{"id":"https://openalex.org/W2594221001","doi":"https://doi.org/10.1093/bib/bbx026","title":"An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data","display_name":"An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data","publication_year":2017,"publication_date":"2017-02-15","ids":{"openalex":"https://openalex.org/W2594221001","doi":"https://doi.org/10.1093/bib/bbx026","mag":"2594221001","pmid":"https://pubmed.ncbi.nlm.nih.gov/28334268"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbx026","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx026","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5017344694","display_name":"Bingqiang Liu","orcid":"https://orcid.org/0000-0002-5734-1135"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bingqiang Liu","raw_affiliation_strings":["School of Mathematics, Shandong University, Jinan Shandong, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan Shandong, P. R. China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049718088","display_name":"Jinyu Yang","orcid":"https://orcid.org/0000-0002-7004-3570"},"institutions":[{"id":"https://openalex.org/I177156846","display_name":"South Dakota State University","ror":"https://ror.org/015jmes13","country_code":"US","type":"education","lineage":["https://openalex.org/I177156846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinyu Yang","raw_affiliation_strings":["Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA","institution_ids":["https://openalex.org/I177156846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100421627","display_name":"Yang Li","orcid":"https://orcid.org/0000-0002-7677-9028"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Li","raw_affiliation_strings":["School of Mathematics, Shandong University, Jinan Shandong, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan Shandong, P. R. China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032867744","display_name":"Adam McDermaid","orcid":"https://orcid.org/0000-0001-8616-1574"},"institutions":[{"id":"https://openalex.org/I177156846","display_name":"South Dakota State University","ror":"https://ror.org/015jmes13","country_code":"US","type":"education","lineage":["https://openalex.org/I177156846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam McDermaid","raw_affiliation_strings":["Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA","institution_ids":["https://openalex.org/I177156846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022408570","display_name":"Qin Ma","orcid":"https://orcid.org/0000-0002-3264-8392"},"institutions":[{"id":"https://openalex.org/I177156846","display_name":"South Dakota State University","ror":"https://ror.org/015jmes13","country_code":"US","type":"education","lineage":["https://openalex.org/I177156846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qin Ma","raw_affiliation_strings":["Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA","institution_ids":["https://openalex.org/I177156846"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017344694"],"corresponding_institution_ids":["https://openalex.org/I154099455"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.3312,"has_fulltext":false,"cited_by_count":50,"citation_normalized_percentile":{"value":0.89073824,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"19","issue":"5","first_page":"1069","last_page":"1081"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9994999766349792,"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/T10604","display_name":"RNA Research and Splicing","score":0.9987000226974487,"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/motif","display_name":"Motif (music)","score":0.700096070766449},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.614302933216095},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5689669251441956},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4388246536254883},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4153466820716858},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32924556732177734},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3055781126022339},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2177976369857788},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18629968166351318},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13462847471237183},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.09614390134811401},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.07238602638244629}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.700096070766449},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.614302933216095},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5689669251441956},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4388246536254883},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4153466820716858},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32924556732177734},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3055781126022339},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2177976369857788},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18629968166351318},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13462847471237183},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.09614390134811401},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.07238602638244629},{"id":"https://openalex.org/C107038049","wikidata":"https://www.wikidata.org/wiki/Q35986","display_name":"Aesthetics","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","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":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbx026","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx026","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28334268","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28334268","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6800000071525574,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G3040862546","display_name":"\u57fa\u4e8e\u9ad8\u901a\u91cfRNA-seq\u6570\u636e\u8f6c\u5f55\u7ec4\u62fc\u63a5\u7684\u5173\u952e\u6280\u672f\u4e0e\u7b97\u6cd5\u7814\u7a76","funder_award_id":"61432010","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4232076736","display_name":null,"funder_award_id":"61303084","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":132,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1552913826","https://openalex.org/W1580213736","https://openalex.org/W1592870802","https://openalex.org/W1861050171","https://openalex.org/W1966354073","https://openalex.org/W1966558370","https://openalex.org/W1974614108","https://openalex.org/W1979353384","https://openalex.org/W1981509058","https://openalex.org/W1983983428","https://openalex.org/W1984053739","https://openalex.org/W1986105390","https://openalex.org/W1988294855","https://openalex.org/W1988871238","https://openalex.org/W1998300401","https://openalex.org/W2003967338","https://openalex.org/W2006439377","https://openalex.org/W2006853093","https://openalex.org/W2012139697","https://openalex.org/W2019160435","https://openalex.org/W2019522436","https://openalex.org/W2019896510","https://openalex.org/W2020749481","https://openalex.org/W2029201460","https://openalex.org/W2031140266","https://openalex.org/W2032231928","https://openalex.org/W2034206030","https://openalex.org/W2036131961","https://openalex.org/W2038093918","https://openalex.org/W2039317795","https://openalex.org/W2039458303","https://openalex.org/W2041726559","https://openalex.org/W2042465823","https://openalex.org/W2044937161","https://openalex.org/W2050151193","https://openalex.org/W2051640319","https://openalex.org/W2052562387","https://openalex.org/W2058852389","https://openalex.org/W2060064237","https://openalex.org/W2069985409","https://openalex.org/W2071042066","https://openalex.org/W2071116416","https://openalex.org/W2072388876","https://openalex.org/W2073850887","https://openalex.org/W2074307047","https://openalex.org/W2076985742","https://openalex.org/W2077377665","https://openalex.org/W2083861085","https://openalex.org/W2086273821","https://openalex.org/W2087598350","https://openalex.org/W2095150428","https://openalex.org/W2095791120","https://openalex.org/W2096629558","https://openalex.org/W2097175728","https://openalex.org/W2097220641","https://openalex.org/W2097396311","https://openalex.org/W2098412979","https://openalex.org/W2101835893","https://openalex.org/W2102231586","https://openalex.org/W2102663142","https://openalex.org/W2102904139","https://openalex.org/W2103441770","https://openalex.org/W2104865962","https://openalex.org/W2108539079","https://openalex.org/W2109275727","https://openalex.org/W2110455321","https://openalex.org/W2110707963","https://openalex.org/W2110738405","https://openalex.org/W2113117122","https://openalex.org/W2114446330","https://openalex.org/W2114650383","https://openalex.org/W2115577355","https://openalex.org/W2115761267","https://openalex.org/W2118393799","https://openalex.org/W2121356022","https://openalex.org/W2121967239","https://openalex.org/W2124201730","https://openalex.org/W2124807683","https://openalex.org/W2124985265","https://openalex.org/W2125598804","https://openalex.org/W2128091972","https://openalex.org/W2128397771","https://openalex.org/W2135221645","https://openalex.org/W2138891173","https://openalex.org/W2139398143","https://openalex.org/W2141222038","https://openalex.org/W2141395444","https://openalex.org/W2141408320","https://openalex.org/W2143837300","https://openalex.org/W2144609215","https://openalex.org/W2144955337","https://openalex.org/W2145091349","https://openalex.org/W2147055980","https://openalex.org/W2149118429","https://openalex.org/W2149769193","https://openalex.org/W2150573567","https://openalex.org/W2156553342","https://openalex.org/W2157009395","https://openalex.org/W2157485293","https://openalex.org/W2157758083","https://openalex.org/W2157952888","https://openalex.org/W2159324718","https://openalex.org/W2161951664","https://openalex.org/W2162530919","https://openalex.org/W2164814636","https://openalex.org/W2166425625","https://openalex.org/W2167077887","https://openalex.org/W2167296922","https://openalex.org/W2171111703","https://openalex.org/W2171286893","https://openalex.org/W2171808845","https://openalex.org/W2180785263","https://openalex.org/W2247766769","https://openalex.org/W2277218877","https://openalex.org/W2294265159","https://openalex.org/W2301598169","https://openalex.org/W2395238275","https://openalex.org/W2408658366","https://openalex.org/W2444103466","https://openalex.org/W2508081817","https://openalex.org/W4205097856","https://openalex.org/W4237853625","https://openalex.org/W4247053599","https://openalex.org/W6632975688","https://openalex.org/W6634719314","https://openalex.org/W6635200387","https://openalex.org/W6655548692","https://openalex.org/W6669145357","https://openalex.org/W6676479977","https://openalex.org/W6694897849","https://openalex.org/W6711757063"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2605676258","https://openalex.org/W2368037387","https://openalex.org/W190186656","https://openalex.org/W2902352756","https://openalex.org/W2377079823","https://openalex.org/W2953439652","https://openalex.org/W2599962286"],"abstract_inverted_index":{"Transcription":[0],"factors":[1],"are":[2],"proteins":[3],"that":[4],"bind":[5],"to":[6,65,90,109,151],"specific":[7,152],"DNA":[8],"sequences":[9],"and":[10,40,121,144,159,166],"play":[11],"important":[12,147],"roles":[13],"in":[14,99,174],"controlling":[15],"the":[16,75,100],"expression":[17],"levels":[18],"of":[19,25,77,94,105,176],"their":[20],"target":[21],"genes.":[22],"Hence,":[23],"prediction":[24,89],"transcription":[26],"factor":[27],"binding":[28],"sites":[29],"(TFBSs)":[30],"provides":[31],"a":[32,45],"solid":[33],"foundation":[34],"for":[35,44,57,87,114,168],"inferring":[36],"gene":[37],"regulatory":[38,42],"mechanisms":[39],"building":[41],"networks":[43],"genome.":[46],"Chromatin":[47],"immunoprecipitation":[48],"sequencing":[49],"(ChIP-seq)":[50],"technology":[51],"can":[52],"generate":[53],"large-scale":[54],"experimental":[55],"data":[56,97,116],"such":[58],"protein-DNA":[59],"interactions,":[60],"providing":[61],"an":[62,118],"unprecedented":[63],"opportunity":[64],"identify":[66],"TFBSs":[67],"(a.k.a.":[68],"cis-regulatory":[69],"motifs).":[70],"The":[71,103,129],"bottleneck,":[72],"however,":[73],"is":[74,108],"lack":[76],"robust":[78],"mathematical":[79],"models,":[80],"as":[81,83],"well":[82],"efficient":[84],"computational":[85,124],"methods":[86,113,131],"TFBS":[88],"make":[91],"effective":[92],"use":[93],"massive":[95],"ChIP-seq":[96,115],"sets":[98],"public":[101],"domain.":[102],"purpose":[104],"this":[106,127],"study":[107],"review":[110],"existing":[111],"motif-finding":[112,138,170],"from":[117],"algorithmic":[119],"perspective":[120],"provide":[122],"new":[123],"insight":[125],"into":[126],"field.":[128],"state-of-the-art":[130],"were":[132,172],"shown":[133],"through":[134],"summarizing":[135],"eight":[136],"representative":[137],"algorithms":[139],"along":[140],"with":[141],"corresponding":[142],"challenges,":[143],"introducing":[145],"some":[146],"relative":[148],"functions":[149],"according":[150],"biological":[153],"demands,":[154],"including":[155],"discriminative":[156],"motif":[157],"finding":[158],"cofactor":[160],"motifs":[161],"analysis.":[162],"Finally,":[163],"potential":[164],"directions":[165],"plans":[167],"ChIP-seq-based":[169],"tools":[171],"showcased":[173],"support":[175],"future":[177],"algorithm":[178],"development.":[179]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":10}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
