{"id":"https://openalex.org/W2321308395","doi":"https://doi.org/10.1093/bioinformatics/btw186","title":"iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework","display_name":"iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework","publication_year":2016,"publication_date":"2016-04-08","ids":{"openalex":"https://openalex.org/W2321308395","doi":"https://doi.org/10.1093/bioinformatics/btw186","mag":"2321308395"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw186","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw186","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065663815","display_name":"Bin Liu","orcid":"https://orcid.org/0000-0002-9687-7493"},"institutions":[{"id":"https://openalex.org/I4210098239","display_name":"The Gordon Life Science Institute","ror":"https://ror.org/0135ffj82","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098239"]},{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Bin Liu","raw_affiliation_strings":["1 School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China","2 Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China","3 Gordon Life Science Institute, Belmont, MA 02478, USA"],"affiliations":[{"raw_affiliation_string":"1 School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"2 Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"3 Gordon Life Science Institute, Belmont, MA 02478, USA","institution_ids":["https://openalex.org/I4210098239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067991380","display_name":"Long Ren","orcid":"https://orcid.org/0000-0001-6757-7195"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ren Long","raw_affiliation_strings":["1 School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China"],"affiliations":[{"raw_affiliation_string":"1 School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113500576","display_name":"Kuo\u2010Chen Chou","orcid":null},"institutions":[{"id":"https://openalex.org/I4210098239","display_name":"The Gordon Life Science Institute","ror":"https://ror.org/0135ffj82","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098239"]},{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]}],"countries":["SA","US"],"is_corresponding":false,"raw_author_name":"Kuo-Chen Chou","raw_affiliation_strings":["3 Gordon Life Science Institute, Belmont, MA 02478, USA","4 Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"3 Gordon Life Science Institute, Belmont, MA 02478, USA","institution_ids":["https://openalex.org/I4210098239"]},{"raw_affiliation_string":"4 Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I185163786"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065663815"],"corresponding_institution_ids":["https://openalex.org/I204983213","https://openalex.org/I4210098239"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":24.5092,"has_fulltext":false,"cited_by_count":211,"citation_normalized_percentile":{"value":0.99701029,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"32","issue":"16","first_page":"2411","last_page":"2418"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T12254","display_name":"Machine Learning in Bioinformatics","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9993000030517578,"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":0.9979000091552734,"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/genome","display_name":"Genome","score":0.6506072878837585},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5796922445297241},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49738290905952454},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46806493401527405},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.4303187131881714},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3511672019958496},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31886324286460876}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6506072878837585},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5796922445297241},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49738290905952454},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46806493401527405},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.4303187131881714},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3511672019958496},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31886324286460876},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw186","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw186","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/16/2411","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/16/2411","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.699999988079071,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":75,"referenced_works":["https://openalex.org/W1494484168","https://openalex.org/W1561712938","https://openalex.org/W1612034467","https://openalex.org/W1807324513","https://openalex.org/W1918744929","https://openalex.org/W1943237984","https://openalex.org/W1966991202","https://openalex.org/W1968361401","https://openalex.org/W1969691479","https://openalex.org/W1971057981","https://openalex.org/W1977927254","https://openalex.org/W1982112888","https://openalex.org/W1983808106","https://openalex.org/W1990678622","https://openalex.org/W1991141438","https://openalex.org/W1998064689","https://openalex.org/W2001168095","https://openalex.org/W2004132756","https://openalex.org/W2007794469","https://openalex.org/W2009470087","https://openalex.org/W2010211703","https://openalex.org/W2010979687","https://openalex.org/W2020969907","https://openalex.org/W2022965734","https://openalex.org/W2026463883","https://openalex.org/W2026666393","https://openalex.org/W2030650052","https://openalex.org/W2031085703","https://openalex.org/W2034070267","https://openalex.org/W2036956828","https://openalex.org/W2042491847","https://openalex.org/W2046842005","https://openalex.org/W2047187013","https://openalex.org/W2053963319","https://openalex.org/W2056108729","https://openalex.org/W2063122849","https://openalex.org/W2070159701","https://openalex.org/W2071834506","https://openalex.org/W2082436128","https://openalex.org/W2090561245","https://openalex.org/W2093645389","https://openalex.org/W2098028543","https://openalex.org/W2099665470","https://openalex.org/W2109268993","https://openalex.org/W2114024619","https://openalex.org/W2114973325","https://openalex.org/W2118467383","https://openalex.org/W2118729365","https://openalex.org/W2120026469","https://openalex.org/W2121607820","https://openalex.org/W2123525093","https://openalex.org/W2124266758","https://openalex.org/W2138045300","https://openalex.org/W2141259072","https://openalex.org/W2143635696","https://openalex.org/W2145957695","https://openalex.org/W2149118429","https://openalex.org/W2150047146","https://openalex.org/W2151180344","https://openalex.org/W2156192813","https://openalex.org/W2156678798","https://openalex.org/W2161621183","https://openalex.org/W2162787150","https://openalex.org/W2177510297","https://openalex.org/W2205505631","https://openalex.org/W2209329607","https://openalex.org/W2217901696","https://openalex.org/W2270702445","https://openalex.org/W2278741011","https://openalex.org/W2313411748","https://openalex.org/W2340970647","https://openalex.org/W2911964244","https://openalex.org/W4232096545","https://openalex.org/W6680166665","https://openalex.org/W6681680184"],"related_works":["https://openalex.org/W2382566571","https://openalex.org/W2349321798","https://openalex.org/W2366686860","https://openalex.org/W2350859087","https://openalex.org/W2387118502","https://openalex.org/W4233775131","https://openalex.org/W2158418060","https://openalex.org/W2987420353","https://openalex.org/W1491897707","https://openalex.org/W2034625591"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Regulatory":[2],"DNA":[3],"elements":[4],"are":[5,194],"associated":[6],"with":[7],"DNase":[8],"I":[9],"hypersensitive":[10],"sites":[11],"(DHSs).":[12],"Accordingly,":[13],"identification":[14],"of":[15,27,38,53,85,128],"DHSs":[16],"will":[17,175],"provide":[18],"useful":[19,179],"insights":[20],"for":[21,49,135,149,183],"in-depth":[22],"investigation":[23],"into":[24,69],"the":[25,36,51,81,86,108,113,126,143,163,168],"function":[26],"noncoding":[28],"genomic":[29],"regions.":[30],"Results:":[31],"In":[32],"this":[33],"study,":[34],"using":[35],"strategy":[37],"ensemble":[39,71],"learning":[40],"framework,":[41],"we":[42],"proposed":[43],"a":[44,132,177],"new":[45,109],"predictor":[46,110,146],"called":[47],"iDHS-EL":[48,136,174],"identifying":[50,150],"location":[52],"DHS":[54],"in":[55,117],"human":[56],"genome.":[57],"It":[58,103],"was":[59],"formed":[60],"by":[61,153],"fusing":[62],"three":[63,74,82],"individual":[64],"Random":[65],"Forest":[66],"(RF)":[67],"classifiers":[68],"an":[70],"predictor.":[72],"The":[73],"RF":[75],"operators":[76],"were":[77],"respectively":[78],"based":[79],"on":[80],"special":[83],"modes":[84],"general":[87],"pseudo":[88,100],"nucleotide":[89],"composition":[90],"(PseKNC):":[91],"(i)":[92],"kmer,":[93],"(ii)":[94],"reverse":[95],"complement":[96],"kmer":[97],"and":[98,120,123,152],"(iii)":[99],"dinucleotide":[101],"composition.":[102],"has":[104],"been":[105],"demonstrated":[106],"that":[107,173],"remarkably":[111],"outperforms":[112],"relevant":[114],"state-of-the-art":[115],"methods":[116],"both":[118],"accuracy":[119],"stability.":[121],"Availability":[122],"Implementation:":[124],"For":[125],"convenience":[127],"most":[129],"experimental":[130],"scientists,":[131],"web":[133],"server":[134],"is":[137,142],"established":[138,148],"at":[139,196],"http://bioinformatics.hitsz.edu.cn/iDHS-EL,":[140],"which":[141,154],"first":[144],"web-server":[145],"ever":[147],"DHSs,":[151],"users":[155],"can":[156],"easily":[157],"get":[158],"their":[159],"desired":[160],"results":[161],"without":[162],"need":[164],"to":[165],"go":[166],"through":[167],"mathematical":[169],"details.":[170],"We":[171],"anticipate":[172],"become":[176],"very":[178],"high":[180],"throughput":[181],"tool":[182],"genome":[184],"analysis.":[185],"Contact:":[186],"bliu@gordonlifescience.org":[187],"or":[188],"bliu@insun.hit.edu.cn":[189],"Supplementary":[190,192],"information:":[191],"data":[193],"available":[195],"Bioinformatics":[197],"online.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":27},{"year":2019,"cited_by_count":26},{"year":2018,"cited_by_count":49},{"year":2017,"cited_by_count":50},{"year":2016,"cited_by_count":22}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
