{"id":"https://openalex.org/W2111359483","doi":"https://doi.org/10.1093/bioinformatics/btl147","title":"GAME: detecting <i>cis</i>-regulatory elements using a genetic algorithm","display_name":"GAME: detecting <i>cis</i>-regulatory elements using a genetic algorithm","publication_year":2006,"publication_date":"2006-04-21","ids":{"openalex":"https://openalex.org/W2111359483","doi":"https://doi.org/10.1093/bioinformatics/btl147","mag":"2111359483","pmid":"https://pubmed.ncbi.nlm.nih.gov/16632495"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl147","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl147","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1577/48838104/bioinformatics_22_13_1577.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/22/13/1577/48838104/bioinformatics_22_13_1577.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001916237","display_name":"Zhi Wei","orcid":"https://orcid.org/0000-0001-6059-4267"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhi Wei","raw_affiliation_strings":["Genomics and Computational Biology Graduate Group, University of Pennsylvania School of Medicine 1 \u00a0 1 \u00a0 \u00a0 Philadelphia, PA 19104, USA"],"affiliations":[{"raw_affiliation_string":"Genomics and Computational Biology Graduate Group, University of Pennsylvania School of Medicine 1 \u00a0 1 \u00a0 \u00a0 Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038551920","display_name":"Shane T. Jensen","orcid":"https://orcid.org/0000-0003-0945-5725"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shane T. Jensen","raw_affiliation_strings":["Department of Statistics, The Wharton School, University of Pennsylvania 2 \u00a0 2 \u00a0 \u00a0 Philadelphia, PA 19104, USA"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, The Wharton School, University of Pennsylvania 2 \u00a0 2 \u00a0 \u00a0 Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5001916237"],"corresponding_institution_ids":["https://openalex.org/I79576946"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.7089,"has_fulltext":false,"cited_by_count":97,"citation_normalized_percentile":{"value":0.9362727,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"13","first_page":"1577","last_page":"1584"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9986000061035156,"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":0.9986000061035156,"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":0.9980000257492065,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.992900013923645,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.8201539516448975},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6153863072395325},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.49100807309150696},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4266323149204254},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3781255781650543},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37302184104919434},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37196171283721924},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.36024749279022217},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2115395963191986},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1292075216770172}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.8201539516448975},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6153863072395325},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.49100807309150696},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4266323149204254},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3781255781650543},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37302184104919434},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37196171283721924},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36024749279022217},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2115395963191986},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1292075216770172},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btl147","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl147","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1577/48838104/bioinformatics_22_13_1577.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:16632495","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16632495","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/btl147","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl147","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1577/48838104/bioinformatics_22_13_1577.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":[],"funders":[{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2111359483.pdf","grobid_xml":"https://content.openalex.org/works/W2111359483.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W329913983","https://openalex.org/W1492417045","https://openalex.org/W1511493290","https://openalex.org/W1592870802","https://openalex.org/W1661761688","https://openalex.org/W1965555277","https://openalex.org/W1975924111","https://openalex.org/W1994755936","https://openalex.org/W2003967338","https://openalex.org/W2033765726","https://openalex.org/W2041877620","https://openalex.org/W2048869777","https://openalex.org/W2049114051","https://openalex.org/W2073850887","https://openalex.org/W2077013196","https://openalex.org/W2084908610","https://openalex.org/W2096590200","https://openalex.org/W2106004801","https://openalex.org/W2112444654","https://openalex.org/W2115603438","https://openalex.org/W2117549173","https://openalex.org/W2121298930","https://openalex.org/W2121356022","https://openalex.org/W2128937741","https://openalex.org/W2141224484","https://openalex.org/W2142183404","https://openalex.org/W2145295592","https://openalex.org/W2151638714","https://openalex.org/W2154165587","https://openalex.org/W2158266834","https://openalex.org/W2159831212","https://openalex.org/W2161965550","https://openalex.org/W2166429927","https://openalex.org/W2168786813","https://openalex.org/W2904250082","https://openalex.org/W2913091258","https://openalex.org/W3023540311","https://openalex.org/W4301173492","https://openalex.org/W4387688680","https://openalex.org/W6635200387","https://openalex.org/W6669145357","https://openalex.org/W6677399227","https://openalex.org/W6683187033"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2368037387","https://openalex.org/W190186656","https://openalex.org/W2377079823","https://openalex.org/W2902352756","https://openalex.org/W2605676258","https://openalex.org/W2599962286","https://openalex.org/W2319582300","https://openalex.org/W2890847211"],"abstract_inverted_index":{"We":[0,59],"introduce":[1],"software,":[2],"GAME,":[3],"which":[4,30],"utilizes":[5],"a":[6,23],"genetic":[7,43],"algorithm":[8,91],"to":[9,40,54,97],"find":[10],"optimal":[11],"motifs":[12,18],"in":[13,72],"DNA":[14],"sequences.":[15],"GAME":[16,45,65,90],"evolves":[17],"with":[19,67],"high":[20],"fitness":[21],"from":[22],"population":[24],"of":[25,64,88],"randomly":[26],"generated":[27],"starting":[28],"motifs,":[29],"eliminate":[31],"the":[32,55,61,89,94],"reliance":[33],"on":[34],"additional":[35,49],"motif-finding":[36],"programs.":[37],"In":[38],"addition":[39],"using":[41],"standard":[42],"operations,":[44],"also":[46],"incorporates":[47],"two":[48],"operators":[50],"that":[51,92],"are":[52],"specific":[53],"motif":[56,95],"discovery":[57],"problem.":[58],"demonstrate":[60],"superior":[62],"performance":[63],"compared":[66],"MEME,":[68],"BioProspector":[69],"and":[70],"BioOptimizer":[71],"simulation":[73],"studies":[74],"as":[75,77],"well":[76],"several":[78],"real":[79],"data":[80],"applications":[81],"where":[82],"we":[83],"use":[84],"an":[85],"extended":[86],"version":[87],"allows":[93],"width":[96],"be":[98],"unknown.":[99]},"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":5},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":8}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
