{"id":"https://openalex.org/W3014408508","doi":"https://doi.org/10.1109/bibm.2017.8217912","title":"Higher-order partial least squares for predicting gene expression levels from chromatin states","display_name":"Higher-order partial least squares for predicting gene expression levels from chromatin states","publication_year":2017,"publication_date":"2017-11-01","ids":{"openalex":"https://openalex.org/W3014408508","doi":"https://doi.org/10.1109/bibm.2017.8217912","mag":"3014408508"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2017.8217912","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217912","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5048884064","display_name":"Shiquan Sun","orcid":"https://orcid.org/0000-0002-9150-6992"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiquan Sun","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054219637","display_name":"Xifang Sun","orcid":"https://orcid.org/0000-0002-5739-4624"},"institutions":[{"id":"https://openalex.org/I181903023","display_name":"Xi'an Shiyou University","ror":"https://ror.org/040c7js64","country_code":"CN","type":"education","lineage":["https://openalex.org/I181903023"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xifang Sun","raw_affiliation_strings":["School of Science, Xi'an Shiyou University, Xi'an, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Xi'an Shiyou University, Xi'an, Shaanxi, China","institution_ids":["https://openalex.org/I181903023"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083558362","display_name":"Yan Zheng","orcid":"https://orcid.org/0000-0001-7254-7564"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Zheng","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"419","issue":null,"first_page":"1678","last_page":"1683"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":1.0,"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":1.0,"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/T10184","display_name":"Plant Molecular Biology Research","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.992900013923645,"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/chromatin","display_name":"Chromatin","score":0.8572602272033691},{"id":"https://openalex.org/keywords/h3k4me3","display_name":"H3K4me3","score":0.7686529755592346},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.678449273109436},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5753878951072693},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4905316233634949},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4596331715583801},{"id":"https://openalex.org/keywords/degeneracy","display_name":"Degeneracy (biology)","score":0.45178020000457764},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4501856565475464},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4302251935005188},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42713862657546997},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3515171408653259},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3150840401649475},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.11281129717826843}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.8572602272033691},{"id":"https://openalex.org/C2780914512","wikidata":"https://www.wikidata.org/wiki/Q25323943","display_name":"H3K4me3","level":5,"score":0.7686529755592346},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.678449273109436},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5753878951072693},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4905316233634949},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4596331715583801},{"id":"https://openalex.org/C2777727622","wikidata":"https://www.wikidata.org/wiki/Q5251772","display_name":"Degeneracy (biology)","level":2,"score":0.45178020000457764},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4501856565475464},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4302251935005188},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42713862657546997},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3515171408653259},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3150840401649475},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.11281129717826843},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2017.8217912","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217912","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W273955616","https://openalex.org/W2002698073","https://openalex.org/W2015416439","https://openalex.org/W2017840637","https://openalex.org/W2022936129","https://openalex.org/W2024584416","https://openalex.org/W2042904283","https://openalex.org/W2044826047","https://openalex.org/W2096083625","https://openalex.org/W2102619694","https://openalex.org/W2104326170","https://openalex.org/W2127081697","https://openalex.org/W2130942354","https://openalex.org/W2137183255","https://openalex.org/W2140593657","https://openalex.org/W2142205294","https://openalex.org/W2147524392","https://openalex.org/W2155639125","https://openalex.org/W2163250689","https://openalex.org/W2164116506","https://openalex.org/W2171033594","https://openalex.org/W2384153472","https://openalex.org/W2482092413","https://openalex.org/W2485236528","https://openalex.org/W2557591078","https://openalex.org/W2561789123","https://openalex.org/W2730833391","https://openalex.org/W2950758817","https://openalex.org/W4240255376","https://openalex.org/W6610017368","https://openalex.org/W6710471451","https://openalex.org/W6730465031"],"related_works":["https://openalex.org/W2072087349","https://openalex.org/W2036052587","https://openalex.org/W2372940580","https://openalex.org/W98379584","https://openalex.org/W2413824894","https://openalex.org/W2055566470","https://openalex.org/W3145419749","https://openalex.org/W3038565614","https://openalex.org/W3112469286","https://openalex.org/W2075622490"],"abstract_inverted_index":{"Multiple":[0],"publications":[1],"have":[2],"indicated":[3],"that":[4,119],"gene":[5,39,69,128],"expression":[6,40,70,129],"levels":[7,130],"are":[8],"strongly":[9],"affected":[10],"by":[11],"chromatin":[12,65],"mark":[13],"combinations":[14],"via":[15],"at":[16],"least":[17],"two":[18],"mechanisms,":[19],"i.e.,":[20],"activation":[21],"or":[22],"repression.":[23],"But":[24],"their":[25],"combinatorial":[26],"patterns":[27],"remain":[28],"unresolved.":[29],"To":[30],"further":[31],"understand":[32],"the":[33,90,120,140],"relationship":[34],"between":[35],"histone":[36,106],"modifications":[37,107],"and":[38,84,102,113,146,152],"levels,":[41],"here":[42],"in":[43],"this":[44],"paper,":[45],"we":[46],"introduce":[47],"a":[48],"purely":[49],"geometric":[50],"higher-order":[51],"representation,":[52],"tensor":[53],"(also":[54],"called":[55],"multidimensional":[56],"array),":[57],"which":[58],"might":[59],"contain":[60],"more":[61,124],"hidden":[62],"information":[63],"from":[64,77],"states":[66],"to":[67],"predicting":[68,127],"levels.":[71],"The":[72],"prediction":[73],"models":[74],"were":[75],"learned":[76],"regions":[78],"around":[79],"upstream":[80],"10k":[81,86],"base":[82,87],"pairs":[83,88],"downstream":[85],"of":[89],"transcriptional":[91],"start":[92],"sites":[93],"(TSSs)":[94],"over":[95],"three":[96],"species":[97],"(i.e.,":[98,108],"Human,":[99],"Rhesus":[100],"Macaque,":[101],"Chimpanzee)":[103],"with":[104],"five":[105],"H3K4me1,":[109],"H3K4me3,":[110],"H3K27ac,":[111],"H3K27me3,":[112],"Pol":[114],"II).":[115],"Experimental":[116],"results":[117],"demonstrate":[118],"proposed":[121],"method":[122,138],"is":[123],"powerful":[125],"for":[126],"than":[131],"several":[132],"commonly":[133],"used":[134],"methods.":[135],"Specifically,":[136],"our":[137],"improves":[139],"performance":[141],"on":[142],"both":[143],"criteria,":[144],"R":[145],"RMSE":[147],"as":[148,150],"high":[149],"1.7%":[151],"11%,":[153],"respectively.":[154]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}