{"id":"https://openalex.org/W2114671747","doi":"https://doi.org/10.1109/cibcb.2007.4221240","title":"Hybrid Architecture for Accelerating DNA Codeword Library Searching","display_name":"Hybrid Architecture for Accelerating DNA Codeword Library Searching","publication_year":2007,"publication_date":"2007-04-01","ids":{"openalex":"https://openalex.org/W2114671747","doi":"https://doi.org/10.1109/cibcb.2007.4221240","mag":"2114671747"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2007.4221240","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2007.4221240","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology","raw_type":"proceedings-article"},"type":"conference-paper","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/A5018468480","display_name":"Qinru Qiu","orcid":"https://orcid.org/0000-0003-2546-0655"},"institutions":[{"id":"https://openalex.org/I123946342","display_name":"Binghamton University","ror":"https://ror.org/008rmbt77","country_code":"US","type":"education","lineage":["https://openalex.org/I123946342"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qinru Qiu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Binghamton University, Binghamton, NY, USA","Dept. of Electr. & Comput. Eng., Binghamton Univ., NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Binghamton University, Binghamton, NY, USA","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Binghamton Univ., NY","institution_ids":["https://openalex.org/I123946342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101569957","display_name":"Daniel J. Burns","orcid":null},"institutions":[{"id":"https://openalex.org/I123946342","display_name":"Binghamton University","ror":"https://ror.org/008rmbt77","country_code":"US","type":"education","lineage":["https://openalex.org/I123946342"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Burns","raw_affiliation_strings":["Air Force Research Laboratory, Rome, Italy","Dept. of Electr. & Comput. Eng., Binghamton Univ., NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Air Force Research Laboratory, Rome, Italy","institution_ids":[]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Binghamton Univ., NY","institution_ids":["https://openalex.org/I123946342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100731724","display_name":"Q. M. Jonathan Wu","orcid":"https://orcid.org/0000-0002-5208-7975"},"institutions":[{"id":"https://openalex.org/I123946342","display_name":"Binghamton University","ror":"https://ror.org/008rmbt77","country_code":"US","type":"education","lineage":["https://openalex.org/I123946342"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qing Wu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Binghamton University, Binghamton, NY, USA","Dept. of Electr. & Comput. Eng., Binghamton Univ., NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Binghamton University, Binghamton, NY, USA","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Binghamton Univ., NY","institution_ids":["https://openalex.org/I123946342"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006836561","display_name":"Prakash Mukre","orcid":null},"institutions":[{"id":"https://openalex.org/I123946342","display_name":"Binghamton University","ror":"https://ror.org/008rmbt77","country_code":"US","type":"education","lineage":["https://openalex.org/I123946342"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. Mukre","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Binghamton University, Binghamton, NY, USA","Dept. of Electr. & Comput. Eng., Binghamton Univ., NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Binghamton University, Binghamton, NY, USA","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Binghamton Univ., NY","institution_ids":["https://openalex.org/I123946342"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I123946342"],"apc_list":null,"apc_paid":null,"fwci":4.9593,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.94883652,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"3969","issue":null,"first_page":"323","last_page":"330"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","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/T12029","display_name":"DNA and Biological Computing","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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","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/T11269","display_name":"Algorithms and Data Compression","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7631351947784424},{"id":"https://openalex.org/keywords/code-word","display_name":"Code word","score":0.6491727828979492},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.4876755475997925},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4640829563140869},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.45879149436950684},{"id":"https://openalex.org/keywords/microprocessor","display_name":"Microprocessor","score":0.4419272541999817},{"id":"https://openalex.org/keywords/edit-distance","display_name":"Edit distance","score":0.41120094060897827},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.39282917976379395},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3552568256855011},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33007925748825073},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32422977685928345},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2935599088668823},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.206839919090271},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.13414207100868225}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7631351947784424},{"id":"https://openalex.org/C153207627","wikidata":"https://www.wikidata.org/wiki/Q863873","display_name":"Code word","level":3,"score":0.6491727828979492},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.4876755475997925},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4640829563140869},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.45879149436950684},{"id":"https://openalex.org/C2780728072","wikidata":"https://www.wikidata.org/wiki/Q5297","display_name":"Microprocessor","level":2,"score":0.4419272541999817},{"id":"https://openalex.org/C44359876","wikidata":"https://www.wikidata.org/wiki/Q5338467","display_name":"Edit distance","level":2,"score":0.41120094060897827},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.39282917976379395},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3552568256855011},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33007925748825073},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32422977685928345},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2935599088668823},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.206839919090271},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.13414207100868225},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/cibcb.2007.4221240","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2007.4221240","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.86.867","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.86.867","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://hydrogen.ws.binghamton.edu/~qqiu/papers/CIBCB_07.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5299999713897705}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1504030323","https://openalex.org/W1562861155","https://openalex.org/W1964440534","https://openalex.org/W1970529854","https://openalex.org/W1977312644","https://openalex.org/W2017106829","https://openalex.org/W2096307073","https://openalex.org/W2135995702","https://openalex.org/W2471342003","https://openalex.org/W2912221431","https://openalex.org/W4256415959","https://openalex.org/W6630069870","https://openalex.org/W6633827651"],"related_works":["https://openalex.org/W3044917232","https://openalex.org/W1498160656","https://openalex.org/W2055693471","https://openalex.org/W2119149496","https://openalex.org/W39373273","https://openalex.org/W2139858675","https://openalex.org/W2952580779","https://openalex.org/W2895235410","https://openalex.org/W251429526","https://openalex.org/W2304380675"],"abstract_inverted_index":{"A":[0],"large":[1],"and":[2,53,75,97,138],"reliable":[3,22],"DNA":[4,14,23,62],"codeword":[5],"library":[6],"is":[7,25],"the":[8,11,19,34,59,115,126,132,140],"key":[9],"to":[10,87,105,149],"success":[12],"of":[13,21,48,61,70,117,131],"based":[15],"computing.":[16],"Searching":[17],"for":[18,57,114],"set":[20],"codewords":[24],"an":[26],"NP-hard":[27],"problem,":[28],"which":[29],"can":[30,128],"take":[31],"days":[32],"on":[33],"state-of-art":[35],"high":[36],"performance":[37],"cluster":[38],"computers.":[39],"This":[40],"work":[41],"presents":[42],"a":[43,49,54,78,83,94,98,150],"hybrid":[44,141],"architecture":[45,72,142],"that":[46,81,101,125,139],"consists":[47],"general":[50],"purpose":[51],"microprocessor":[52],"hardware":[55],"accelerator":[56],"accelerating":[58],"discovery":[60],"reverse":[63],"complement,":[64],"edit":[65],"distance":[66],"codes.":[67,120],"Two":[68],"applications":[69],"this":[71],"were":[73],"implemented":[74],"evaluated,":[76],"including":[77],"code":[79,99],"generator":[80],"uses":[82,102],"genetic":[84],"algorithm":[85],"(GA)":[86],"produce":[88,106],"nearly":[89],"locally":[90,107,135],"optimal":[91],"codes":[92,109],"in":[93,110,134],"few":[95],"minutes,":[96],"extender":[100],"exhaustive":[103],"search":[104],"optimum":[108,136],"about":[111],"1.5":[112],"hours":[113],"case":[116],"length":[118],"16":[119],"The":[121],"experimental":[122],"results":[123],"demonstrate":[124],"GA":[127],"find":[129],"~99%":[130],"words":[133],"libraries,":[137],"provides":[143],"more":[144],"than":[145],"1000X":[146],"speed-up":[147],"compared":[148],"software":[151],"only":[152],"implementation":[153]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}