{"id":"https://openalex.org/W2088115849","doi":"https://doi.org/10.1145/2063384.2063459","title":"Highly scalable <i>ab initio</i> genomic motif identification","display_name":"Highly scalable <i>ab initio</i> genomic motif identification","publication_year":2011,"publication_date":"2011-11-08","ids":{"openalex":"https://openalex.org/W2088115849","doi":"https://doi.org/10.1145/2063384.2063459","mag":"2088115849"},"language":"en","primary_location":{"id":"doi:10.1145/2063384.2063459","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2063384.2063459","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis","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/A5011616954","display_name":"Beno\u0131\u0302t Marchand","orcid":"https://orcid.org/0000-0001-5137-3526"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Beno\u00eet Marchand","raw_affiliation_strings":["King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055569646","display_name":"Vladimir B. Baji\u0107","orcid":"https://orcid.org/0000-0001-5435-4750"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Vladimir B. Bajic","raw_affiliation_strings":["King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111841360","display_name":"Dinesh Kaushik","orcid":null},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Dinesh K. Kaushik","raw_affiliation_strings":["King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","KAUST Supercomputing Laboratory (KSL), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"KAUST Supercomputing Laboratory (KSL), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5011616954"],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":null,"apc_paid":null,"fwci":0.6514,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.68326898,"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":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T11269","display_name":"Algorithms and Data Compression","score":0.9980000257492065,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9973000288009644,"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/scalability","display_name":"Scalability","score":0.7623157501220703},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7551823854446411},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.6549076437950134},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6515752673149109},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5559659600257874},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.5330184102058411},{"id":"https://openalex.org/keywords/workload","display_name":"Workload","score":0.518814742565155},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.43127915263175964},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.4216546416282654},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33919310569763184},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.18413615226745605},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1623346209526062},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10871279239654541},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08033311367034912}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7623157501220703},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7551823854446411},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6549076437950134},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6515752673149109},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5559659600257874},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.5330184102058411},{"id":"https://openalex.org/C2778476105","wikidata":"https://www.wikidata.org/wiki/Q628539","display_name":"Workload","level":2,"score":0.518814742565155},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.43127915263175964},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.4216546416282654},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33919310569763184},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18413615226745605},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1623346209526062},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10871279239654541},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08033311367034912},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2063384.2063459","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2063384.2063459","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis","raw_type":"proceedings-article"},{"id":"pmh:oai:repository.kaust.edu.sa:10754/564332","is_oa":false,"landing_page_url":"http://hdl.handle.net/10754/564332","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference Paper"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production","score":0.4699999988079071}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W6041888","https://openalex.org/W145873026","https://openalex.org/W1993030047","https://openalex.org/W2071116416","https://openalex.org/W2102924260","https://openalex.org/W2495184785"],"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/W2027972911","https://openalex.org/W2157978810","https://openalex.org/W2597809628","https://openalex.org/W3012895752"],"abstract_inverted_index":{"We":[0,68],"present":[1],"results":[2],"of":[3,20,27,35,48,76,96,157],"scaling":[4],"an":[5],"ab":[6,61,140],"initio":[7,62,141],"motif":[8,41],"family":[9],"identification":[10],"system,":[11],"Dragon":[12],"Motif":[13],"Finder":[14],"(DMF),":[15],"to":[16,50,58,108,120,135],"65,536":[17,105],"processor":[18],"cores":[19,106,110],"IBM":[21],"Blue":[22],"Gene/P.":[23],"DMF":[24],"seeks":[25],"groups":[26],"mutually":[28],"similar":[29],"polynucleotide":[30],"patterns":[31],"within":[32],"a":[33,74,112,145],"set":[34],"genomic":[36],"sequences":[37],"and":[38,90],"builds":[39],"various":[40],"families":[42],"from":[43],"them.":[44],"Such":[45],"information":[46],"is":[47],"relevance":[49],"many":[51,138],"problems":[52],"in":[53,144],"life":[54],"sciences.":[55],"Prior":[56],"attempts":[57],"scale":[59],"such":[60],"motif-finding":[63,142],"algorithms":[64],"achieved":[65],"limited":[66],"success.":[67],"solve":[69],"the":[70,94,115,121,149],"scalability":[71,95],"issues":[72],"using":[73],"combination":[75],"mixed-mode":[77],"MPI-OpenMP":[78],"parallel":[79,102],"programming,":[80],"master-slave":[81],"work":[82],"assignment,":[83],"multi-level":[84,87],"workload":[85],"distribution,":[86],"MPI":[88],"collectives,":[89],"serial":[91,123,128,151],"optimizations.":[92],"While":[93],"our":[97],"algorithm":[98],"was":[99],"excellent":[100],"(94%":[101],"efficiency":[103],"on":[104,111],"relative":[107],"256":[109],"modest-size":[113],"problem),":[114],"final":[116],"speedup":[117],"with":[118],"respect":[119],"original":[122,150],"code":[124,152],"exceeded":[125],"250,000":[126],"when":[127],"optimizations":[129],"are":[130],"included.":[131],"This":[132],"enabled":[133],"us":[134],"carry":[136],"out":[137],"large-scale":[139],"simulations":[143],"few":[146],"hours":[147],"while":[148],"would":[153],"have":[154],"needed":[155],"decades":[156],"execution":[158],"time.":[159]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
