{"id":"https://openalex.org/W2109487010","doi":"https://doi.org/10.3390/a2010582","title":"Recent Advances in the Computational Discovery of Transcription Factor Binding Sites","display_name":"Recent Advances in the Computational Discovery of Transcription Factor Binding Sites","publication_year":2009,"publication_date":"2009-03-24","ids":{"openalex":"https://openalex.org/W2109487010","doi":"https://doi.org/10.3390/a2010582","mag":"2109487010"},"language":"en","primary_location":{"id":"doi:10.3390/a2010582","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a2010582","pdf_url":"https://www.mdpi.com/1999-4893/2/1/582/pdf?version=1237902985","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1999-4893/2/1/582/pdf?version=1237902985","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100642009","display_name":"Tung Nguyen","orcid":"https://orcid.org/0000-0003-4232-0566"},"institutions":[{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]},{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tung T. Nguyen","raw_affiliation_strings":["BioMaPS Institute for Quantitative Biology, Rutgers University, New Jersey 08854, USA"],"affiliations":[{"raw_affiliation_string":"BioMaPS Institute for Quantitative Biology, Rutgers University, New Jersey 08854, USA","institution_ids":["https://openalex.org/I4210098931","https://openalex.org/I102322142"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049184270","display_name":"Ioannis P. Androulakis","orcid":"https://orcid.org/0000-0002-3795-3628"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ioannis P. Androulakis","raw_affiliation_strings":["Biomedical Engineering Department, Rutgers University, New Jersey 08854, USA"],"affiliations":[{"raw_affiliation_string":"Biomedical Engineering Department, Rutgers University, New Jersey 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5049184270","https://openalex.org/A5100642009"],"corresponding_institution_ids":["https://openalex.org/I102322142","https://openalex.org/I4210098931"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":1.0784,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.76609662,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2","issue":"1","first_page":"582","last_page":"605"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987999796867371,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987999796867371,"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":0.9939000010490417,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9905999898910522,"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/dna-binding-site","display_name":"DNA binding site","score":0.7048014402389526},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5967792272567749},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.592399001121521},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5880791544914246},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.578150749206543},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4936295747756958},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.41854721307754517},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35490018129348755},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31874024868011475},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.2762987017631531},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2681694030761719},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17181739211082458}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.7048014402389526},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5967792272567749},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.592399001121521},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5880791544914246},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.578150749206543},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4936295747756958},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.41854721307754517},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35490018129348755},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31874024868011475},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.2762987017631531},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2681694030761719},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17181739211082458},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3390/a2010582","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a2010582","pdf_url":"https://www.mdpi.com/1999-4893/2/1/582/pdf?version=1237902985","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.309.6469","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.309.6469","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.mdpi.com/1999-4893/2/1/582/pdf/","raw_type":"text"},{"id":"pmh:oai:alma.01RUT_INST:11663470960004646","is_oa":false,"landing_page_url":"https://scholarship.libraries.rutgers.edu/esploro/outputs/journalArticle/Recent-Advances-in-the-Computational-Discovery/991031654640204646","pdf_url":null,"source":{"id":"https://openalex.org/S4210197018","display_name":"View","issn_l":"2688-268X","issn":["2688-268X","2688-3988"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:a731557d1e534348a69739e27438b46f","is_oa":true,"landing_page_url":"https://doaj.org/article/a731557d1e534348a69739e27438b46f","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms, Vol 2, Iss 1, Pp 582-605 (2009)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1999-4893/2/1/582/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/a2010582","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms; Volume 2; Issue 1; Pages: 582-605","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/a2010582","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a2010582","pdf_url":"https://www.mdpi.com/1999-4893/2/1/582/pdf?version=1237902985","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109487010.pdf","grobid_xml":"https://content.openalex.org/works/W2109487010.grobid-xml"},"referenced_works_count":142,"referenced_works":["https://openalex.org/W1518026427","https://openalex.org/W1525734744","https://openalex.org/W1586891520","https://openalex.org/W1592870802","https://openalex.org/W1593132348","https://openalex.org/W1637197683","https://openalex.org/W1815199292","https://openalex.org/W1838422459","https://openalex.org/W1861050171","https://openalex.org/W1951165114","https://openalex.org/W1966448776","https://openalex.org/W1968384393","https://openalex.org/W1972386855","https://openalex.org/W1972813594","https://openalex.org/W1974614108","https://openalex.org/W1978173716","https://openalex.org/W1984053739","https://openalex.org/W1986014242","https://openalex.org/W1987122345","https://openalex.org/W1987187756","https://openalex.org/W1988393300","https://openalex.org/W1998300401","https://openalex.org/W2001400919","https://openalex.org/W2001785106","https://openalex.org/W2002804418","https://openalex.org/W2003967338","https://openalex.org/W2006300267","https://openalex.org/W2009566340","https://openalex.org/W2009570821","https://openalex.org/W2009596137","https://openalex.org/W2009659265","https://openalex.org/W2011282682","https://openalex.org/W2013739996","https://openalex.org/W2014411636","https://openalex.org/W2019462186","https://openalex.org/W2020634541","https://openalex.org/W2023825247","https://openalex.org/W2025289680","https://openalex.org/W2027349221","https://openalex.org/W2027662098","https://openalex.org/W2029144080","https://openalex.org/W2041726559","https://openalex.org/W2053852189","https://openalex.org/W2054042001","https://openalex.org/W2054984882","https://openalex.org/W2056033769","https://openalex.org/W2058682865","https://openalex.org/W2061123083","https://openalex.org/W2063732674","https://openalex.org/W2064879068","https://openalex.org/W2066310505","https://openalex.org/W2071753700","https://openalex.org/W2072522723","https://openalex.org/W2074530889","https://openalex.org/W2078733137","https://openalex.org/W2079450159","https://openalex.org/W2080498142","https://openalex.org/W2082213640","https://openalex.org/W2083482432","https://openalex.org/W2084908610","https://openalex.org/W2085955339","https://openalex.org/W2086914764","https://openalex.org/W2090730621","https://openalex.org/W2092390808","https://openalex.org/W2094036688","https://openalex.org/W2094074349","https://openalex.org/W2095617232","https://openalex.org/W2097040991","https://openalex.org/W2098222328","https://openalex.org/W2100558818","https://openalex.org/W2102424972","https://openalex.org/W2103447044","https://openalex.org/W2103465619","https://openalex.org/W2103673639","https://openalex.org/W2104730528","https://openalex.org/W2106756765","https://openalex.org/W2106882534","https://openalex.org/W2108145648","https://openalex.org/W2108595723","https://openalex.org/W2108887668","https://openalex.org/W2109314645","https://openalex.org/W2109830628","https://openalex.org/W2110455321","https://openalex.org/W2110472417","https://openalex.org/W2112717966","https://openalex.org/W2113206920","https://openalex.org/W2114783261","https://openalex.org/W2115776426","https://openalex.org/W2115979107","https://openalex.org/W2118151959","https://openalex.org/W2118628540","https://openalex.org/W2118767738","https://openalex.org/W2126468786","https://openalex.org/W2126598626","https://openalex.org/W2127084782","https://openalex.org/W2127230663","https://openalex.org/W2128937741","https://openalex.org/W2129175797","https://openalex.org/W2133027051","https://openalex.org/W2133147430","https://openalex.org/W2134591904","https://openalex.org/W2135000328","https://openalex.org/W2135221645","https://openalex.org/W2137144878","https://openalex.org/W2140885056","https://openalex.org/W2141408320","https://openalex.org/W2144362290","https://openalex.org/W2144824022","https://openalex.org/W2145133452","https://openalex.org/W2146202528","https://openalex.org/W2146393977","https://openalex.org/W2147848023","https://openalex.org/W2148056478","https://openalex.org/W2148503087","https://openalex.org/W2149271848","https://openalex.org/W2149769193","https://openalex.org/W2150612336","https://openalex.org/W2151945801","https://openalex.org/W2153550523","https://openalex.org/W2155237411","https://openalex.org/W2155717510","https://openalex.org/W2156246479","https://openalex.org/W2158962723","https://openalex.org/W2159057006","https://openalex.org/W2159164310","https://openalex.org/W2161711244","https://openalex.org/W2164814636","https://openalex.org/W2166187656","https://openalex.org/W2167190345","https://openalex.org/W2168341106","https://openalex.org/W2168786813","https://openalex.org/W2170465332","https://openalex.org/W2172121366","https://openalex.org/W2172186301","https://openalex.org/W2408658366","https://openalex.org/W2414421951","https://openalex.org/W3019267280","https://openalex.org/W4245023496","https://openalex.org/W4248318091","https://openalex.org/W6635200387","https://openalex.org/W6676479977","https://openalex.org/W6678667821"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2152664145","https://openalex.org/W2153561273","https://openalex.org/W2079197459","https://openalex.org/W2379997263","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W1557222478","https://openalex.org/W2367493320","https://openalex.org/W2131580913"],"abstract_inverted_index":{"The":[0],"discovery":[1],"of":[2,37,79,86,96,108,163,215],"gene":[3,24],"regulatory":[4,20,217],"elements":[5,88],"requires":[6],"the":[7,18,34,51,57,76,80,104,133,145,164,176,205,212],"synergism":[8],"between":[9],"computational":[10,97,149,213],"and":[11,31,91,117,126,171,189],"experimental":[12,39],"techniques":[13,177],"in":[14,26,43,56,124,130,148],"order":[15],"to":[16,28,49,68,74,102,178],"reveal":[17],"underlying":[19],"mechanisms":[21],"that":[22],"drive":[23],"expression":[25],"response":[27],"external":[29],"cues":[30],"signals.":[32],"Utilizing":[33],"large":[35,94],"amount":[36],"high-throughput":[38],"data,":[40],"constantly":[41],"growing":[42],"recent":[44,146],"years,":[45],"researchers":[46],"have":[47,99,120],"attempted":[48],"decipher":[50],"patterns":[52],"which":[53,71],"are":[54,64,72,114],"hidden":[55],"genomic":[58],"sequences.":[59],"These":[60],"patterns,":[61],"called":[62],"motifs,":[63],"potential":[65],"binding":[66,154,168,184],"sites":[67,185],"transcription":[69,81,152],"factors":[70],"hypothesized":[73],"be":[75],"main":[77],"regulators":[78],"process.":[82],"Consequently,":[83],"precise":[84],"detection":[85],"these":[87,209],"is":[89],"required":[90],"thus":[92],"a":[93,137,160],"number":[95],"approaches":[98,113,166,210],"been":[100],"developed":[101],"support":[103],"de":[105],"novo":[106],"identification":[107,214],"TFBSs.":[109],"Even":[110],"though":[111],"novel":[112],"continuously":[115],"proposed":[116],"almost":[118],"all":[119],"reported":[121],"some":[122,194],"success":[123],"yeast":[125],"other":[127],"lower":[128],"organisms,":[129],"higher":[131],"organisms":[132],"problem":[134],"still":[135],"remains":[136],"challenge.":[138],"In":[139],"this":[140],"paper,":[141],"we":[142,202],"therefore":[143],"review":[144,162],"developments":[147],"methods":[150],"for":[151,167,207],"factor":[153],"site":[155,169],"prediction.":[156],"We":[157],"start":[158],"with":[159],"brief":[161],"basic":[165],"representation":[170],"promoter":[172],"identification,":[173],"then":[174],"discuss":[175],"locate":[179],"physical":[180],"TFBSs,":[181],"identify":[182],"functional":[183,191],"using":[186],"orthologous":[187],"information,":[188],"infer":[190],"TFBSs":[192],"within":[193],"context":[195],"defined":[196],"by":[197],"additional":[198],"prior":[199],"knowledge.":[200],"Finally,":[201],"briefly":[203],"explore":[204],"opportunities":[206],"expanding":[208],"towards":[211],"transcriptional":[216],"networks.":[218]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
