{"id":"https://openalex.org/W2127284131","doi":"https://doi.org/10.1186/1471-2105-7-279","title":"Optimized mixed Markov models for motif identification","display_name":"Optimized mixed Markov models for motif identification","publication_year":2006,"publication_date":"2006-06-02","ids":{"openalex":"https://openalex.org/W2127284131","doi":"https://doi.org/10.1186/1471-2105-7-279","mag":"2127284131","pmid":"https://pubmed.ncbi.nlm.nih.gov/16749929"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-279","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-279","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-279","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-279","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003273569","display_name":"Weichun Huang","orcid":"https://orcid.org/0000-0002-9149-0599"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]},{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]},{"id":"https://openalex.org/I4210153043","display_name":"Duke University Hospital","ror":"https://ror.org/04bct7p84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876","https://openalex.org/I4210144876","https://openalex.org/I4210153043"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weichun Huang","raw_affiliation_strings":["Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA. huang6@niehs.nih.gov","Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, USA","Bioinformatics Research Center, North Carolina State University, Raleigh, USA","Institute for Genome Sciences & Policy, Duke University Medical Center, Durham, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA. huang6@niehs.nih.gov","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, USA","institution_ids":["https://openalex.org/I1299303238"]},{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Institute for Genome Sciences & Policy, Duke University Medical Center, Durham, USA","institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210153043","https://openalex.org/I4210126298"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036278452","display_name":"David M. Umbach","orcid":"https://orcid.org/0000-0002-7142-2812"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210095140","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210095140"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David M Umbach","raw_affiliation_strings":["Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, NC, 27709, USA","Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, NC, 27709, USA","institution_ids":["https://openalex.org/I4210095140","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, USA","institution_ids":["https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000077668","display_name":"Uwe Ohler","orcid":"https://orcid.org/0000-0002-0881-3116"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]},{"id":"https://openalex.org/I4210153043","display_name":"Duke University Hospital","ror":"https://ror.org/04bct7p84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876","https://openalex.org/I4210144876","https://openalex.org/I4210153043"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Uwe Ohler","raw_affiliation_strings":["Institute for Genome Sciences & Policy, Duke University Medical Center, Durham, NC, 27708, USA","Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Genome Sciences & Policy, Duke University Medical Center, Durham, NC, 27708, USA","institution_ids":["https://openalex.org/I4210153043","https://openalex.org/I4210126298"]},{"raw_affiliation_string":"Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, USA","institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210153043","https://openalex.org/I4210126298"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100408451","display_name":"Leping Li","orcid":"https://orcid.org/0000-0003-4208-0259"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210095140","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210095140"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leping Li","raw_affiliation_strings":["Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, NC, 27709, USA","Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, NC, 27709, USA","institution_ids":["https://openalex.org/I4210095140","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, USA","institution_ids":["https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.091,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.75742281,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"7","issue":"1","first_page":"279","last_page":"279"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9567999839782715,"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":0.9567999839782715,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.013700000010430813,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.007000000216066837,"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/computer-science","display_name":"Computer science","score":0.719788134098053},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.7043287754058838},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.6488460302352905},{"id":"https://openalex.org/keywords/maximum-entropy-markov-model","display_name":"Maximum-entropy Markov model","score":0.6443424820899963},{"id":"https://openalex.org/keywords/markov-model","display_name":"Markov model","score":0.6371846795082092},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5841537117958069},{"id":"https://openalex.org/keywords/model-selection","display_name":"Model selection","score":0.48242124915122986},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4572067856788635},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4483349919319153},{"id":"https://openalex.org/keywords/principle-of-maximum-entropy","display_name":"Principle of maximum entropy","score":0.42162764072418213},{"id":"https://openalex.org/keywords/entropy","display_name":"Entropy (arrow of time)","score":0.41826802492141724},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40822333097457886},{"id":"https://openalex.org/keywords/variable-order-markov-model","display_name":"Variable-order Markov model","score":0.351305216550827},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3467786908149719}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.719788134098053},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7043287754058838},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.6488460302352905},{"id":"https://openalex.org/C196956702","wikidata":"https://www.wikidata.org/wiki/Q6795829","display_name":"Maximum-entropy Markov model","level":5,"score":0.6443424820899963},{"id":"https://openalex.org/C163836022","wikidata":"https://www.wikidata.org/wiki/Q6771326","display_name":"Markov model","level":3,"score":0.6371846795082092},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5841537117958069},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.48242124915122986},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4572067856788635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4483349919319153},{"id":"https://openalex.org/C9679016","wikidata":"https://www.wikidata.org/wiki/Q1417473","display_name":"Principle of maximum entropy","level":2,"score":0.42162764072418213},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.41826802492141724},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40822333097457886},{"id":"https://openalex.org/C54907487","wikidata":"https://www.wikidata.org/wiki/Q7915688","display_name":"Variable-order Markov model","level":4,"score":0.351305216550827},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3467786908149719},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-7-279","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-279","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-279","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16749929","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16749929","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:fe257ce19c154a0f86ef553111433b6e","is_oa":true,"landing_page_url":"https://doaj.org/article/fe257ce19c154a0f86ef553111433b6e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 7, Iss 1, p 279 (2006)","raw_type":"article"},{"id":"pmh:oai:edoc.mdc-berlin.de:12597","is_oa":false,"landing_page_url":"https://edoc.mdc-berlin.de/12597/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1534070","is_oa":true,"landing_page_url":"http://doi.org/10.1186/1471-2105-7-279","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-279","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-279","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-279","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2127284131.pdf","grobid_xml":"https://content.openalex.org/works/W2127284131.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1981019623","https://openalex.org/W2006101370","https://openalex.org/W2011485152","https://openalex.org/W2015622114","https://openalex.org/W2032548898","https://openalex.org/W2032870665","https://openalex.org/W2034691490","https://openalex.org/W2035564383","https://openalex.org/W2040616538","https://openalex.org/W2048695079","https://openalex.org/W2050294416","https://openalex.org/W2054624670","https://openalex.org/W2055660520","https://openalex.org/W2056967728","https://openalex.org/W2064879068","https://openalex.org/W2071753700","https://openalex.org/W2074703985","https://openalex.org/W2079450159","https://openalex.org/W2085442947","https://openalex.org/W2094036688","https://openalex.org/W2097706568","https://openalex.org/W2100558818","https://openalex.org/W2101025813","https://openalex.org/W2107787782","https://openalex.org/W2109553965","https://openalex.org/W2110863141","https://openalex.org/W2118600301","https://openalex.org/W2124195715","https://openalex.org/W2131000278","https://openalex.org/W2133147430","https://openalex.org/W2141936300","https://openalex.org/W2142635246","https://openalex.org/W2142890842","https://openalex.org/W2146393977","https://openalex.org/W2148381206","https://openalex.org/W2154514071","https://openalex.org/W2158266834","https://openalex.org/W2166187656","https://openalex.org/W2166429927","https://openalex.org/W2166711485","https://openalex.org/W2168175751","https://openalex.org/W2433480171","https://openalex.org/W4247292500"],"related_works":["https://openalex.org/W2382132287","https://openalex.org/W2130519334","https://openalex.org/W2161328464","https://openalex.org/W1985664346","https://openalex.org/W3113307220","https://openalex.org/W2379333870","https://openalex.org/W1542903750","https://openalex.org/W3164302780","https://openalex.org/W2363310627","https://openalex.org/W2118728396"],"abstract_inverted_index":{"BACKGROUND:":[0],"Identifying":[1],"functional":[2],"elements,":[3],"such":[4],"as":[5],"transcriptional":[6],"factor":[7],"binding":[8],"sites,":[9],"is":[10,139,154,183],"a":[11,21,35,178],"fundamental":[12],"step":[13],"in":[14,120],"reconstructing":[15],"gene":[16],"regulatory":[17],"networks":[18],"and":[19,37,46,86,102,107,186,188],"remains":[20],"challenging":[22],"issue,":[23],"largely":[24],"due":[25],"to":[26,49,115,136,169],"limited":[27],"availability":[28],"of":[29,52,122,127,149,163],"training":[30,90,128],"samples.":[31],"RESULTS:":[32],"We":[33],"introduce":[34],"novel":[36],"flexible":[38],"model,":[39],"the":[40,69,79,93,116,140,150,170],"Optimized":[41],"Mixture":[42],"Markov":[43,83,164],"model":[44,53,75,182],"(OMiMa),":[45],"related":[47],"methods":[48,119,172],"allow":[50],"adjustment":[51],"complexity":[54],"for":[55,173],"different":[56],"motifs.":[57],"In":[58],"comparison":[59],"with":[60],"other":[61,117,197],"leading":[62,118,198],"methods,":[63],"OMiMa":[64,73,87,134,153],"can":[65,189],"incorporate":[66],"more":[67],"than":[68,78,92],"NNSplice's":[70],"pairwise":[71],"dependencies;":[72],"avoids":[74],"over-fitting":[76],"better":[77],"Permuted":[80],"Variable":[81],"Length":[82],"Model":[84,96],"(PVLMM);":[85],"requires":[88],"smaller":[89],"samples":[91],"Maximum":[94],"Entropy":[95],"(MEM).":[97],"Testing":[98],"on":[99],"both":[100],"simulated":[101],"actual":[103],"data":[104,129],"(regulatory":[105],"cis-elements":[106],"splice":[108],"sites),":[109],"we":[110],"found":[111],"OMiMa's":[112],"performance":[113],"superior":[114],"terms":[121],"prediction":[123,191],"accuracy,":[124],"required":[125],"size":[126],"or":[130],"computational":[131,194],"time.":[132],"Our":[133,160,181],"system,":[135],"our":[137],"knowledge,":[138],"only":[141],"motif":[142],"finding":[143],"tool":[144],"that":[145],"incorporates":[146],"automatic":[147],"selection":[148],"best":[151],"model.":[152],"freely":[155],"available":[156],"at":[157],"1.":[158],"CONCLUSION:":[159],"optimized":[161],"mixture":[162],"models":[165],"represents":[166],"an":[167],"alternative":[168],"existing":[171],"modeling":[174],"dependent":[175],"structures":[176],"within":[177],"biological":[179],"motif.":[180],"conceptually":[184],"simple":[185],"effective,":[187],"improve":[190],"accuracy":[192],"and/or":[193],"speed":[195],"over":[196],"methods.":[199]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
