{"id":"https://openalex.org/W2774691683","doi":"https://doi.org/10.1109/bibm.2017.8217829","title":"Prediction of enhancer RNA activity levels from ChIP-seq-derived histone modification combinatorial codes","display_name":"Prediction of enhancer RNA activity levels from ChIP-seq-derived histone modification combinatorial codes","publication_year":2017,"publication_date":"2017-11-01","ids":{"openalex":"https://openalex.org/W2774691683","doi":"https://doi.org/10.1109/bibm.2017.8217829","mag":"2774691683"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2017.8217829","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217829","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/A5070708809","display_name":"Nawanol Theera-Ampornpunt","orcid":"https://orcid.org/0000-0002-7594-8061"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nawanol Theera-Ampornpunt","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, Indiana, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, Indiana, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055585728","display_name":"Somali Chaterji","orcid":"https://orcid.org/0000-0002-3651-6362"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Somali Chaterji","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, Indiana, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, Indiana, USA","institution_ids":["https://openalex.org/I219193219"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I219193219"],"apc_list":null,"apc_paid":null,"fwci":0.9001,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.80013004,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"153","issue":null,"first_page":"1206","last_page":"1214"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T11482","display_name":"RNA modifications and cancer","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"}}],"keywords":[{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.9035120010375977},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6865500211715698},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6204684376716614},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.5989255905151367},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.5552185773849487},{"id":"https://openalex.org/keywords/epigenome","display_name":"Epigenome","score":0.5519638657569885},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4945635497570038},{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.4717225432395935},{"id":"https://openalex.org/keywords/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.4340023398399353},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4305607080459595},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4113362431526184},{"id":"https://openalex.org/keywords/enhancer-rnas","display_name":"Enhancer RNAs","score":0.4107932150363922},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.38678178191185},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36465713381767273},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.312150239944458},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.30412745475769043},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.2186708152294159}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.9035120010375977},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6865500211715698},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6204684376716614},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5989255905151367},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.5552185773849487},{"id":"https://openalex.org/C117717151","wikidata":"https://www.wikidata.org/wiki/Q3589155","display_name":"Epigenome","level":5,"score":0.5519638657569885},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4945635497570038},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.4717225432395935},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.4340023398399353},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4305607080459595},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4113362431526184},{"id":"https://openalex.org/C21784809","wikidata":"https://www.wikidata.org/wiki/Q17119097","display_name":"Enhancer RNAs","level":5,"score":0.4107932150363922},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.38678178191185},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36465713381767273},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.312150239944458},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.30412745475769043},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.2186708152294159}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2017.8217829","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217829","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":41,"referenced_works":["https://openalex.org/W1968083284","https://openalex.org/W1971578941","https://openalex.org/W1981030303","https://openalex.org/W1986865417","https://openalex.org/W1992696908","https://openalex.org/W1997590968","https://openalex.org/W2007844697","https://openalex.org/W2015416439","https://openalex.org/W2034510261","https://openalex.org/W2036619779","https://openalex.org/W2039705224","https://openalex.org/W2048263136","https://openalex.org/W2060316084","https://openalex.org/W2060396676","https://openalex.org/W2077624120","https://openalex.org/W2083245183","https://openalex.org/W2088722891","https://openalex.org/W2091533196","https://openalex.org/W2100847260","https://openalex.org/W2112001233","https://openalex.org/W2112741367","https://openalex.org/W2113945915","https://openalex.org/W2128817132","https://openalex.org/W2134854530","https://openalex.org/W2159164310","https://openalex.org/W2166770943","https://openalex.org/W2171111703","https://openalex.org/W2176525427","https://openalex.org/W2204875887","https://openalex.org/W2207178401","https://openalex.org/W2259938310","https://openalex.org/W2308092540","https://openalex.org/W2412192467","https://openalex.org/W2475924856","https://openalex.org/W2560048654","https://openalex.org/W2748933472","https://openalex.org/W2752064279","https://openalex.org/W2760000637","https://openalex.org/W2765303113","https://openalex.org/W6688221503","https://openalex.org/W6744803420"],"related_works":["https://openalex.org/W2424092526","https://openalex.org/W2507790420","https://openalex.org/W2212710981","https://openalex.org/W4200376839","https://openalex.org/W2795223073","https://openalex.org/W2151543286","https://openalex.org/W2418239907","https://openalex.org/W2142890267","https://openalex.org/W4280600268","https://openalex.org/W2474086683"],"abstract_inverted_index":{"Motivation:":[0],"Transcription-regulatory":[1],"elements":[2],"(TREs)":[3],"are":[4,23,34,154,222],"critical":[5],"modulators":[6],"of":[7,40,81,87,132,149,159,172,178,230,249],"gene":[8,18],"transcription,":[9],"with":[10,165,194,241],"promoters":[11],"and":[12,33,119],"enhancers":[13,22,56,89],"being":[14,116],"major":[15],"hubs":[16],"for":[17,168,180,199],"regulation.":[19],"Of":[20],"these,":[21],"distal":[24],"regulatory":[25,52],"elements,":[26],"typically":[27],"short":[28],"50-150":[29],"basepairs":[30],"DNA":[31],"regions":[32,42],"identified":[35],"via":[36],"the":[37,82,130,137,147,169,181,210,219,234,239,252],"large":[38],"numbers":[39],"genomic":[41],"displaying":[43],"enhancer-like":[44],"chromatin":[45],"features,":[46],"such":[47,100],"as":[48,101,140,145],"histone":[49,151],"modifications":[50,152],"at":[51,58,121],"sites.":[53],"Given":[54],"that":[55,153,218],"operate":[57],"sites":[59],"vastly":[60],"removed":[61],"from":[62],"their":[63,66],"cognate":[64],"genes,":[65],"computational":[67,197],"prediction":[68],"is":[69,114,209],"challenging.":[70],"While":[71],"ChIP-seq":[72,133],"datasets":[73],"have":[74,90,103],"been":[75,91,104],"used":[76,105],"to":[77,93,106,135,156,233],"map":[78],"out":[79],"parts":[80],"epigenome,":[83],"only":[84],"a":[85,191,195,242],"fraction":[86],"predicted":[88],"found":[92],"be":[94,157],"functionally":[95,108],"active.":[96],"Thus,":[97],"recent":[98],"methods,":[99],"GRO-seq,":[102,143],"elucidate":[107],"active":[109],"enhancers.":[110,160],"However,":[111],"GRO-seq":[112],"data":[113,134],"sparse,":[115],"experimentally":[117],"complex,":[118],"often":[120],"insufficient":[122],"resolution.":[123],"Hence,":[124],"in":[125],"this":[126],"paper,":[127],"we":[128],"evaluate":[129],"ability":[131],"predict":[136],"eRNA":[138,173],"activity,":[139,174],"given":[141],"by":[142],"using":[144],"inputs":[146],"signatures":[148],"key":[150],"known":[155],"predictive":[158],"We":[161,188,225],"implement":[162],"two":[163],"models":[164],"accurate":[166],"performance":[167],"entire":[170],"range":[171],"spanning":[175],"5":[176],"orders":[177],"magnitude,":[179],"human":[182],"embryonic":[183],"stem":[184],"cell":[185],"type":[186],"H1.":[187],"then":[189],"perform":[190],"detailed":[192],"comparison":[193,240],"prior":[196,243,253],"approach":[198],"(binary)":[200],"enhancer":[201],"activity":[202],"classification.":[203],"Results:":[204],"Our":[205],"best":[206],"performing":[207],"model":[208,246],"Convolutional":[211],"Neural":[212],"Network":[213],"(CNN)-based":[214],"regression":[215],"model,":[216],"indicating":[217],"epigenetic":[220],"patterns":[221],"location":[223],"invariant.":[224],"achieve":[226],"an":[227],"overall":[228],"RMSE":[229],"0.82":[231],"compared":[232],"baseline's":[235],"(ZeroR)":[236],"1.30.":[237],"In":[238],"approach,":[244],"our":[245],"achieves":[247],"AUC":[248],"0.75":[250],"against":[251],"approach's":[254],"0.56.":[255]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
