625"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9927999973297119,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.984499990940094,"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/tata-box","display_name":"TATA box","score":0.7799167633056641},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6317702531814575},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5901037454605103},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32125741243362427},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2337442934513092},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1150626540184021}],"concepts":[{"id":"https://openalex.org/C65888428","wikidata":"https://www.wikidata.org/wiki/Q1413955","display_name":"TATA box","level":5,"score":0.7799167633056641},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6317702531814575},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5901037454605103},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32125741243362427},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2337442934513092},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1150626540184021},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D000163","descriptor_name":"Acquired Immunodeficiency Syndrome","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D000163","descriptor_name":"Acquired Immunodeficiency Syndrome","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D000163","descriptor_name":"Acquired Immunodeficiency Syndrome","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D000163","descriptor_name":"Acquired Immunodeficiency Syndrome","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000163","descriptor_name":"Acquired Immunodeficiency Syndrome","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000163","descriptor_name":"Acquired Immunodeficiency Syndrome","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D004196","descriptor_name":"Disease Outbreaks","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015995","descriptor_name":"Prevalence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015995","descriptor_name":"Prevalence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015995","descriptor_name":"Prevalence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016385","descriptor_name":"TATA Box","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016385","descriptor_name":"TATA Box","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016385","descriptor_name":"TATA Box","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D038622","descriptor_name":"Internationality","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D038622","descriptor_name":"Internationality","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D038622","descriptor_name":"Internationality","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720010004677","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010004677","pdf_url":null,"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:20556865","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20556865","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":null,"sustainable_development_goals":[{"score":0.8500000238418579,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321770","display_name":"Siberian Branch, Russian Academy of Sciences","ror":"https://ror.org/02frkq021"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1518967339","https://openalex.org/W1582891190","https://openalex.org/W1597865451","https://openalex.org/W1892036989","https://openalex.org/W1897005832","https://openalex.org/W1966975236","https://openalex.org/W1970301294","https://openalex.org/W1973381207","https://openalex.org/W1974238583","https://openalex.org/W1986473194","https://openalex.org/W1989468850","https://openalex.org/W1991144403","https://openalex.org/W1991330646","https://openalex.org/W1994203761","https://openalex.org/W1999027354","https://openalex.org/W1999966058","https://openalex.org/W2002899891","https://openalex.org/W2006362317","https://openalex.org/W2023479104","https://openalex.org/W2029353650","https://openalex.org/W2031830783","https://openalex.org/W2034488184","https://openalex.org/W2041880278","https://openalex.org/W2044811718","https://openalex.org/W2045950998","https://openalex.org/W2048750844","https://openalex.org/W2048978761","https://openalex.org/W2057927013","https://openalex.org/W2064311051","https://openalex.org/W2064703363","https://openalex.org/W2068170981","https://openalex.org/W2071227538","https://openalex.org/W2073990872","https://openalex.org/W2081539383","https://openalex.org/W2086679686","https://openalex.org/W2088493593","https://openalex.org/W2096658573","https://openalex.org/W2098601534","https://openalex.org/W2104834748","https://openalex.org/W2114282483","https://openalex.org/W2125374553","https://openalex.org/W2128969076","https://openalex.org/W2140665904","https://openalex.org/W2142593273","https://openalex.org/W2143849684","https://openalex.org/W2151625863","https://openalex.org/W2155388660","https://openalex.org/W2157115700","https://openalex.org/W2164640003","https://openalex.org/W2165608108","https://openalex.org/W2166464288","https://openalex.org/W2285146487","https://openalex.org/W2415100485","https://openalex.org/W2419429512","https://openalex.org/W2466139592","https://openalex.org/W2496173866","https://openalex.org/W4254980429"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W1641042124","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802","https://openalex.org/W2051339581","https://openalex.org/W4234157524"],"abstract_inverted_index":{"Evolutionary":[0],"trends":[1,132],"have":[2,61],"been":[3,62],"examined":[4],"in":[5,96,133,158],"146":[6],"HIV-1":[7,42,60,74,92,134],"forms":[8],"(2662":[9],"copies,":[10],"2311":[11],"isolates)":[12],"polymorphic":[13],"for":[14,22],"the":[15,19,27,69,78,100,109,115,130,139,146,159,162],"TATA":[16,28,40,81,93,141,149],"box":[17,41,82,94,150],"using":[18],"\"DNA":[20],"sequence-->affinity":[21],"TBP\"":[23],"regression":[24],"(TBP":[25],"is":[26,75,124],"binding":[29],"protein).":[30],"As":[31],"a":[32,34,46],"result,":[33],"statistically":[35],"significant":[36],"excess":[37,70],"of":[38,49,59,71,102,108,114,121,129,161],"low-affinity":[39],"variants":[43],"corresponding":[44],"to":[45],"low":[47],"level":[48],"both":[50],"basal":[51],"and":[52,111],"TAT-dependent":[53],"expression":[54],"and,":[55],"consequently,":[56],"slow":[57],"replication":[58],"detected.":[63],"A":[64],"detailed":[65],"analysis":[66],"revealed":[67,99],"that":[68,119],"slowly":[72,147,163],"replicating":[73,148,164],"associated":[76,126],"with":[77,127],"subtype":[79],"E-associated":[80],"core":[83,151],"sequence":[84,152],"\"CATAAAA\".":[85],"Principal":[86],"Component":[87],"Analysis":[88],"performed":[89],"on":[90],"2662":[91],"copies":[95],"70":[97],"countries":[98,123],"presence":[101],"two":[103],"principal":[104],"components,":[105],"PC1":[106],"(75.7%":[107],"variance)":[110],"PC2":[112],"(23.3%":[113],"variance).":[116],"They":[117],"indicate":[118],"each":[120],"these":[122],"specifically":[125],"one":[128],"following":[131],"evolution:":[135],"neutral":[136,143],"drift":[137,144],"around":[138,145],"normal":[140],"box;":[142],"(phylogenetic":[153],"inertia);":[154],"an":[155],"adaptive":[156],"increase":[157],"frequency":[160],"form.":[165]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
