{"id":"https://openalex.org/W3005149796","doi":"https://doi.org/10.1109/bibm47256.2019.8983074","title":"SURFr: Algorithm for identification and analysis of ncRNA-derived RNAs","display_name":"SURFr: Algorithm for identification and analysis of ncRNA-derived RNAs","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3005149796","doi":"https://doi.org/10.1109/bibm47256.2019.8983074","mag":"3005149796"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983074","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983074","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5017519521","display_name":"Mohan Vamsi Kasukurthi","orcid":null},"institutions":[{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mohan Vamsi Kasukurthi","raw_affiliation_strings":["School of Computing, University of South Alabama,Mobile,AL,U.S.A","School of Computing, University of South Alabama, Mobile, AL, U.S.A"],"affiliations":[{"raw_affiliation_string":"School of Computing, University of South Alabama,Mobile,AL,U.S.A","institution_ids":["https://openalex.org/I83809506"]},{"raw_affiliation_string":"School of Computing, University of South Alabama, Mobile, AL, U.S.A","institution_ids":["https://openalex.org/I83809506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024399921","display_name":"Dihua Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Dihua Zhang","raw_affiliation_strings":["Sun Yat-sen University,Nephrology Department,Guangzhou,China","School of Computing, University of South Alabama, Mobile, AL, U.S.A"],"affiliations":[{"raw_affiliation_string":"Sun Yat-sen University,Nephrology Department,Guangzhou,China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Computing, University of South Alabama, Mobile, AL, U.S.A","institution_ids":["https://openalex.org/I83809506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083366494","display_name":"Mika Housevera","orcid":null},"institutions":[{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mika Housevera","raw_affiliation_strings":["University of South Alabama,Department of Pharmacology,Mobile,AL,U.S.A","Department of Pharmacology, University of South Alabama, Mobile, AL, U.S.A"],"affiliations":[{"raw_affiliation_string":"University of South Alabama,Department of Pharmacology,Mobile,AL,U.S.A","institution_ids":["https://openalex.org/I83809506"]},{"raw_affiliation_string":"Department of Pharmacology, University of South Alabama, Mobile, AL, U.S.A","institution_ids":["https://openalex.org/I83809506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102022713","display_name":"Yulong Huang","orcid":"https://orcid.org/0000-0002-6188-5178"},"institutions":[{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yulong Huang","raw_affiliation_strings":["College of Allied Health Professions, University of South Alabama,Mobile,AL,U.S.A","School of Computing, University of South Alabama, Mobile, AL, U.S.A"],"affiliations":[{"raw_affiliation_string":"College of Allied Health Professions, University of South Alabama,Mobile,AL,U.S.A","institution_ids":["https://openalex.org/I83809506"]},{"raw_affiliation_string":"School of Computing, University of South Alabama, Mobile, AL, U.S.A","institution_ids":["https://openalex.org/I83809506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021721710","display_name":"Shaobo Tan","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Shaobo Tan","raw_affiliation_strings":["School of Computing, University of South Alabama,Mobile,AL,U.S.A","Nephrology Department, Sun Yat-sen University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Computing, University of South Alabama,Mobile,AL,U.S.A","institution_ids":["https://openalex.org/I83809506"]},{"raw_affiliation_string":"Nephrology Department, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100749729","display_name":"Bin Ma","orcid":"https://orcid.org/0000-0001-7649-6696"},"institutions":[{"id":"https://openalex.org/I152269853","display_name":"Qilu University of Technology","ror":"https://ror.org/04hyzq608","country_code":"CN","type":"education","lineage":["https://openalex.org/I152269853"]},{"id":"https://openalex.org/I4210142748","display_name":"Shandong Academy of Sciences","ror":"https://ror.org/04y8d6y55","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210142748"]},{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Bin Ma","raw_affiliation_strings":["Qilu University of Technology, Shandong Academy of Science,Jinan,Shandong,China","Department of Pharmacology, University of South Alabama, Mobile, AL, U.S.A"],"affiliations":[{"raw_affiliation_string":"Qilu University of Technology, Shandong Academy of Science,Jinan,Shandong,China","institution_ids":["https://openalex.org/I152269853","https://openalex.org/I4210142748"]},{"raw_affiliation_string":"Department of Pharmacology, University of South Alabama, Mobile, AL, U.S.A","institution_ids":["https://openalex.org/I83809506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101746855","display_name":"Dongqi Li","orcid":"https://orcid.org/0000-0002-0421-2161"},"institutions":[{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dongqi Li","raw_affiliation_strings":["School of Computing, University of South Alabama,Mobile,AL,U.S.A","College of Allied Health Professions, University of South Alabama, Mobile, AL, U.S.A"],"affiliations":[{"raw_affiliation_string":"School of Computing, University of South Alabama,Mobile,AL,U.S.A","institution_ids":["https://openalex.org/I83809506"]},{"raw_affiliation_string":"College of Allied Health Professions, University of South Alabama, Mobile, AL, U.S.A","institution_ids":["https://openalex.org/I83809506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005864826","display_name":"Ryan Benton","orcid":"https://orcid.org/0000-0001-9616-6221"},"institutions":[{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Benton","raw_affiliation_strings":["School of Computing, University of South Alabama,Mobile,AL,U.S.A","School of Computing, University of South Alabama, Mobile, AL, U.S.A"],"affiliations":[{"raw_affiliation_string":"School of Computing, University of South Alabama,Mobile,AL,U.S.A","institution_ids":["https://openalex.org/I83809506"]},{"raw_affiliation_string":"School of Computing, University of South Alabama, Mobile, AL, U.S.A","institution_ids":["https://openalex.org/I83809506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042202985","display_name":"Jingwei Lin","orcid":"https://orcid.org/0000-0002-2476-9928"},"institutions":[{"id":"https://openalex.org/I152269853","display_name":"Qilu University of Technology","ror":"https://ror.org/04hyzq608","country_code":"CN","type":"education","lineage":["https://openalex.org/I152269853"]},{"id":"https://openalex.org/I80947539","display_name":"Fuzhou University","ror":"https://ror.org/011xvna82","country_code":"CN","type":"education","lineage":["https://openalex.org/I80947539"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingwei Lin","raw_affiliation_strings":["Ocean School, Fuzhou University,Fuzhou,China","Qilu University of Technology, Shandong Academy of Science, Jinan, Shandong, China"],"affiliations":[{"raw_affiliation_string":"Ocean School, Fuzhou University,Fuzhou,China","institution_ids":["https://openalex.org/I80947539"]},{"raw_affiliation_string":"Qilu University of Technology, Shandong Academy of Science, Jinan, Shandong, China","institution_ids":["https://openalex.org/I152269853"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108853916","display_name":"Shengyu Li","orcid":null},"institutions":[{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shengyu Li","raw_affiliation_strings":["School of Computing, University of South Alabama,Mobile,AL,U.S.A","School of Computing, University of South Alabama, Mobile, AL, U.S.A"],"affiliations":[{"raw_affiliation_string":"School of Computing, University of South Alabama,Mobile,AL,U.S.A","institution_ids":["https://openalex.org/I83809506"]},{"raw_affiliation_string":"School of Computing, University of South Alabama, Mobile, AL, U.S.A","institution_ids":["https://openalex.org/I83809506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066027793","display_name":"Glen M. Borchert","orcid":"https://orcid.org/0000-0002-6182-7154"},"institutions":[{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Glen M. Borchert","raw_affiliation_strings":["University of South Alabama,Department of Pharmacology,Mobile,AL,U.S.A","School of Computing, University of South Alabama, Mobile, AL, U.S.A"],"affiliations":[{"raw_affiliation_string":"University of South Alabama,Department of Pharmacology,Mobile,AL,U.S.A","institution_ids":["https://openalex.org/I83809506"]},{"raw_affiliation_string":"School of Computing, University of South Alabama, Mobile, AL, U.S.A","institution_ids":["https://openalex.org/I83809506"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103191466","display_name":"Jingshan Huang","orcid":"https://orcid.org/0000-0003-2408-2883"},"institutions":[{"id":"https://openalex.org/I80947539","display_name":"Fuzhou University","ror":"https://ror.org/011xvna82","country_code":"CN","type":"education","lineage":["https://openalex.org/I80947539"]},{"id":"https://openalex.org/I83809506","display_name":"University of South Alabama","ror":"https://ror.org/01s7b5y08","country_code":"US","type":"education","lineage":["https://openalex.org/I83809506"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jingshan Huang","raw_affiliation_strings":["School of Computing, University of South Alabama,Mobile,AL,U.S.A","Ocean School, Fuzhou University, Fuzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Computing, University of South Alabama,Mobile,AL,U.S.A","institution_ids":["https://openalex.org/I83809506"]},{"raw_affiliation_string":"Ocean School, Fuzhou University, Fuzhou, China","institution_ids":["https://openalex.org/I80947539"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5017519521"],"corresponding_institution_ids":["https://openalex.org/I83809506"],"apc_list":null,"apc_paid":null,"fwci":0.382,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.55996514,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1504","last_page":"1507"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9998999834060669,"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"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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/small-nucleolar-rna","display_name":"Small nucleolar RNA","score":0.9442378282546997},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.6965901851654053},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6576536893844604},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.5851888656616211},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5733543634414673},{"id":"https://openalex.org/keywords/long-non-coding-rna","display_name":"Long non-coding RNA","score":0.4846354126930237},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.483573853969574},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4609471261501312},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4507772624492645},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3622991442680359},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2736670672893524},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19314974546432495}],"concepts":[{"id":"https://openalex.org/C179255354","wikidata":"https://www.wikidata.org/wiki/Q284416","display_name":"Small nucleolar RNA","level":5,"score":0.9442378282546997},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.6965901851654053},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6576536893844604},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.5851888656616211},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5733543634414673},{"id":"https://openalex.org/C62203573","wikidata":"https://www.wikidata.org/wiki/Q15087973","display_name":"Long non-coding RNA","level":4,"score":0.4846354126930237},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.483573853969574},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4609471261501312},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4507772624492645},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3622991442680359},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2736670672893524},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19314974546432495},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983074","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983074","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1964016141","https://openalex.org/W1970760326","https://openalex.org/W1974371134","https://openalex.org/W1996021349","https://openalex.org/W1997393600","https://openalex.org/W2055043387","https://openalex.org/W2074231493","https://openalex.org/W2095968788","https://openalex.org/W2099964107","https://openalex.org/W2100555999","https://openalex.org/W2124985265","https://openalex.org/W2138664009","https://openalex.org/W2147495091","https://openalex.org/W2168130065","https://openalex.org/W2522746842","https://openalex.org/W2735747624","https://openalex.org/W2769912973","https://openalex.org/W2807674901","https://openalex.org/W4205744525"],"related_works":["https://openalex.org/W2982161529","https://openalex.org/W2810951145","https://openalex.org/W2984596260","https://openalex.org/W2753767186","https://openalex.org/W2217522595","https://openalex.org/W2403309656","https://openalex.org/W2094292925","https://openalex.org/W2954286598","https://openalex.org/W4239397632","https://openalex.org/W4313827290"],"abstract_inverted_index":{"Noncoding":[0],"RNAs":[1,20,62,67,106],"(ncRNAs)":[2],"regulate":[3],"gene":[4],"expression":[5],"in":[6,14,38,82],"essential":[7],"cellular":[8,85],"processes":[9],"and":[10,41,44,87,102,111,137],"play":[11],"key":[12],"roles":[13],"many":[15,46],"human":[16],"diseases.":[17],"Small":[18],"nucleolar":[19],"(snoRNAs)":[21],"are":[22],"a":[23,94],"relatively":[24],"large":[25],"group":[26],"of":[27,35,47,104,126],"ncRNAs.":[28],"Many":[29],"studies":[30],"have":[31,50,68],"identified":[32],"significant":[33],"alterations":[34],"different":[36],"snoRNAs":[37,49],"prostate,":[39],"breast,":[40],"lung":[42],"malignancies":[43],"that":[45],"these":[48],"been":[51,71],"shown":[52],"to":[53,73,80,143],"be":[54,74],"processed":[55],"into":[56],"microRNA-like":[57],"molecules":[58],"known":[59],"as":[60],"snoRNA-derived":[61],"(sdRNAs).":[63],"Similarly,":[64],"several":[65,133],"small":[66],"also":[69],"recently":[70],"found":[72],"excised":[75],"from":[76],"well":[77],"characterized":[78],"tRNAs":[79],"function":[81],"both":[83],"normal":[84],"metabolism":[86],"disease.":[88],"In":[89],"this":[90],"paper,":[91],"we":[92],"present":[93],"new":[95],"computational":[96],"methodology":[97],"for":[98,116],"the":[99,124],"identification,":[100],"analysis,":[101],"visualization":[103],"ncRNA-derived":[105],"(ndRNAs)":[107],"with":[108],"linear":[109],"time":[110,130],"space":[112],"complexity":[113],"(named":[114],"SURFr":[115],"Short":[117],"Uncharacterized":[118],"R":[119],"NA":[120],"Finder).":[121],"We":[122],"provide":[123],"results":[125],"our":[127,144],"algorithm's":[128],"running":[129],"by":[131],"analyzing":[132],"publicly":[134],"available":[135],"datasets":[136],"finally":[138],"discuss":[139],"future":[140],"research":[141],"directions":[142],"work.":[145]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4}],"updated_date":"2026-03-25T23:56:10.502304","created_date":"2025-10-10T00:00:00"}