{"id":"https://openalex.org/W4205136918","doi":"https://doi.org/10.1109/tcbb.2021.3139634","title":"Differential Gene Expression Prediction by Ensemble Deep Networks on Histone Modification Data","display_name":"Differential Gene Expression Prediction by Ensemble Deep Networks on Histone Modification Data","publication_year":2021,"publication_date":"2021-12-31","ids":{"openalex":"https://openalex.org/W4205136918","doi":"https://doi.org/10.1109/tcbb.2021.3139634","pmid":"https://pubmed.ncbi.nlm.nih.gov/34971538"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3139634","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3139634","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Zimo Huang","orcid":"https://orcid.org/0000-0003-1027-880X"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zimo Huang","raw_affiliation_strings":["School of Software, Shandong University, Jinan, Shandong, China"],"raw_orcid":"https://orcid.org/0000-0003-1027-880X","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jun Wang","orcid":"https://orcid.org/0000-0002-5890-0365"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Wang","raw_affiliation_strings":["Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University, Jinan, Shandong, China"],"raw_orcid":"https://orcid.org/0000-0002-5890-0365","affiliations":[{"raw_affiliation_string":"Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhongmin Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhongmin Yan","raw_affiliation_strings":["School of Software, Shandong University, Jinan, Shandong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lin Wan","orcid":"https://orcid.org/0000-0003-2627-8775"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Wan","raw_affiliation_strings":["School of Software, Shandong University, Jinan, Shandong, China"],"raw_orcid":"https://orcid.org/0000-0003-2627-8775","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"last","author":{"id":null,"display_name":"Maozu Guo","orcid":"https://orcid.org/0000-0001-6228-6276"},"institutions":[{"id":"https://openalex.org/I62853816","display_name":"Beijing University of Civil Engineering and Architecture","ror":"https://ror.org/02yj0p855","country_code":"CN","type":"education","lineage":["https://openalex.org/I62853816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Maozu Guo","raw_affiliation_strings":["College of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-6228-6276","affiliations":[{"raw_affiliation_string":"College of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China","institution_ids":["https://openalex.org/I62853816"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1327489,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"20","issue":"1","first_page":"340","last_page":"351"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.38109999895095825,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.38109999895095825,"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":0.21860000491142273,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.11969999969005585,"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/feature","display_name":"Feature (linguistics)","score":0.5701000094413757},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5217999815940857},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4837000072002411},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4787999987602234},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.47530001401901245},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.4413999915122986},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.4235999882221222},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.40610000491142273},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.3515999913215637}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.586899995803833},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5740000009536743},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5701000094413757},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5217999815940857},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4837000072002411},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4787999987602234},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.47530001401901245},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.4413999915122986},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.42809998989105225},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.4235999882221222},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4099999964237213},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.40610000491142273},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.3515999913215637},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34850001335144043},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.3353999853134155},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3303000032901764},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3301999866962433},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.32820001244544983},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3280999958515167},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.3199000060558319},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.3163999915122986},{"id":"https://openalex.org/C156273044","wikidata":"https://www.wikidata.org/wiki/Q4913766","display_name":"Bin","level":2,"score":0.31369999051094055},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.303600013256073},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.30059999227523804},{"id":"https://openalex.org/C155512373","wikidata":"https://www.wikidata.org/wiki/Q287450","display_name":"Residual","level":2,"score":0.29100000858306885},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2840000092983246},{"id":"https://openalex.org/C119898033","wikidata":"https://www.wikidata.org/wiki/Q3433888","display_name":"Ensemble forecasting","level":2,"score":0.2825999855995178},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.27810001373291016},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27160000801086426},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.27129998803138733},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.2637999951839447},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.2619999945163727},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.25540000200271606}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3139634","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3139634","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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:34971538","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34971538","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":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6836859050","display_name":null,"funder_award_id":"62031003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8056994637","display_name":"\u764c\u75c7\u8de8\u6027\u72b6\u534f\u540c\u9a71\u52a8\u901a\u8def\u8bc6\u522b\u7814\u7a76","funder_award_id":"62072380","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W630889805","https://openalex.org/W1565746575","https://openalex.org/W2001004762","https://openalex.org/W2002698073","https://openalex.org/W2017840637","https://openalex.org/W2017952818","https://openalex.org/W2026343134","https://openalex.org/W2048186818","https://openalex.org/W2056415893","https://openalex.org/W2064675550","https://openalex.org/W2069717852","https://openalex.org/W2076154138","https://openalex.org/W2089689396","https://openalex.org/W2089865437","https://openalex.org/W2096083625","https://openalex.org/W2112796928","https://openalex.org/W2122609635","https://openalex.org/W2123564569","https://openalex.org/W2125805216","https://openalex.org/W2127081697","https://openalex.org/W2133381800","https://openalex.org/W2134087142","https://openalex.org/W2142205294","https://openalex.org/W2143658931","https://openalex.org/W2147524392","https://openalex.org/W2154431984","https://openalex.org/W2161435642","https://openalex.org/W2164116506","https://openalex.org/W2194775991","https://openalex.org/W2259938310","https://openalex.org/W2479945688","https://openalex.org/W2509725501","https://openalex.org/W2551929191","https://openalex.org/W2748881498","https://openalex.org/W2749182114","https://openalex.org/W2784154277","https://openalex.org/W2789926271","https://openalex.org/W2804331675","https://openalex.org/W2911658010","https://openalex.org/W2963582649","https://openalex.org/W2969086705","https://openalex.org/W2990720125","https://openalex.org/W3076243292","https://openalex.org/W3096958321","https://openalex.org/W3127152040","https://openalex.org/W3159102436","https://openalex.org/W6631190155","https://openalex.org/W6679434410","https://openalex.org/W6742092700"],"related_works":[],"abstract_inverted_index":{"Predicting":[0],"differential":[1,22,48,213],"gene":[2,23,214],"expression":[3,49,215],"(DGE)":[4],"from":[5,193],"Histone":[6],"modifications":[7],"(HM)":[8],"signal":[9,118,139,154],"is":[10],"crucial":[11],"to":[12,32,46,75,143,181],"understand":[13],"how":[14],"HM":[15,34,71,117,138],"controls":[16],"cell":[17,53,56,203],"functional":[18],"heterogeneity":[19],"through":[20],"influencing":[21],"regulation.":[24],"Most":[25],"existing":[26],"prediction":[27,88,179],"methods":[28],"use":[29],"fixed-length":[30],"bins":[31,39],"represent":[33],"signals":[35],"and":[36,73,124,147,156],"transmit":[37],"these":[38,91],"into":[40],"a":[41,171],"single":[42,52,82],"machine":[43],"learning":[44,83,134],"model":[45,84,176],"predict":[47],"genes":[50],"of":[51,68,81,149,160,185],"type":[54,57,204],"or":[55],"pair.":[58],"However,":[59],"the":[60,66,69,79,87,126,145,158,164,183,190,194,209],"inappropriate":[61],"bin":[62,122],"length":[63],"may":[64,85],"cause":[65],"splitting":[67],"important":[70],"segment":[72],"lead":[74],"information":[76,151],"loss.":[77],"Furthermore,":[78],"bias":[80,159],"limit":[86],"accuracy.":[89],"Considering":[90],"problems,":[92],"in":[93,152],"this":[94],"paper,":[95],"we":[96,168],"proposes":[97],"an":[98],"Ensemble":[99,132],"deep":[100],"neural":[101],"networks":[102],"framework":[103],"for":[104,129,201,212],"predicting":[105],"Differential":[106],"Gene":[107],"Expression":[108],"(EnDGE).":[109],"EnDGE":[110,206],"employs":[111],"different":[112,121,137],"feature":[113,127,166,186],"extractors":[114],"on":[115,189],"input":[116],"data":[119],"with":[120,136,177],"lengths":[123],"fuses":[125],"vectors":[128],"DGE":[130],"prediction.":[131,216],"multiple":[133],"models":[135],"cutting":[140],"strategies":[141],"helps":[142],"keep":[144],"integrity":[146],"consistency":[148],"genetic":[150],"each":[153],"segment,":[155],"offset":[157],"individual":[161],"models.":[162],"Besides":[163],"popular":[165],"extractors,":[167],"also":[169],"propose":[170],"new":[172],"Residual":[173],"Network":[174],"based":[175],"higher":[178],"accuracy":[180],"increase":[182],"diversity":[184],"extractors.":[187],"Experiments":[188],"real":[191],"datasets":[192],"Roadmap":[195],"Epigenome":[196],"Project":[197],"(REMC)":[198],"show":[199],"that":[200],"all":[202],"pairs,":[205],"significantly":[207],"outperforms":[208],"state-of-the-art":[210],"baselines":[211]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2022-01-26T00:00:00"}
