{"id":"https://openalex.org/W2132365957","doi":"https://doi.org/10.1109/csb.2004.1332418","title":"Compressed pattern matching in DNA sequences","display_name":"Compressed pattern matching in DNA sequences","publication_year":2004,"publication_date":"2004-11-08","ids":{"openalex":"https://openalex.org/W2132365957","doi":"https://doi.org/10.1109/csb.2004.1332418","mag":"2132365957","pmid":"https://pubmed.ncbi.nlm.nih.gov/16448000"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2004.1332418","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332418","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5064062823","display_name":"Lei Chen","orcid":"https://orcid.org/0000-0002-4912-3293"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lei Chen","raw_affiliation_strings":["Wayne State University, USA. ak3230@wayne.edu","Wayne State University Detroit MI USA"],"affiliations":[{"raw_affiliation_string":"Wayne State University, USA. ak3230@wayne.edu","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Wayne State University Detroit MI USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044023807","display_name":"Shiyong Lu","orcid":"https://orcid.org/0000-0002-7864-1815"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shiyong Lu","raw_affiliation_strings":["Wayne State University, USA","Wayne State University Detroit MI USA"],"affiliations":[{"raw_affiliation_string":"Wayne State University, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Wayne State University Detroit MI USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081790732","display_name":"Jeffrey L. Ram","orcid":"https://orcid.org/0000-0002-1063-546X"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Ram","raw_affiliation_strings":["Wayne State University, USA","Wayne State University Detroit MI USA"],"affiliations":[{"raw_affiliation_string":"Wayne State University, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Wayne State University Detroit MI USA","institution_ids":["https://openalex.org/I185443292"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5064062823"],"corresponding_institution_ids":["https://openalex.org/I185443292"],"apc_list":null,"apc_paid":null,"fwci":1.6844,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.85004643,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"39","issue":null,"first_page":"59","last_page":"65"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998999834060669,"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":0.9940999746322632,"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/T12326","display_name":"Network Packet Processing and Optimization","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/string-searching-algorithm","display_name":"String searching algorithm","score":0.73444664478302},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.710986852645874},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5988825559616089},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5614466071128845},{"id":"https://openalex.org/keywords/compressed-suffix-array","display_name":"Compressed suffix array","score":0.5583794116973877},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.545081615447998},{"id":"https://openalex.org/keywords/data-compression","display_name":"Data compression","score":0.543308436870575},{"id":"https://openalex.org/keywords/commentz-walter-algorithm","display_name":"Commentz-Walter algorithm","score":0.4866979420185089},{"id":"https://openalex.org/keywords/alphabet","display_name":"Alphabet","score":0.47992926836013794},{"id":"https://openalex.org/keywords/compression","display_name":"Compression (physics)","score":0.41583240032196045},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.40177950263023376},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.34113287925720215},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.303688645362854},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1994476318359375}],"concepts":[{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.73444664478302},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.710986852645874},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5988825559616089},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5614466071128845},{"id":"https://openalex.org/C100903775","wikidata":"https://www.wikidata.org/wiki/Q5157028","display_name":"Compressed suffix array","level":4,"score":0.5583794116973877},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.545081615447998},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.543308436870575},{"id":"https://openalex.org/C13052355","wikidata":"https://www.wikidata.org/wiki/Q5152399","display_name":"Commentz-Walter algorithm","level":4,"score":0.4866979420185089},{"id":"https://openalex.org/C112876837","wikidata":"https://www.wikidata.org/wiki/Q837518","display_name":"Alphabet","level":2,"score":0.47992926836013794},{"id":"https://openalex.org/C180016635","wikidata":"https://www.wikidata.org/wiki/Q2712821","display_name":"Compression (physics)","level":2,"score":0.41583240032196045},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.40177950263023376},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34113287925720215},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.303688645362854},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1994476318359375},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1109/csb.2004.1332418","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332418","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},{"id":"pmid:16448000","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16448000","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. IEEE Computational Systems Bioinformatics Conference","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.258.5184","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.258.5184","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.wayne.edu/%7Eshiyong/papers/csb2004_chen.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.404.825","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.404.825","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://ftp.dec.com/pub/toomany/005_lu_s_patternMatching.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.75.2354","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.75.2354","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.wayne.edu/~shiyong/papers/csb04.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.5799999833106995}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W46679369","https://openalex.org/W938539187","https://openalex.org/W1480106357","https://openalex.org/W1499930986","https://openalex.org/W1510807444","https://openalex.org/W1512616185","https://openalex.org/W1514337702","https://openalex.org/W1521067712","https://openalex.org/W1530918642","https://openalex.org/W1569173524","https://openalex.org/W1883832029","https://openalex.org/W1986106281","https://openalex.org/W1990061958","https://openalex.org/W2003093253","https://openalex.org/W2019724649","https://openalex.org/W2026315272","https://openalex.org/W2045821558","https://openalex.org/W2062657631","https://openalex.org/W2104098945","https://openalex.org/W2108278098","https://openalex.org/W2133248397","https://openalex.org/W2134826720","https://openalex.org/W2160748429","https://openalex.org/W2460736511","https://openalex.org/W2610179052","https://openalex.org/W4285719527","https://openalex.org/W6601894380","https://openalex.org/W6630503602","https://openalex.org/W6631160372"],"related_works":["https://openalex.org/W3145288231","https://openalex.org/W2257399947","https://openalex.org/W2371263218","https://openalex.org/W4398785990","https://openalex.org/W2245915510","https://openalex.org/W2182332549","https://openalex.org/W2141423589","https://openalex.org/W2355168454","https://openalex.org/W2019219986","https://openalex.org/W2132365957"],"abstract_inverted_index":{"We":[0],"propose":[1],"derivative":[2],"Boyer-Moore":[3,20,124],"(d-BM),":[4],"a":[5,102],"new":[6],"compressed":[7,58],"pattern":[8,59,90],"matching":[9,30,60,91],"algorithm":[10,15,61,115],"in":[11,130],"DNA":[12,38,64,96],"sequences.":[13],"This":[14],"is":[16,23,85,116],"based":[17],"on":[18],"the":[19,26,75,80,88,110,114,119,123],"method,":[21],"which":[22,84],"one":[24],"of":[25,79,95,106,113,122],"most":[27],"popular":[28],"string":[29],"algorithms.":[31],"In":[32,108],"this":[33,57,99],"approach,":[34],"we":[35],"compress":[36],"both":[37],"sequences":[39,97],"and":[40],"patterns":[41,65],"by":[42,98],"using":[43],"two":[44],"bits":[45],"to":[46,118,135],"represent":[47],"each":[48],"A,":[49],"T,":[50],"C,":[51],"G":[52],"character.":[53],"Experiments":[54],"indicate":[55],"that":[56],"searches":[62],"long":[63],"(length":[66],">":[67],"50)":[68],"more":[69],"than":[70,74],"10":[71],"times":[72],"faster":[73],"exact":[76],"match":[77],"routine":[78],"software":[81],"package":[82],"Agrep,":[83],"known":[86],"as":[87],"fastest":[89],"tool.":[92],"Moreover,":[93],"compression":[94],"method":[100,125],"gives":[101],"guaranteed":[103],"space":[104],"saving":[105],"75%.":[107],"part":[109],"enhanced":[111],"speed":[112],"due":[117],"increased":[120],"efficiency":[121],"resulting":[126],"from":[127,133],"an":[128],"increase":[129],"alphabet":[131],"size":[132],"4":[134],"256.":[136]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
