{"id":"https://openalex.org/W4367042085","doi":"https://doi.org/10.1093/bib/bbad156","title":"A survey on algorithms to characterize transcription factor binding sites","display_name":"A survey on algorithms to characterize transcription factor binding sites","publication_year":2023,"publication_date":"2023-04-25","ids":{"openalex":"https://openalex.org/W4367042085","doi":"https://doi.org/10.1093/bib/bbad156"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad156","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad156","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad156/51102056/bbad156.pdf","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":"review","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad156/51102056/bbad156.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026130676","display_name":"Manuel Tognon","orcid":"https://orcid.org/0000-0002-6707-2071"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]},{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Manuel Tognon","raw_affiliation_strings":["Broad Institute of MIT and Harvard , Cambridge, Massachusetts , United States of America","Computer Science Department, University of Verona , Verona, Italy","Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital , Charlestown, Massachusetts , United States of America"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, Massachusetts , United States of America","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Computer Science Department, University of Verona , Verona, Italy","institution_ids":["https://openalex.org/I119439378"]},{"raw_affiliation_string":"Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital , Charlestown, Massachusetts , United States of America","institution_ids":["https://openalex.org/I4210149717","https://openalex.org/I4210087915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002057785","display_name":"Rosalba Giugno","orcid":"https://orcid.org/0000-0001-9843-7638"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Rosalba Giugno","raw_affiliation_strings":["Computer Science Department, University of Verona , Verona, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of Verona , Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078228499","display_name":"Luca Pinello","orcid":"https://orcid.org/0000-0003-1195-9607"},"institutions":[{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Luca Pinello","raw_affiliation_strings":["Broad Institute of MIT and Harvard , Cambridge, Massachusetts , United States of America","Department of Pathology, Harvard Medical School , Boston, Massachusetts , United States of America","Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital , Charlestown, Massachusetts , United States of America"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, Massachusetts , United States of America","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Pathology, Harvard Medical School , Boston, Massachusetts , United States of America","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital , Charlestown, Massachusetts , United States of America","institution_ids":["https://openalex.org/I4210149717","https://openalex.org/I4210087915"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5002057785","https://openalex.org/A5078228499"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I119439378","https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210149717"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.2536,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.94654261,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"24","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T11482","display_name":"RNA modifications and cancer","score":0.9943000078201294,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.991100013256073,"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/transcription-factor","display_name":"Transcription factor","score":0.5656439065933228},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49766090512275696},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46078455448150635},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.42724713683128357},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3900986909866333},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2849646806716919},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1697092354297638},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.16920459270477295},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10087329149246216},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07602030038833618}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5656439065933228},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49766090512275696},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46078455448150635},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.42724713683128357},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3900986909866333},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2849646806716919},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1697092354297638},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.16920459270477295},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10087329149246216},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07602030038833618}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad156","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad156","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad156/51102056/bbad156.pdf","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":"pmh:oai:pubmedcentral.nih.gov:10422928","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10422928","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10422928/pdf/bbad156.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad156","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad156","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad156/51102056/bbad156.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3828530024","display_name":null,"funder_award_id":"R35HG010717","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4614449928","display_name":null,"funder_award_id":"2019-466-037","funder_id":"https://openalex.org/F4320314158","funder_display_name":"EU Joint Programme \u2013 Neurodegenerative Disease Research"},{"id":"https://openalex.org/G4956428346","display_name":null,"funder_award_id":"Horizon 2020 research and innovatio","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5456788263","display_name":null,"funder_award_id":"JPND2019-466-037","funder_id":"https://openalex.org/F4320314158","funder_display_name":"EU Joint Programme \u2013 Neurodegenerative Disease Research"},{"id":"https://openalex.org/G655460490","display_name":null,"funder_award_id":"814978","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320308349","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78"},{"id":"https://openalex.org/F4320314158","display_name":"EU Joint Programme \u2013 Neurodegenerative Disease Research","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322875","display_name":"Universit\u00e0 degli Studi di Parma","ror":"https://ror.org/02k7wn190"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4367042085.pdf"},"referenced_works_count":220,"referenced_works":["https://openalex.org/W110099204","https://openalex.org/W247170787","https://openalex.org/W314528818","https://openalex.org/W1019830208","https://openalex.org/W1123205372","https://openalex.org/W1214546200","https://openalex.org/W1500328508","https://openalex.org/W1553587640","https://openalex.org/W1592870802","https://openalex.org/W1672219033","https://openalex.org/W1768880427","https://openalex.org/W1783247684","https://openalex.org/W1885076136","https://openalex.org/W1963911710","https://openalex.org/W1964963969","https://openalex.org/W1965267927","https://openalex.org/W1967085530","https://openalex.org/W1968475238","https://openalex.org/W1972792790","https://openalex.org/W1976093396","https://openalex.org/W1979353384","https://openalex.org/W1980825481","https://openalex.org/W1988393300","https://openalex.org/W1988581590","https://openalex.org/W1989080074","https://openalex.org/W1989338936","https://openalex.org/W1989419347","https://openalex.org/W1994122295","https://openalex.org/W1994383643","https://openalex.org/W1995837988","https://openalex.org/W1995918845","https://openalex.org/W1998000745","https://openalex.org/W1998300401","https://openalex.org/W2002122781","https://openalex.org/W2003967338","https://openalex.org/W2011282682","https://openalex.org/W2012114217","https://openalex.org/W2013887116","https://openalex.org/W2013989044","https://openalex.org/W2014677321","https://openalex.org/W2015324225","https://openalex.org/W2019937806","https://openalex.org/W2020816856","https://openalex.org/W2022736304","https://openalex.org/W2026690931","https://openalex.org/W2026731344","https://openalex.org/W2029201460","https://openalex.org/W2032609519","https://openalex.org/W2033169664","https://openalex.org/W2033781392","https://openalex.org/W2037940015","https://openalex.org/W2038849570","https://openalex.org/W2039317795","https://openalex.org/W2040745508","https://openalex.org/W2041726559","https://openalex.org/W2041877620","https://openalex.org/W2045273474","https://openalex.org/W2046842005","https://openalex.org/W2048869777","https://openalex.org/W2050284387","https://openalex.org/W2050833533","https://openalex.org/W2051640319","https://openalex.org/W2054984882","https://openalex.org/W2061834804","https://openalex.org/W2064675550","https://openalex.org/W2065419951","https://openalex.org/W2065579185","https://openalex.org/W2067899297","https://openalex.org/W2073661767","https://openalex.org/W2073850887","https://openalex.org/W2074307047","https://openalex.org/W2076439598","https://openalex.org/W2078059415","https://openalex.org/W2080291586","https://openalex.org/W2081277704","https://openalex.org/W2083861085","https://openalex.org/W2084160423","https://openalex.org/W2084620487","https://openalex.org/W2085239230","https://openalex.org/W2087347434","https://openalex.org/W2090804789","https://openalex.org/W2097175728","https://openalex.org/W2097936772","https://openalex.org/W2099229391","https://openalex.org/W2101025813","https://openalex.org/W2102473929","https://openalex.org/W2103777723","https://openalex.org/W2109897790","https://openalex.org/W2110738405","https://openalex.org/W2113117122","https://openalex.org/W2115761267","https://openalex.org/W2117757143","https://openalex.org/W2118393799","https://openalex.org/W2119804413","https://openalex.org/W2121356022","https://openalex.org/W2123490534","https://openalex.org/W2126468786","https://openalex.org/W2129795133","https://openalex.org/W2132955708","https://openalex.org/W2136945519","https://openalex.org/W2137465688","https://openalex.org/W2140952049","https://openalex.org/W2141224484","https://openalex.org/W2141408320","https://openalex.org/W2141781797","https://openalex.org/W2142890842","https://openalex.org/W2143658931","https://openalex.org/W2145091349","https://openalex.org/W2145295592","https://openalex.org/W2146393977","https://openalex.org/W2146890600","https://openalex.org/W2148014281","https://openalex.org/W2149769193","https://openalex.org/W2150573567","https://openalex.org/W2151845703","https://openalex.org/W2151945801","https://openalex.org/W2152121035","https://openalex.org/W2153561273","https://openalex.org/W2154855927","https://openalex.org/W2155844132","https://openalex.org/W2156661861","https://openalex.org/W2157952888","https://openalex.org/W2158485480","https://openalex.org/W2158962723","https://openalex.org/W2159324718","https://openalex.org/W2161313889","https://openalex.org/W2161849959","https://openalex.org/W2162530919","https://openalex.org/W2162778212","https://openalex.org/W2163922914","https://openalex.org/W2164814636","https://openalex.org/W2165102934","https://openalex.org/W2165649312","https://openalex.org/W2166086559","https://openalex.org/W2166277117","https://openalex.org/W2168157737","https://openalex.org/W2168642461","https://openalex.org/W2168786813","https://openalex.org/W2170960297","https://openalex.org/W2171808845","https://openalex.org/W2185560378","https://openalex.org/W2198371822","https://openalex.org/W2198606573","https://openalex.org/W2212528563","https://openalex.org/W2259938310","https://openalex.org/W2278401009","https://openalex.org/W2305687918","https://openalex.org/W2330303612","https://openalex.org/W2336509392","https://openalex.org/W2338148720","https://openalex.org/W2340182364","https://openalex.org/W2345512687","https://openalex.org/W2385696187","https://openalex.org/W2413160504","https://openalex.org/W2433743436","https://openalex.org/W2479945688","https://openalex.org/W2479952736","https://openalex.org/W2481378334","https://openalex.org/W2554247923","https://openalex.org/W2561544479","https://openalex.org/W2588039758","https://openalex.org/W2594221001","https://openalex.org/W2603734366","https://openalex.org/W2605409611","https://openalex.org/W2739174192","https://openalex.org/W2767749844","https://openalex.org/W2785792383","https://openalex.org/W2790023639","https://openalex.org/W2800857888","https://openalex.org/W2801527818","https://openalex.org/W2884914958","https://openalex.org/W2891494568","https://openalex.org/W2893880892","https://openalex.org/W2901027836","https://openalex.org/W2907025617","https://openalex.org/W2918598256","https://openalex.org/W2919115771","https://openalex.org/W2921983621","https://openalex.org/W2943967679","https://openalex.org/W2947608130","https://openalex.org/W2949588195","https://openalex.org/W2951218167","https://openalex.org/W2951410692","https://openalex.org/W2952239877","https://openalex.org/W2952602201","https://openalex.org/W2962038738","https://openalex.org/W2963266267","https://openalex.org/W2988716798","https://openalex.org/W3035587935","https://openalex.org/W3047670845","https://openalex.org/W3081278968","https://openalex.org/W3090491025","https://openalex.org/W3108737349","https://openalex.org/W3112390879","https://openalex.org/W3121486818","https://openalex.org/W3127538277","https://openalex.org/W3130819465","https://openalex.org/W3139265997","https://openalex.org/W3152218910","https://openalex.org/W3152892280","https://openalex.org/W3164076681","https://openalex.org/W3175931262","https://openalex.org/W3188230161","https://openalex.org/W3200848929","https://openalex.org/W3203588026","https://openalex.org/W3210860076","https://openalex.org/W3212111676","https://openalex.org/W4245581330","https://openalex.org/W4282011047","https://openalex.org/W4290672942","https://openalex.org/W6628147189","https://openalex.org/W6635200387","https://openalex.org/W6655478935","https://openalex.org/W6659963394","https://openalex.org/W6669145357","https://openalex.org/W6710305905","https://openalex.org/W6729963616","https://openalex.org/W6736518430","https://openalex.org/W6769944288","https://openalex.org/W6801727856"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2379997263","https://openalex.org/W1557222478","https://openalex.org/W2367493320","https://openalex.org/W2112717966","https://openalex.org/W2131580913","https://openalex.org/W2125854412","https://openalex.org/W3083097828","https://openalex.org/W2796029694","https://openalex.org/W2499916532"],"abstract_inverted_index":{"Abstract":[0],"Transcription":[1],"factors":[2],"(TFs)":[3],"are":[4],"key":[5],"regulatory":[6,37],"proteins":[7],"that":[8,134],"control":[9],"the":[10,36,40,46,83,95,137,141],"transcriptional":[11,41],"rate":[12],"of":[13,43,82],"cells":[14],"by":[15],"binding":[16,23],"short":[17],"DNA":[18,57,77,119],"sequences":[19,58],"called":[20],"transcription":[21],"factor":[22],"sites":[24],"(TFBS)":[25],"or":[26],"motifs.":[27],"Identifying":[28],"and":[29,70,90,105,108,114,124,131],"characterizing":[30],"TFBS":[31,72,116],"is":[32,80,91],"fundamental":[33],"to":[34,55,68,93,112],"understanding":[35],"mechanisms":[38],"governing":[39],"state":[42],"cells.":[44],"During":[45],"last":[47],"decades,":[48],"several":[49],"experimental":[50,107],"methods":[51,64,110],"have":[52,65],"been":[53,66],"developed":[54,111],"recover":[56],"containing":[59],"TFBS.":[60],"In":[61,99],"parallel,":[62],"computational":[63,109],"proposed":[67],"discover":[69,113],"identify":[71],"motifs":[73,117],"based":[74],"on":[75],"these":[76],"sequences.":[78],"This":[79],"one":[81],"most":[84],"widely":[85],"investigated":[86],"problems":[87],"in":[88,118,140],"bioinformatics":[89],"referred":[92],"as":[94],"motif":[96],"discovery":[97],"problem.":[98],"this":[100],"manuscript,":[101],"we":[102],"review":[103],"classical":[104],"novel":[106],"characterize":[115],"sequences,":[120],"highlighting":[121],"their":[122],"advantages":[123],"drawbacks.":[125],"We":[126],"also":[127],"discuss":[128],"open":[129],"challenges":[130],"future":[132],"perspectives":[133],"could":[135],"fill":[136],"remaining":[138],"gaps":[139],"field.":[142]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
