{"id":"https://openalex.org/W2004902010","doi":"https://doi.org/10.1109/bibe.2007.4375664","title":"FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data","display_name":"FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data","publication_year":2007,"publication_date":"2007-10-01","ids":{"openalex":"https://openalex.org/W2004902010","doi":"https://doi.org/10.1109/bibe.2007.4375664","mag":"2004902010"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2007.4375664","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375664","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","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/A5001266986","display_name":"Jason D. Bakos","orcid":"https://orcid.org/0000-0002-0821-6258"},"institutions":[{"id":"https://openalex.org/I155781252","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903","country_code":"US","type":"education","lineage":["https://openalex.org/I155781252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason D. Bakos","raw_affiliation_strings":["Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA","University of South Carolina, Columbia;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA","institution_ids":["https://openalex.org/I155781252"]},{"raw_affiliation_string":"University of South Carolina, Columbia;","institution_ids":["https://openalex.org/I155781252"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076415234","display_name":"Panormitis E. Elenis","orcid":null},"institutions":[{"id":"https://openalex.org/I155781252","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903","country_code":"US","type":"education","lineage":["https://openalex.org/I155781252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Panormitis E. Elenis","raw_affiliation_strings":["Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA","University of South Carolina, Columbia;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA","institution_ids":["https://openalex.org/I155781252"]},{"raw_affiliation_string":"University of South Carolina, Columbia;","institution_ids":["https://openalex.org/I155781252"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001619694","display_name":"Jijun Tang","orcid":"https://orcid.org/0000-0002-6377-536X"},"institutions":[{"id":"https://openalex.org/I155781252","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903","country_code":"US","type":"education","lineage":["https://openalex.org/I155781252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jijun Tang","raw_affiliation_strings":["Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA","University of South Carolina, Columbia;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA","institution_ids":["https://openalex.org/I155781252"]},{"raw_affiliation_string":"University of South Carolina, Columbia;","institution_ids":["https://openalex.org/I155781252"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.2733,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.81185562,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"888","last_page":"895"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.998199999332428,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9977999925613403,"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/speedup","display_name":"Speedup","score":0.9357651472091675},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.7201855182647705},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6917129755020142},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6530101895332336},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6390763521194458},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.607014536857605},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.5507321953773499},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5317071080207825},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.36107760667800903},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35147541761398315},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.13604864478111267},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11456716060638428},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0737684965133667}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.9357651472091675},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.7201855182647705},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6917129755020142},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6530101895332336},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6390763521194458},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.607014536857605},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.5507321953773499},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5317071080207825},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.36107760667800903},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35147541761398315},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.13604864478111267},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11456716060638428},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0737684965133667},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibe.2007.4375664","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375664","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.162.818","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.162.818","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cse.sc.edu/~jbakos/papers/bibe07_paper.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W152315924","https://openalex.org/W1567890695","https://openalex.org/W1572531572","https://openalex.org/W1592788845","https://openalex.org/W1594983821","https://openalex.org/W1794479819","https://openalex.org/W1975922463","https://openalex.org/W1985530443","https://openalex.org/W2026452889","https://openalex.org/W2027350882","https://openalex.org/W2041797002","https://openalex.org/W2043887813","https://openalex.org/W2069010522","https://openalex.org/W2095140504","https://openalex.org/W2097706568","https://openalex.org/W2100665964","https://openalex.org/W2107356030","https://openalex.org/W2132154112","https://openalex.org/W2133090982","https://openalex.org/W2140350225","https://openalex.org/W2146058063","https://openalex.org/W2147015565","https://openalex.org/W2157312689","https://openalex.org/W2168698047","https://openalex.org/W2169039127","https://openalex.org/W2750757353","https://openalex.org/W3140730966","https://openalex.org/W4255466524","https://openalex.org/W4302445777","https://openalex.org/W6633852976","https://openalex.org/W6635422531","https://openalex.org/W6680058235","https://openalex.org/W6845193463"],"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/W2146872326","https://openalex.org/W2518118925","https://openalex.org/W2532502681","https://openalex.org/W3159273459"],"abstract_inverted_index":{"In":[0],"this":[1,76],"paper":[2,77],"we":[3,59],"describe":[4],"our":[5,51],"design":[6,23],"and":[7,33],"characterization":[8],"of":[9,28,38,65],"a":[10,25,45,83],"co-processor":[11],"architecture":[12],"to":[13],"accelerate":[14],"median-based":[15],"phylogenetic":[16,70,89],"reconstruction":[17,71],"for":[18,40,86],"gene-rearrangement":[19],"data.":[20],"Our":[21],"current":[22],"performs":[24],"parallelized":[26],"version":[27],"the":[29,56,68],"breakpoint":[30],"median":[31,53],"computation":[32,54],"achieves":[34],"an":[35,62],"average":[36,63],"speedup":[37,64],"876":[39],"simulated":[41],"input":[42],"data":[43],"having":[44],"high":[46],"evolution":[47],"rate.":[48],"After":[49],"integrating":[50],"hardware-based":[52],"into":[55],"GRAPPA":[57],"toolset,":[58],"have":[60],"achieved":[61],"189":[66],"over":[67],"entire":[69],"procedure.":[72],"The":[73],"results":[74],"in":[75],"suggest":[78],"that":[79,91],"FPGA-based":[80],"acceleration":[81],"is":[82],"promising":[84],"approach":[85],"computationally":[87],"expensive":[88],"problems":[90],"are":[92],"based":[93],"on":[94],"combinatorial":[95],"optimization.":[96]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
