{"id":"https://openalex.org/W1968083284","doi":"https://doi.org/10.1186/1471-2105-9-547","title":"Prediction of regulatory elements in mammalian genomes using chromatin signatures","display_name":"Prediction of regulatory elements in mammalian genomes using chromatin signatures","publication_year":2008,"publication_date":"2008-12-01","ids":{"openalex":"https://openalex.org/W1968083284","doi":"https://doi.org/10.1186/1471-2105-9-547","mag":"1968083284","pmid":"https://pubmed.ncbi.nlm.nih.gov/19094206","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2657164"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-547","doi":"https://doi.org/10.1186/1471-2105-9-547","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-547","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-547","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,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-547","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060918471","display_name":"Kyoung\u2010Jae Won","orcid":"https://orcid.org/0000-0002-2924-9630","observed_orcids":["https://orcid.org/0000-0002-2924-9630"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyoung-Jae Won","raw_affiliation_strings":["Dept of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0359, USA. kwon@ucsd.edu","Department of Chemistry & Biochemistry, University of California San Diego,La Jolla,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0359, USA. kwon@ucsd.edu","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Chemistry & Biochemistry, University of California San Diego,La Jolla,USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047970786","display_name":"Iouri Chepelev","orcid":"https://orcid.org/0000-0002-2121-8805","observed_orcids":["https://orcid.org/0000-0002-2121-8805"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Iouri Chepelev","raw_affiliation_strings":["Dept of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0359, USA","Department of Chemistry & Biochemistry, University of California San Diego,La Jolla,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0359, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Chemistry & Biochemistry, University of California San Diego,La Jolla,USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073855965","display_name":"Bing Ren","orcid":"https://orcid.org/0000-0002-5435-1127","observed_orcids":["https://orcid.org/0000-0002-5435-1127","https://orcid.org/0009-0002-3454-085X","https://orcid.org/0009-0004-0708-2069"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210150094","display_name":"Ludwig Cancer Research","ror":"https://ror.org/05qdwtz81","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210150094"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bing Ren","raw_affiliation_strings":["Ludwig Institute for Cancer Research, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0653, USA","Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ludwig Institute for Cancer Research, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0653, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I4210150094"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100392035","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-6346-2216","observed_orcids":["https://orcid.org/0000-0002-6346-2216"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Wang","raw_affiliation_strings":["Dept of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0359, USA","Department of Chemistry & Biochemistry, University of California San Diego,La Jolla,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0359, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Chemistry & Biochemistry, University of California San Diego,La Jolla,USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100392035"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":3.1505,"has_fulltext":true,"cited_by_count":94,"citation_normalized_percentile":{"value":0.92025584,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"547","last_page":"547"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9990000128746033,"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":0.9990000128746033,"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":0.00019999999494757503,"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/T12820","display_name":"Chromatin Remodeling and Cancer","score":9.999999747378752e-05,"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/promoter-recognition","display_name":"promoter identification","score":0.875},{"id":"https://openalex.org/keywords/enhancer-prediction","display_name":"enhancer prediction","score":0.9990000128746033},{"id":"https://openalex.org/keywords/chromatin-signatures","display_name":"chromatin signatures","score":0.7879999876022339},{"id":"https://openalex.org/keywords/histone-modifications","display_name":"histone modifications","score":0.9739999771118164},{"id":"https://openalex.org/keywords/hidden-markov-models","display_name":"hidden Markov models","score":0.9509999752044678},{"id":"https://openalex.org/keywords/simulated-annealing","display_name":"simulated annealing","score":0.9509999752044678},{"id":"https://openalex.org/keywords/chip-seq","display_name":"ChIP-seq","score":0.7369999885559082},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.6740000247955322},{"id":"https://openalex.org/keywords/mouse-cell-lines","display_name":"mouse cell lines","score":0.7429999709129333},{"id":"https://openalex.org/keywords/human-genome","display_name":"human genome","score":0.4429999887943268}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.819490373134613},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.762639045715332},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7148135304450989},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.666439950466156},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.622437596321106},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.6132856011390686},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.6120898127555847},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5980038642883301},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5820066928863525},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5814084410667419},{"id":"https://openalex.org/C67258246","wikidata":"https://www.wikidata.org/wiki/Q5065897","display_name":"ChIA-PET","level":5,"score":0.5756974816322327},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.5172984600067139},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4792789816856384},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45812663435935974},{"id":"https://openalex.org/C2780914512","wikidata":"https://www.wikidata.org/wiki/Q25323943","display_name":"H3K4me3","level":5,"score":0.4276901185512543},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3934362530708313},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3637459874153137},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27605581283569336},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.21655422449111938},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18929046392440796}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-547","doi":"https://doi.org/10.1186/1471-2105-9-547","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-547","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-547","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,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"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":"pmh:oai:pubmedcentral.nih.gov:2657164","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2657164","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmid:19094206","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19094206","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,"listed_in":[],"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":"Journal Article"},{"id":"pmh:oai:doaj.org/article:86f3f3354a3f4471aeb63521f2a4ddda","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/86f3f3354a3f4471aeb63521f2a4ddda","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,"listed_in":[],"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 9, Iss 1, p 547 (2008)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-547","doi":"https://doi.org/10.1186/1471-2105-9-547","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-547","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-547","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,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"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":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1968083284.pdf","grobid_xml":"https://content.openalex.org/works/W1968083284.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W2005281324","https://openalex.org/W2015416439","https://openalex.org/W2017840637","https://openalex.org/W2023700110","https://openalex.org/W2024060531","https://openalex.org/W2026882865","https://openalex.org/W2057692691","https://openalex.org/W2065173155","https://openalex.org/W2077132193","https://openalex.org/W2085442947","https://openalex.org/W2095617232","https://openalex.org/W2100990361","https://openalex.org/W2106004801","https://openalex.org/W2112717966","https://openalex.org/W2118628540","https://openalex.org/W2125838338","https://openalex.org/W2128016314","https://openalex.org/W2128937741","https://openalex.org/W2129061533","https://openalex.org/W2129795133","https://openalex.org/W2134087142","https://openalex.org/W2150009446","https://openalex.org/W2168602111","https://openalex.org/W3214380909","https://openalex.org/W4232420716","https://openalex.org/W4245668478","https://openalex.org/W4248318091"],"related_works":["https://openalex.org/W2941445363","https://openalex.org/W2128817132","https://openalex.org/W2168602111","https://openalex.org/W1950782631","https://openalex.org/W2118671962","https://openalex.org/W7096157757","https://openalex.org/W2006918465","https://openalex.org/W2039098454","https://openalex.org/W2949326540","https://openalex.org/W4391012465"],"abstract_inverted_index":{"BACKGROUND:":[0],"Recent":[1],"genomic":[2],"scale":[3],"survey":[4],"of":[5,31,41,48,149,166,208,222,234,262],"epigenetic":[6],"states":[7],"in":[8,35,45,127,190,246],"the":[9,36,46,105,117,128,140,145,155,158,163,171,178,186,206,215,232],"mammalian":[10],"genomes":[11],"has":[12],"shown":[13],"that":[14,182,198,214],"promoters":[15,88,111,192,257],"and":[16,51,89,112,114,144,176,193,219,251,255],"enhancers":[17,90],"are":[18,75],"correlated":[19],"with":[20,154,258],"distinct":[21],"chromatin":[22,42,55,95],"signatures,":[23],"providing":[24],"a":[25,82,132],"pragmatic":[26],"way":[27],"for":[28,109,139],"systematic":[29],"mapping":[30,191],"these":[32,73],"regulatory":[33,63],"elements":[34],"genome.":[37,130],"With":[38],"rapid":[39],"accumulation":[40],"modification":[43,96,107],"profiles":[44],"genome":[47,242],"various":[49],"organisms":[50],"cell":[52,249],"types,":[53],"this":[54],"based":[56,91],"approach":[57],"promises":[58],"to":[59,68,86,120,240],"uncover":[60],"many":[61],"new":[62],"elements,":[64],"but":[65],"computational":[66],"methods":[67],"effectively":[69],"extract":[70],"information":[71,224],"from":[72,170,225],"datasets":[74],"still":[76],"limited.":[77],"RESULTS:":[78],"We":[79,98,195],"present":[80],"here":[81],"supervised":[83],"learning":[84],"method":[85,160,184,189],"predict":[87],"on":[92,104],"their":[93],"unique":[94],"signatures.":[97],"trained":[99,118],"Hidden":[100],"Markov":[101],"models":[102],"(HMMs)":[103],"histone":[106,150,167,201,227],"data":[108,245],"known":[110],"enhancers,":[113],"then":[115],"used":[116],"HMMs":[119],"identify":[121],"promoter":[122],"or":[123],"enhancer":[124],"like":[125],"sequences":[126],"human":[129],"Using":[131],"simulated":[133],"annealing":[134],"(SA)":[135],"procedure,":[136],"we":[137,237],"searched":[138],"most":[141],"informative":[142],"combination":[143],"optimal":[146],"window":[147],"size":[148],"marks.":[151,228],"CONCLUSION:":[152],"Compared":[153],"previous":[156,187],"methods,":[157],"HMM":[159,216],"can":[161,203],"capture":[162],"complex":[164],"patterns":[165],"modifications":[168],"particularly":[169],"weak":[172],"signals.":[173],"Cross":[174],"validation":[175],"scanning":[177],"ENCODE":[179],"regions":[180],"showed":[181,197],"our":[183,209,235],"outperforms":[185],"profile-based":[188],"enhancers.":[194],"also":[196],"including":[199],"more":[200,263],"marks":[202],"further":[204,230],"boost":[205],"performance":[207],"method.":[210],"This":[211],"observation":[212],"suggests":[213],"is":[217,220,268],"robust":[218],"capable":[221],"integrating":[223],"multiple":[226],"To":[229],"demonstrate":[231],"usefulness":[233],"method,":[236],"applied":[238],"it":[239],"analyzing":[241],"wide":[243],"ChIP-Seq":[244],"three":[247],"mouse":[248],"lines":[250],"correctly":[252],"predicted":[253],"active":[254],"inactive":[256],"positive":[259],"predictive":[260],"values":[261],"than":[264],"80%.":[265],"The":[266],"software":[267],"available":[269],"at":[270],"http://http:/nash.ucsd.edu/chromatin.tar.gz.":[271]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":7}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}