{"id":"https://openalex.org/W2001114224","doi":"https://doi.org/10.1109/embc.2014.6944687","title":"A novel genome-wide polyadenylation sites recognition system based on condition random field","display_name":"A novel genome-wide polyadenylation sites recognition system based on condition random field","publication_year":2014,"publication_date":"2014-08-01","ids":{"openalex":"https://openalex.org/W2001114224","doi":"https://doi.org/10.1109/embc.2014.6944687","mag":"2001114224","pmid":"https://pubmed.ncbi.nlm.nih.gov/25571055"},"language":"en","primary_location":{"id":"doi:10.1109/embc.2014.6944687","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2014.6944687","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society","raw_type":"proceedings-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":"https://openalex.org/A5101571055","display_name":"Jiuqiang Han","orcid":"https://orcid.org/0000-0002-5642-5935"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiuqiang Han","raw_affiliation_strings":["School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China","School of Electronic and Information Engineering, Xi\u2019an Jiaotong University, Xi\u2019an 710049 China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Electronic and Information Engineering, Xi\u2019an Jiaotong University, Xi\u2019an 710049 China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054713955","display_name":"Shanxin Zhang","orcid":"https://orcid.org/0000-0002-7948-9202"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shanxin Zhang","raw_affiliation_strings":["School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China","School of Electronic and Information Engineering, Xi\u2019an Jiaotong University, Xi\u2019an 710049 China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Electronic and Information Engineering, Xi\u2019an Jiaotong University, Xi\u2019an 710049 China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100361740","display_name":"Jun Liu","orcid":"https://orcid.org/0000-0002-0077-1919"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Liu","raw_affiliation_strings":["School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China","School of Electronic and Information Engineering, Xi\u2019an Jiaotong University, Xi\u2019an 710049 China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Electronic and Information Engineering, Xi\u2019an Jiaotong University, Xi\u2019an 710049 China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101853939","display_name":"Ruiling Liu","orcid":"https://orcid.org/0000-0002-0107-6352"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruiling Liu","raw_affiliation_strings":["School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China","School of Electronic and Information Engineering, Xi\u2019an Jiaotong University, Xi\u2019an 710049 China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Electronic and Information Engineering, Xi\u2019an Jiaotong University, Xi\u2019an 710049 China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101571055"],"corresponding_institution_ids":["https://openalex.org/I87445476"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0643377,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2014","issue":null,"first_page":"4755","last_page":"4758"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","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/T10604","display_name":"RNA Research and Splicing","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/T11482","display_name":"RNA modifications and cancer","score":0.9991999864578247,"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":0.998199999332428,"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/polyadenylation","display_name":"Polyadenylation","score":0.9712638854980469},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6904791593551636},{"id":"https://openalex.org/keywords/cleavage-and-polyadenylation-specificity-factor","display_name":"Cleavage and polyadenylation specificity factor","score":0.634223461151123},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48498913645744324},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4446408450603485},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.43984276056289673},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4232708513736725},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.41870319843292236},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39759621024131775},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36860212683677673},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.36388373374938965},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36115968227386475},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3525143265724182},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2877603769302368}],"concepts":[{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.9712638854980469},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6904791593551636},{"id":"https://openalex.org/C62531158","wikidata":"https://www.wikidata.org/wiki/Q21100335","display_name":"Cleavage and polyadenylation specificity factor","level":5,"score":0.634223461151123},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48498913645744324},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4446408450603485},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.43984276056289673},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4232708513736725},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.41870319843292236},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39759621024131775},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36860212683677673},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.36388373374938965},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36115968227386475},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3525143265724182},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2877603769302368}],"mesh":[{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/embc.2014.6944687","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2014.6944687","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society","raw_type":"proceedings-article"},{"id":"pmid:25571055","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25571055","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1997699426","https://openalex.org/W2018384224","https://openalex.org/W2032009534","https://openalex.org/W2034164729","https://openalex.org/W2039781333","https://openalex.org/W2065213545","https://openalex.org/W2096465161","https://openalex.org/W2097979901","https://openalex.org/W2099305989","https://openalex.org/W2099915768","https://openalex.org/W2101459357","https://openalex.org/W2102307373","https://openalex.org/W2108264419","https://openalex.org/W2113635738","https://openalex.org/W2118031210","https://openalex.org/W2128016314","https://openalex.org/W2130907011","https://openalex.org/W2132640619","https://openalex.org/W2140303894","https://openalex.org/W2141653569","https://openalex.org/W2156976607","https://openalex.org/W2170669858","https://openalex.org/W3029457946"],"related_works":["https://openalex.org/W2166494447","https://openalex.org/W1972484052","https://openalex.org/W2006563243","https://openalex.org/W2092590107","https://openalex.org/W1991230146","https://openalex.org/W2142574026","https://openalex.org/W2151562469","https://openalex.org/W2093641665","https://openalex.org/W1764884856","https://openalex.org/W2009700107"],"abstract_inverted_index":{"Polyadenylation":[0],"including":[1],"the":[2,14,38,47,113,124,144],"cleavage":[3],"of":[4,8,11,20,29,73,86,95,132],"pre-mRNA":[5,21],"and":[6,35,37,43],"addition":[7],"a":[9,81,93,105,140],"stretch":[10],"adenosines":[12],"to":[13,49,70,79],"3'-end":[15],"is":[16,77,157],"an":[17,158],"essential":[18],"step":[19],"processing":[22],"in":[23,31,161],"eukayotes.":[24],"The":[25,151],"known":[26],"regulatory":[27],"role":[28],"polyadenylation":[30,52],"mRNA":[32],"localization,":[33],"stability,":[34],"translation":[36],"emerging":[39],"link":[40],"between":[41],"poly(A)":[42,62,87,96,108,133,164],"disease":[44],"states":[45],"underline":[46],"necessary":[48,78],"fully":[50],"characterize":[51],"sites.":[53,88],"Several":[54],"artificial":[55],"intelligence":[56],"methods":[57,67],"have":[58,91],"been":[59],"proposed":[60,104],"for":[61,83,130],"sites":[63,134,165],"recognition.":[64,166],"However,":[65],"these":[66],"are":[68],"suitable":[69],"small":[71],"subsets":[72],"genome":[74,162],"sequences.":[75],"It":[76],"propose":[80],"method":[82,110,138,156,160],"genome-wide":[84,107],"recognition":[85,109],"Recent":[89],"efforts":[90],"found":[92],"lot":[94],"related":[97],"factors":[98],"on":[99,112],"DNA":[100],"level.":[101],"Here,":[102],"we":[103],"novel":[106],"based":[111],"Condition":[114],"Random":[115],"Field":[116],"(CRF)":[117],"by":[118],"integrating":[119],"multiple":[120],"features.":[121],"Compared":[122],"with":[123,143],"polya_svm":[125],"(the":[126],"most":[127],"accurate":[128],"program":[129],"prediction":[131],"till":[135],"date),":[136],"our":[137,155],"had":[139],"higher":[141],"performance":[142],"area":[145],"under":[146],"ROC":[147],"curve(0.8621":[148],"versus":[149],"0.6796).":[150],"result":[152],"suggests":[153],"that":[154],"effective":[159],"wide":[163]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}