{"id":"https://openalex.org/W4288388964","doi":"https://doi.org/10.1109/jcsse54890.2022.9836262","title":"A Computational Workflow for Estimation of Short RNA Polyadenylation using Direct RNA Nanopore Sequencing with Polyuridylation","display_name":"A Computational Workflow for Estimation of Short RNA Polyadenylation using Direct RNA Nanopore Sequencing with Polyuridylation","publication_year":2022,"publication_date":"2022-06-22","ids":{"openalex":"https://openalex.org/W4288388964","doi":"https://doi.org/10.1109/jcsse54890.2022.9836262"},"language":"en","primary_location":{"id":"doi:10.1109/jcsse54890.2022.9836262","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jcsse54890.2022.9836262","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 19th International Joint Conference on Computer Science and Software Engineering (JCSSE)","raw_type":"proceedings-article"},"type":"article","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/A5038767661","display_name":"Jirachote Karunyakorn","orcid":null},"institutions":[{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":true,"raw_author_name":"Jirachote Karunyakorn","raw_affiliation_strings":["Program in Bioinformatics and Computational Biology, Graduate school, Chulalongkorn University,Bangkok,Thailand,10330"],"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Computational Biology, Graduate school, Chulalongkorn University,Bangkok,Thailand,10330","institution_ids":["https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028196556","display_name":"Ploy N. Pratanwanich","orcid":"https://orcid.org/0000-0003-3684-6967"},"institutions":[{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Naruemon Pratanwanich","raw_affiliation_strings":["Center of Excellence in Computational Molecular Biology, Chulalongkorn University,Faculty of Science,Department of Mathematics and Computer Science,Bangkok,Thailand,10330"],"affiliations":[{"raw_affiliation_string":"Center of Excellence in Computational Molecular Biology, Chulalongkorn University,Faculty of Science,Department of Mathematics and Computer Science,Bangkok,Thailand,10330","institution_ids":["https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044963170","display_name":"Monnat Pongpanich","orcid":"https://orcid.org/0000-0003-3228-3351"},"institutions":[{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Monnat Pongpanich","raw_affiliation_strings":["Chulalongkorn University,Faculty of Science,Department of Mathematics and Computer Science,Bangkok,Thailand,10330"],"affiliations":[{"raw_affiliation_string":"Chulalongkorn University,Faculty of Science,Department of Mathematics and Computer Science,Bangkok,Thailand,10330","institution_ids":["https://openalex.org/I158708052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044369330","display_name":"Pornchai Kaewsapsak","orcid":"https://orcid.org/0000-0001-7921-0868"},"institutions":[{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Pornchai Kaewsapsak","raw_affiliation_strings":["Chulalongkorn University,Faculty of Medicine, Research Unit of Systems Microbiology,Department of Biochemistry,Bangkok,Thailand,10330"],"affiliations":[{"raw_affiliation_string":"Chulalongkorn University,Faculty of Medicine, Research Unit of Systems Microbiology,Department of Biochemistry,Bangkok,Thailand,10330","institution_ids":["https://openalex.org/I158708052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5038767661"],"corresponding_institution_ids":["https://openalex.org/I158708052"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0741756,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T10604","display_name":"RNA Research and Splicing","score":0.9983000159263611,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9898999929428101,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.7918359041213989},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6115328669548035},{"id":"https://openalex.org/keywords/nanopore","display_name":"Nanopore","score":0.5915729999542236},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5896173715591431},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5764684081077576},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.5595173239707947},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4988281726837158},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22160902619361877},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21213558316230774},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.2110450267791748},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1372775435447693},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.09353521466255188},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.0912889838218689}],"concepts":[{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.7918359041213989},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6115328669548035},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.5915729999542236},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5896173715591431},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5764684081077576},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.5595173239707947},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4988281726837158},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22160902619361877},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21213558316230774},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2110450267791748},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1372775435447693},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.09353521466255188},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.0912889838218689},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/jcsse54890.2022.9836262","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jcsse54890.2022.9836262","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 19th International Joint Conference on Computer Science and Software Engineering (JCSSE)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321557","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W943422790","https://openalex.org/W1519765314","https://openalex.org/W2001932825","https://openalex.org/W2030230281","https://openalex.org/W2032109039","https://openalex.org/W2076510291","https://openalex.org/W2108234281","https://openalex.org/W2124075935","https://openalex.org/W2133973346","https://openalex.org/W2153289333","https://openalex.org/W2159666069","https://openalex.org/W2168539350","https://openalex.org/W2550586733","https://openalex.org/W2789843538","https://openalex.org/W2900085273","https://openalex.org/W2909693411","https://openalex.org/W2950063384","https://openalex.org/W2951278111","https://openalex.org/W2953562574","https://openalex.org/W2989499631","https://openalex.org/W3202060848"],"related_works":["https://openalex.org/W2774675543","https://openalex.org/W2119052929","https://openalex.org/W2326282944","https://openalex.org/W2330402197","https://openalex.org/W3197006535","https://openalex.org/W3201371206","https://openalex.org/W2420153309","https://openalex.org/W2096970964","https://openalex.org/W3175842380","https://openalex.org/W2107323267"],"abstract_inverted_index":{"Polyadenylation":[0],"or":[1],"poly(A)":[2,23,37,62,85,106,124,131,141,150],"tail":[3,63,86,125,132,151],"at":[4],"the":[5,34,36,47,69,120],"3\u2019-end":[6],"of":[7,12],"RNA":[8,17,55,72],"is":[9],"a":[10,100],"type":[11],"post-transcriptional":[13],"modification":[14],"that":[15,60],"regulates":[16],"biological":[18],"functions":[19],"and":[20,31,44,98,108,138,156,165],"stability.":[21],"While":[22],"tails":[24,38,107],"in":[25,39,66,90,95,153],"eukaryotes":[26],"are":[27,41],"80\u2013200":[28],"nucleotides":[29],"long":[30],"generally":[32],"stabilize":[33],"RNAs,":[35,87],"prokaryotes":[40],"significantly":[42],"shorter":[43],"usually":[45],"destabilize":[46],"RNAs.":[48],"Although":[49],"Oxford":[50],"Nanopore":[51],"Technologies":[52],"(ONT)":[53],"direct":[54],"sequencing":[56,59,77,136],"provides":[57,119],"long-read":[58],"allows":[61],"length":[64,126,133,152],"estimation":[65,127],"recent":[67],"years,":[68],"standard":[70],"nanopore":[71],"library":[73],"preparation,":[74],"which":[75],"requires":[76],"oligo(dT)":[78],"adapter":[79],"ligation,":[80],"could":[81,145],"not":[82],"capture":[83],"short":[84,123],"especially":[88],"RNAs":[89,114],"prokaryotes.":[91],"Hence,":[92],"we":[93],"introduced":[94],"vitro":[96],"uridylation":[97],"developed":[99],"computational":[101],"processing":[102],"workflow":[103,121,144],"to":[104,148],"dissect":[105],"estimate":[109],"their":[110,161],"length.":[111],"Using":[112],"synthetic":[113],"as":[115],"standard,":[116],"this":[117],"study":[118],"for":[122],"by":[128],"reassigning":[129],"underestimated":[130],"using":[134],"base-called":[135],"data":[137],"re-segmenting":[139],"misassigned":[140],"tail.":[142],"This":[143],"be":[146],"beneficial":[147],"obtain":[149],"different":[154],"organisms":[155],"potentially":[157],"provide":[158],"insights":[159],"into":[160],"gene":[162],"expression,":[163],"regulation,":[164],"modification.":[166]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
