{"id":"https://openalex.org/W2060091836","doi":"https://doi.org/10.1109/tcbb.2014.2359444","title":"CMStalker: A Combinatorial Tool for Composite Motif Discovery","display_name":"CMStalker: A Combinatorial Tool for Composite Motif Discovery","publication_year":2014,"publication_date":"2014-11-05","ids":{"openalex":"https://openalex.org/W2060091836","doi":"https://doi.org/10.1109/tcbb.2014.2359444","mag":"2060091836","pmid":"https://pubmed.ncbi.nlm.nih.gov/26451824"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2359444","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2359444","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://iris.unimore.it/bitstream/11380/1060670/1/CMStalker.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082430235","display_name":"Mauro Leoncini","orcid":"https://orcid.org/0000-0002-1999-3132"},"institutions":[{"id":"https://openalex.org/I122346577","display_name":"University of Modena and Reggio Emilia","ror":"https://ror.org/02d4c4y02","country_code":"IT","type":"education","lineage":["https://openalex.org/I122346577"]},{"id":"https://openalex.org/I4210130157","display_name":"Institute of Informatics and Telematics","ror":"https://ror.org/02gdcn153","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210130157","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mauro Leoncini","raw_affiliation_strings":["Department of Physics, Computer Science, and Mathematics, University of Modena and Reggio Emilia, Italy","IIT-CNR, Pisa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Computer Science, and Mathematics, University of Modena and Reggio Emilia, Italy","institution_ids":["https://openalex.org/I122346577"]},{"raw_affiliation_string":"IIT-CNR, Pisa, Italy","institution_ids":["https://openalex.org/I4210130157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002315056","display_name":"Manuela Montangero","orcid":"https://orcid.org/0000-0001-8827-5495"},"institutions":[{"id":"https://openalex.org/I122346577","display_name":"University of Modena and Reggio Emilia","ror":"https://ror.org/02d4c4y02","country_code":"IT","type":"education","lineage":["https://openalex.org/I122346577"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Manuela Montangero","raw_affiliation_strings":["Department of Physics, Computer Science, and Mathematics, University of Modena and Reggio Emilia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Computer Science, and Mathematics, University of Modena and Reggio Emilia, Italy","institution_ids":["https://openalex.org/I122346577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028551838","display_name":"Marco Pellegrini","orcid":"https://orcid.org/0000-0003-3151-9481"},"institutions":[{"id":"https://openalex.org/I4210130157","display_name":"Institute of Informatics and Telematics","ror":"https://ror.org/02gdcn153","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210130157","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Pellegrini","raw_affiliation_strings":["IIT-CNR, Pisa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IIT-CNR, Pisa, Italy","institution_ids":["https://openalex.org/I4210130157"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072658944","display_name":"Karina Panucia Till\u00e1n","orcid":null},"institutions":[{"id":"https://openalex.org/I122346577","display_name":"University of Modena and Reggio Emilia","ror":"https://ror.org/02d4c4y02","country_code":"IT","type":"education","lineage":["https://openalex.org/I122346577"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Karina Panucia Tillan","raw_affiliation_strings":["Department of Science and Methods for Engineering, University of Modena and Reggio Emilia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Science and Methods for Engineering, University of Modena and Reggio Emilia, Italy","institution_ids":["https://openalex.org/I122346577"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":0.2621,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.56866795,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":"5","first_page":"1123","last_page":"1136"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9984999895095825,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9984999895095825,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9919000267982483,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9904000163078308,"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":0.7432573437690735},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5278361439704895},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39125150442123413},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22596043348312378},{"id":"https://openalex.org/keywords/art","display_name":"Art","score":0.14211228489875793}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7432573437690735},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5278361439704895},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39125150442123413},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22596043348312378},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.14211228489875793},{"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":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":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1109/tcbb.2014.2359444","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2359444","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26451824","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26451824","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:iris.unimore.it:11380/1060670","is_oa":true,"landing_page_url":"http://hdl.handle.net/11380/1060670","pdf_url":"https://iris.unimore.it/bitstream/11380/1060670/1/CMStalker.pdf","source":{"id":"https://openalex.org/S4306400718","display_name":"IRIS UNIMORE (University of Modena and Reggio Emilia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122346577","host_organization_name":"University of Modena and Reggio Emilia","host_organization_lineage":["https://openalex.org/I122346577"],"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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.714.2629","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.714.2629","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://wwwold.iit.cnr.it/staff/marco.pellegrini/papiri/cmstalker-final-2015.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.719.2130","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.719.2130","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://algogroup.unimore.it/people/manuela/Papers/CMStalker.pdf","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:iris.unimore.it:11380/1060670","is_oa":true,"landing_page_url":"http://hdl.handle.net/11380/1060670","pdf_url":"https://iris.unimore.it/bitstream/11380/1060670/1/CMStalker.pdf","source":{"id":"https://openalex.org/S4306400718","display_name":"IRIS UNIMORE (University of Modena and Reggio Emilia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122346577","host_organization_name":"University of Modena and Reggio Emilia","host_organization_lineage":["https://openalex.org/I122346577"],"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":null,"raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320322651","display_name":"Consiglio Nazionale delle Ricerche","ror":"https://ror.org/04zaypm56"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2060091836.pdf","grobid_xml":"https://content.openalex.org/works/W2060091836.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W614012683","https://openalex.org/W1518105754","https://openalex.org/W1580213736","https://openalex.org/W1966833356","https://openalex.org/W1976148686","https://openalex.org/W1988393300","https://openalex.org/W2029201460","https://openalex.org/W2049154263","https://openalex.org/W2054984882","https://openalex.org/W2062872358","https://openalex.org/W2063732674","https://openalex.org/W2068011423","https://openalex.org/W2076985742","https://openalex.org/W2077431563","https://openalex.org/W2081264480","https://openalex.org/W2084620487","https://openalex.org/W2089528193","https://openalex.org/W2094036688","https://openalex.org/W2095617232","https://openalex.org/W2097220641","https://openalex.org/W2101476067","https://openalex.org/W2101913589","https://openalex.org/W2102473929","https://openalex.org/W2102818379","https://openalex.org/W2103495476","https://openalex.org/W2103697116","https://openalex.org/W2110065044","https://openalex.org/W2111676148","https://openalex.org/W2115979107","https://openalex.org/W2116672274","https://openalex.org/W2117549173","https://openalex.org/W2119033016","https://openalex.org/W2119985126","https://openalex.org/W2125246942","https://openalex.org/W2126620167","https://openalex.org/W2128091972","https://openalex.org/W2129920058","https://openalex.org/W2130796889","https://openalex.org/W2132215769","https://openalex.org/W2132633385","https://openalex.org/W2136292095","https://openalex.org/W2141408320","https://openalex.org/W2142136518","https://openalex.org/W2147055980","https://openalex.org/W2148441137","https://openalex.org/W2149841955","https://openalex.org/W2150612336","https://openalex.org/W2151845703","https://openalex.org/W2154514071","https://openalex.org/W2155717510","https://openalex.org/W2156885385","https://openalex.org/W2160829210","https://openalex.org/W2165466912","https://openalex.org/W2165735666","https://openalex.org/W2172186301","https://openalex.org/W2765689719","https://openalex.org/W6630895896","https://openalex.org/W6634719314"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2368037387","https://openalex.org/W190186656","https://openalex.org/W2902352756","https://openalex.org/W2377079823","https://openalex.org/W2605676258","https://openalex.org/W2599962286"],"abstract_inverted_index":{"Controlling":[0],"the":[1,27,76,91,147,169,179],"differential":[2],"expression":[3],"of":[4,17,61,93,96,108,149,168,172,178],"many":[5],"thousands":[6],"different":[7],"genes":[8],"at":[9],"any":[10],"given":[11,103],"time":[12],"is":[13,24,65,190],"a":[14,47,50,85,106,121,130,135,140,175],"fundamental":[15],"task":[16,53],"metazoan":[18],"organisms":[19],"and":[20,73,158],"this":[21,81],"complex":[22,32],"orchestration":[23],"controlled":[25],"by":[26],"so-called":[28],"regulatory":[29,33],"genome":[30],"encoding":[31],"networks:":[34],"several":[35],"Transcription":[36,109],"Factors":[37],"bind":[38],"to":[39,44,90,144,188],"precise":[40],"DNA":[41],"regions,":[42],"so":[43],"perform":[45],"in":[46,58,75,100,104,184],"cooperative":[48],"manner":[49],"specific":[51],"regulation":[52],"for":[54,124],"nearby":[55],"genes.":[56],"The":[57],"silico":[59],"prediction":[60],"these":[62],"binding":[63,98],"sites":[64,99],"still":[66],"an":[67,165],"open":[68],"problem,":[69],"notwithstanding":[70],"continuous":[71],"progress":[72],"activity":[74],"last":[77],"two":[78],"decades.":[79],"In":[80],"paper,":[82],"we":[83],"describe":[84],"new":[86,131],"efficient":[87],"combinatorial":[88],"approach":[89,132],"problem":[92],"detecting":[94],"sets":[95,157],"cooperating":[97],"promoter":[101],"sequences,":[102],"input":[105],"database":[107],"Factor":[110],"Binding":[111],"Sites":[112],"encoded":[113],"as":[114],"Position":[115],"Weight":[116],"Matrices.":[117],"We":[118],"present":[119],"CMStalker,":[120],"software":[122],"tool":[123],"composite":[125],"motif":[126],"discovery":[127],"which":[128],"embodies":[129],"that":[133],"combines":[134],"constraint":[136],"satisfaction":[137],"formulation":[138],"with":[139,154],"parameter":[141],"relaxation":[142],"technique":[143],"explore":[145],"efficiently":[146],"space":[148],"possible":[150],"solutions.":[151],"Extensive":[152],"experiments":[153],"12":[155],"data":[156],"11":[159],"state-of-the-art":[160],"tools":[161],"are":[162],"reported,":[163],"showing":[164],"average":[166],"value":[167,176],"correlation":[170],"coefficient":[171],"0.54":[173],"(against":[174],"0.41":[177],"closest":[180],"competitor).":[181],"This":[182],"improvements":[183],"output":[185],"quality":[186],"due":[187],"CMStalker":[189],"statistically":[191],"significant.":[192]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
