{"id":"https://openalex.org/W1965933988","doi":"https://doi.org/10.1109/bibe.2012.6399733","title":"Opportunities from the use of FPGAs as platforms for bioinformatics algorithms","display_name":"Opportunities from the use of FPGAs as platforms for bioinformatics algorithms","publication_year":2012,"publication_date":"2012-11-01","ids":{"openalex":"https://openalex.org/W1965933988","doi":"https://doi.org/10.1109/bibe.2012.6399733","mag":"1965933988"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2012.6399733","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2012.6399733","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 12th International Conference on Bioinformatics &amp; Bioengineering (BIBE)","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/A5106235705","display_name":"Grigorios Chrysos","orcid":null},"institutions":[{"id":"https://openalex.org/I55741626","display_name":"Technical University of Crete","ror":"https://ror.org/03f8bz564","country_code":"GR","type":"education","lineage":["https://openalex.org/I55741626"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Grigorios Chrysos","raw_affiliation_strings":["Technical University of Crete, Chania, Greece","Technical University of Crete; Chania; Greece"],"affiliations":[{"raw_affiliation_string":"Technical University of Crete, Chania, Greece","institution_ids":["https://openalex.org/I55741626"]},{"raw_affiliation_string":"Technical University of Crete; Chania; Greece","institution_ids":["https://openalex.org/I55741626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113700477","display_name":"Euripides Sotiriades","orcid":null},"institutions":[{"id":"https://openalex.org/I55741626","display_name":"Technical University of Crete","ror":"https://ror.org/03f8bz564","country_code":"GR","type":"education","lineage":["https://openalex.org/I55741626"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Euripides Sotiriades","raw_affiliation_strings":["Technical University of Crete, Chania, Greece","Technical University of Crete; Chania; Greece"],"affiliations":[{"raw_affiliation_string":"Technical University of Crete, Chania, Greece","institution_ids":["https://openalex.org/I55741626"]},{"raw_affiliation_string":"Technical University of Crete; Chania; Greece","institution_ids":["https://openalex.org/I55741626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009693923","display_name":"Christos Rousopoulos","orcid":null},"institutions":[{"id":"https://openalex.org/I55741626","display_name":"Technical University of Crete","ror":"https://ror.org/03f8bz564","country_code":"GR","type":"education","lineage":["https://openalex.org/I55741626"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Christos Rousopoulos","raw_affiliation_strings":["Technical University of Crete, Chania, Greece","Technical University of Crete; Chania; Greece"],"affiliations":[{"raw_affiliation_string":"Technical University of Crete, Chania, Greece","institution_ids":["https://openalex.org/I55741626"]},{"raw_affiliation_string":"Technical University of Crete; Chania; Greece","institution_ids":["https://openalex.org/I55741626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056983242","display_name":"Apostolos Dollas","orcid":null},"institutions":[{"id":"https://openalex.org/I55741626","display_name":"Technical University of Crete","ror":"https://ror.org/03f8bz564","country_code":"GR","type":"education","lineage":["https://openalex.org/I55741626"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Apostolos Dollas","raw_affiliation_strings":["Technical University of Crete, Chania, Greece","Technical University of Crete; Chania; Greece"],"affiliations":[{"raw_affiliation_string":"Technical University of Crete, Chania, Greece","institution_ids":["https://openalex.org/I55741626"]},{"raw_affiliation_string":"Technical University of Crete; Chania; Greece","institution_ids":["https://openalex.org/I55741626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053246465","display_name":"Agathoklis Papadopoulos","orcid":null},"institutions":[{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Agathoklis Papadopoulos","raw_affiliation_strings":["University of Cyprus, Nicosia, Cyprus","University of Cyprus Nicosia Cyprus"],"affiliations":[{"raw_affiliation_string":"University of Cyprus, Nicosia, Cyprus","institution_ids":["https://openalex.org/I34771391"]},{"raw_affiliation_string":"University of Cyprus Nicosia Cyprus","institution_ids":["https://openalex.org/I34771391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022031344","display_name":"Ioannis Kirmitzoglou","orcid":null},"institutions":[{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Ioannis Kirmitzoglou","raw_affiliation_strings":["University of Cyprus, Nicosia, Cyprus","University of Cyprus Nicosia Cyprus"],"affiliations":[{"raw_affiliation_string":"University of Cyprus, Nicosia, Cyprus","institution_ids":["https://openalex.org/I34771391"]},{"raw_affiliation_string":"University of Cyprus Nicosia Cyprus","institution_ids":["https://openalex.org/I34771391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070268749","display_name":"Vasilis J. Promponas","orcid":"https://orcid.org/0000-0003-3352-4831"},"institutions":[{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Vasilis Promponas","raw_affiliation_strings":["University of Cyprus, Nicosia, Cyprus","University of Cyprus Nicosia Cyprus"],"affiliations":[{"raw_affiliation_string":"University of Cyprus, Nicosia, Cyprus","institution_ids":["https://openalex.org/I34771391"]},{"raw_affiliation_string":"University of Cyprus Nicosia Cyprus","institution_ids":["https://openalex.org/I34771391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041366767","display_name":"Theocharis Theocharides","orcid":"https://orcid.org/0000-0001-7222-9152"},"institutions":[{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Theocharis Theocharides","raw_affiliation_strings":["University of Cyprus, Nicosia, Cyprus","University of Cyprus Nicosia Cyprus"],"affiliations":[{"raw_affiliation_string":"University of Cyprus, Nicosia, Cyprus","institution_ids":["https://openalex.org/I34771391"]},{"raw_affiliation_string":"University of Cyprus Nicosia Cyprus","institution_ids":["https://openalex.org/I34771391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007563998","display_name":"George Petihakis","orcid":"https://orcid.org/0000-0002-4290-3588"},"institutions":[{"id":"https://openalex.org/I4210131924","display_name":"Hellenic Centre for Marine Research","ror":"https://ror.org/038kffh84","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210131924"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"George Petihakis","raw_affiliation_strings":["Hellenic Center for Marine Research, Heraklion, Greece"],"affiliations":[{"raw_affiliation_string":"Hellenic Center for Marine Research, Heraklion, Greece","institution_ids":["https://openalex.org/I4210131924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107466162","display_name":"Jacques Lagnel","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131924","display_name":"Hellenic Centre for Marine Research","ror":"https://ror.org/038kffh84","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210131924"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Jacques Lagnel","raw_affiliation_strings":["Hellenic Center for Marine Research, Heraklion, Greece"],"affiliations":[{"raw_affiliation_string":"Hellenic Center for Marine Research, Heraklion, Greece","institution_ids":["https://openalex.org/I4210131924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058109221","display_name":"Panagiotis Vavylis","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131924","display_name":"Hellenic Centre for Marine Research","ror":"https://ror.org/038kffh84","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210131924"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Panagiotis Vavylis","raw_affiliation_strings":["Hellenic Center for Marine Research, Heraklion, Greece"],"affiliations":[{"raw_affiliation_string":"Hellenic Center for Marine Research, Heraklion, Greece","institution_ids":["https://openalex.org/I4210131924"]}]},{"author_position":"last","author":{"id":null,"display_name":"George Kotoulas","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131924","display_name":"Hellenic Centre for Marine Research","ror":"https://ror.org/038kffh84","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210131924"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"George Kotoulas","raw_affiliation_strings":["Hellenic Center for Marine Research, Heraklion, Greece"],"affiliations":[{"raw_affiliation_string":"Hellenic Center for Marine Research, Heraklion, Greece","institution_ids":["https://openalex.org/I4210131924"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5106235705"],"corresponding_institution_ids":["https://openalex.org/I55741626"],"apc_list":null,"apc_paid":null,"fwci":0.5379,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.64233121,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"453","issue":null,"first_page":"559","last_page":"565"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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":0.9973999857902527,"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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9861999750137329,"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/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.8022966384887695},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7326993942260742},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5524927973747253},{"id":"https://openalex.org/keywords/mainstream","display_name":"Mainstream","score":0.5407471656799316},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4678804278373718},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.4418627917766571},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4300912618637085},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.38489997386932373},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.30410224199295044},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.20104756951332092},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09518405795097351},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09451553225517273}],"concepts":[{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.8022966384887695},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7326993942260742},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5524927973747253},{"id":"https://openalex.org/C2777617010","wikidata":"https://www.wikidata.org/wiki/Q18957","display_name":"Mainstream","level":2,"score":0.5407471656799316},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4678804278373718},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.4418627917766571},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4300912618637085},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.38489997386932373},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.30410224199295044},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.20104756951332092},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09518405795097351},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09451553225517273},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C27206212","wikidata":"https://www.wikidata.org/wiki/Q34178","display_name":"Theology","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2012.6399733","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2012.6399733","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 12th International Conference on Bioinformatics &amp; Bioengineering (BIBE)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1972097354","https://openalex.org/W1981644820","https://openalex.org/W2006362317","https://openalex.org/W2025763720","https://openalex.org/W2032870665","https://openalex.org/W2043198910","https://openalex.org/W2051916497","https://openalex.org/W2055043387","https://openalex.org/W2095783058","https://openalex.org/W2097335492","https://openalex.org/W2102502076","https://openalex.org/W2103644816","https://openalex.org/W2104412724","https://openalex.org/W2120428067","https://openalex.org/W2121840477","https://openalex.org/W2122942724","https://openalex.org/W2133008414","https://openalex.org/W2133142974","https://openalex.org/W2140350225","https://openalex.org/W2143180875","https://openalex.org/W2144362290","https://openalex.org/W2154240181","https://openalex.org/W2164824418","https://openalex.org/W2166624903","https://openalex.org/W2168696662","https://openalex.org/W2397578107","https://openalex.org/W2400250419","https://openalex.org/W3140730966","https://openalex.org/W3150677990","https://openalex.org/W4236236547","https://openalex.org/W6661183049","https://openalex.org/W6712582925"],"related_works":["https://openalex.org/W2004215917","https://openalex.org/W2948014085","https://openalex.org/W1974956921","https://openalex.org/W2139695554","https://openalex.org/W2103737249","https://openalex.org/W1972247471","https://openalex.org/W1486249959","https://openalex.org/W2166325055","https://openalex.org/W2885386129","https://openalex.org/W2089499735"],"abstract_inverted_index":{"This":[0,78],"paper":[1],"presents":[2,81],"an":[3],"in-depth":[4],"look":[5],"of":[6,17,30],"how":[7],"FPGA":[8,67,94],"computing":[9,95],"can":[10],"offer":[11],"substantial":[12],"speedups":[13],"in":[14,91,101],"the":[15],"execution":[16],"bioinformatics":[18],"algorithms,":[19],"with":[20],"specific":[21],"results":[22],"achieved":[23],"to":[24,88,96],"date":[25],"for":[26,38,93],"a":[27,98],"broad":[28],"range":[29],"algorithms.":[31],"Examples":[32],"and":[33,49,59,83],"case":[34],"studies":[35],"are":[36],"presented":[37],"sequence":[39,44],"comparison":[40],"(BLAST,":[41],"CAST),":[42],"multiple":[43],"alignment":[45],"(MAFFT,":[46],"T-Coffee),":[47],"RNA":[48],"protein":[50],"secondary":[51],"structure":[52],"prediction":[53,57],"(Zuker,":[54],"Predator),":[55],"gene":[56],"(Glimmer/GlimmerHMM)":[58],"phylogenetic":[60],"tree":[61],"computation":[62],"(RAxML),":[63],"running":[64],"on":[65],"mainstream":[66,99],"technologies":[68],"as":[69,71],"well":[70],"high-end":[72],"FPGA-based":[73],"systems":[74],"(Convey":[75],"HC1,":[76],"BeeCube).":[77],"work":[79],"also":[80],"technological":[82],"other":[84],"obstacles":[85],"that":[86],"need":[87],"be":[89],"overcome":[90],"order":[92],"become":[97],"technology":[100],"Bioinformatics.":[102]},"counts_by_year":[{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
