{"id":"https://openalex.org/W2973176396","doi":"https://doi.org/10.1109/bhi.2019.8834539","title":"circFA: a FPGA-based circular RNA aligner","display_name":"circFA: a FPGA-based circular RNA aligner","publication_year":2019,"publication_date":"2019-05-01","ids":{"openalex":"https://openalex.org/W2973176396","doi":"https://doi.org/10.1109/bhi.2019.8834539","mag":"2973176396"},"language":"en","primary_location":{"id":"doi:10.1109/bhi.2019.8834539","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi.2019.8834539","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE EMBS International Conference on Biomedical &amp; Health Informatics (BHI)","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/A5005739756","display_name":"Alberto Zeni","orcid":"https://orcid.org/0000-0003-4005-6036"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Alberto Zeni","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059732655","display_name":"Francesco Peverelli","orcid":"https://orcid.org/0000-0002-0569-3446"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesco Peverelli","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069586669","display_name":"Enrico Cabri","orcid":"https://orcid.org/0000-0003-4852-6944"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Enrico Cabri","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109198457","display_name":"Lorenzo Di Tucci","orcid":null},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Lorenzo di Tucci","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034473176","display_name":"Luca Cerina","orcid":"https://orcid.org/0000-0001-8571-3971"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luca Cerina","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010543929","display_name":"Marco D. Santambrogio","orcid":"https://orcid.org/0000-0002-9883-9693"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco D. Santambrogio","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5005739756"],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":null,"apc_paid":null,"fwci":0.0856,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.47834936,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"147","issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11765","display_name":"Circular RNAs in diseases","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/T11765","display_name":"Circular RNAs in diseases","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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9954000115394592,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9939000010490417,"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/speedup","display_name":"Speedup","score":0.8375473022460938},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.7513583898544312},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7138262987136841},{"id":"https://openalex.org/keywords/circular-rna","display_name":"Circular RNA","score":0.6871022582054138},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5950844883918762},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.5826853513717651},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.557031512260437},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5184030532836914},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4403221309185028},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3211892247200012},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.2824317216873169},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.27944159507751465},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14536386728286743}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.8375473022460938},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.7513583898544312},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7138262987136841},{"id":"https://openalex.org/C2775893923","wikidata":"https://www.wikidata.org/wiki/Q17113455","display_name":"Circular RNA","level":4,"score":0.6871022582054138},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5950844883918762},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.5826853513717651},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.557031512260437},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5184030532836914},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4403221309185028},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3211892247200012},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.2824317216873169},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.27944159507751465},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14536386728286743},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bhi.2019.8834539","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi.2019.8834539","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE EMBS International Conference on Biomedical &amp; Health Informatics (BHI)","raw_type":"proceedings-article"},{"id":"pmh:oai:re.public.polimi.it:11311/1127933","is_oa":false,"landing_page_url":"http://hdl.handle.net/11311/1127933","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","score":0.5099999904632568,"display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1966557314","https://openalex.org/W2006899413","https://openalex.org/W2060940710","https://openalex.org/W2087064593","https://openalex.org/W2095799789","https://openalex.org/W2097521167","https://openalex.org/W2123714662","https://openalex.org/W2133540884","https://openalex.org/W2137476312","https://openalex.org/W2140729960","https://openalex.org/W2146379626","https://openalex.org/W2166081493","https://openalex.org/W2328854742","https://openalex.org/W2606268188","https://openalex.org/W2613537099","https://openalex.org/W2617715606","https://openalex.org/W2734945090","https://openalex.org/W2769746516","https://openalex.org/W2794160361"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W3138386522","https://openalex.org/W2499279132","https://openalex.org/W2264746079","https://openalex.org/W3012895752"],"abstract_inverted_index":{"Circular":[0,85],"RNAs":[1,9,13,101],"(CircRNAs)":[2],"are":[3,29,37,51],"a":[4,18,59,68,76,90,113,142,160,171,176,188],"widespread":[5],"form":[6],"of":[7,47,93,131,144,166,168,173,180,197],"Non-Coding":[8],"(ncRNAs).":[10],"Although":[11],"circular":[12,100],"have":[14],"been":[15],"known":[16],"for":[17,44,98,148],"long":[19,64],"time,":[20],"it":[21],"is":[22],"only":[23],"recently":[24],"that":[25,35],"their":[26,56,72],"therapeutic":[27],"implications":[28],"being":[30],"investigated.":[31],"Research":[32],"has":[33],"shown":[34],"they":[36,50],"suitable":[38],"candidates":[39],"to":[40,71,74,107,117,203],"be":[41],"genetic":[42,123],"biomarkers":[43],"different":[45],"types":[46],"cancer":[48],"since":[49],"implied":[52],"in":[53,191],"Carcinogenesis.":[54],"However,":[55],"identification":[57,102],"involves":[58],"computationally":[60],"intensive":[61],"and":[62,78,111,170,199,207],"very":[63],"process.":[65],"This":[66],"represents":[67],"serious":[69],"obstacle":[70],"ability":[73],"provide":[75],"fast":[77],"accurate":[79],"life-saving":[80],"diagnosis.":[81],"Here":[82],"we":[83],"present":[84],"RNA":[86],"FPGA":[87],"Aligner":[88],"(circFa),":[89],"hardware":[91],"implementation":[92],"an":[94,195],"alignment":[95],"algorithm":[96,135],"designed":[97],"the":[99,118,127,132,145,163,181,204],"protocol.":[103],"Our":[104,157,184],"solution":[105],"aims":[106],"reduce":[108],"diagnosis":[109],"time":[110],"produces":[112],"pharmacological":[114],"therapy":[115],"tailored":[116],"specific":[119],"patient":[120],"using":[121],"his":[122],"information.":[124],"CircFA":[125],"implements":[126],"same":[128,182],"scalable":[129],"version":[130,165,179],"Smith-Waterman":[133],"(SW)":[134],"with":[136,194,201],"affine":[137],"gaps":[138],"employed":[139],"by":[140],"Bowtie2,":[141],"state":[143],"art":[146],"tool":[147],"sequence":[149],"alignment,":[150],"on":[151],"Field":[152],"Programmable":[153],"Gate":[154],"Array":[155],"(FPGA).":[156],"design":[158],"shows":[159,187],"speedup":[161,172],"over":[162,175],"software":[164,209],"SW":[167],"8.8x,":[169],"1.95x":[174],"parallelized":[177],"multicore":[178,208],"software.":[183],"architecture":[185],"also":[186],"significant":[189],"increase":[190,196],"power":[192],"efficiency":[193],"80.96x":[198],"17.96x":[200],"respect":[202],"single":[205],"core":[206],"respectively.":[210]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
