{"id":"https://openalex.org/W7126042253","doi":"https://doi.org/10.1109/bibm66473.2025.11356792","title":"An Efficient Pattern Matching Approach for Compressed Genomic Sequences","display_name":"An Efficient Pattern Matching Approach for Compressed Genomic Sequences","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126042253","doi":"https://doi.org/10.1109/bibm66473.2025.11356792"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356792","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356792","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5124204850","display_name":"Han Duan","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Han Duan","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences,Beijing,China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences,Beijing,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039277184","display_name":"Chuan Zhi Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuan Hu","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences,Beijing,China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences,Beijing,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044592632","display_name":"Zhihong Shen","orcid":"https://orcid.org/0000-0002-0113-0478"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihong Shen","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences,Beijing,China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences,Beijing,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5124204850"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210108629"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.84045706,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"6527","last_page":"6534"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.98089998960495,"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":0.98089998960495,"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":0.006899999920278788,"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":0.0024999999441206455,"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/search-engine-indexing","display_name":"Search engine indexing","score":0.753600001335144},{"id":"https://openalex.org/keywords/bitmap","display_name":"Bitmap","score":0.6996999979019165},{"id":"https://openalex.org/keywords/data-compression","display_name":"Data compression","score":0.5752999782562256},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.560699999332428},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.5569000244140625},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5040000081062317},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4747999906539917},{"id":"https://openalex.org/keywords/byte","display_name":"Byte","score":0.4691999852657318}],"concepts":[{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.753600001335144},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7035999894142151},{"id":"https://openalex.org/C3115412","wikidata":"https://www.wikidata.org/wiki/Q1194708","display_name":"Bitmap","level":2,"score":0.6996999979019165},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.5752999782562256},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.560699999332428},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.5569000244140625},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5040000081062317},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4747999906539917},{"id":"https://openalex.org/C43364308","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Byte","level":2,"score":0.4691999852657318},{"id":"https://openalex.org/C25797200","wikidata":"https://www.wikidata.org/wiki/Q828137","display_name":"Compression ratio","level":3,"score":0.4219000041484833},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41290000081062317},{"id":"https://openalex.org/C180016635","wikidata":"https://www.wikidata.org/wiki/Q2712821","display_name":"Compression (physics)","level":2,"score":0.4097000062465668},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4011000096797943},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3474000096321106},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.33090001344680786},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.3240000009536743},{"id":"https://openalex.org/C59276292","wikidata":"https://www.wikidata.org/wiki/Q580427","display_name":"Database index","level":3,"score":0.3124000132083893},{"id":"https://openalex.org/C193524817","wikidata":"https://www.wikidata.org/wiki/Q386780","display_name":"Association rule learning","level":2,"score":0.3093999922275543},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.3009999990463257},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.2696000039577484},{"id":"https://openalex.org/C194739806","wikidata":"https://www.wikidata.org/wiki/Q66221","display_name":"Computer data storage","level":2,"score":0.2639999985694885},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2549000084400177}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356792","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356792","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5897372185","display_name":null,"funder_award_id":"2024YFF0729201","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1530918642","https://openalex.org/W1532202009","https://openalex.org/W1537923221","https://openalex.org/W1777016212","https://openalex.org/W2092880969","https://openalex.org/W2138196010","https://openalex.org/W2157745386","https://openalex.org/W2158874082","https://openalex.org/W2580314844","https://openalex.org/W2781268828","https://openalex.org/W2791674087","https://openalex.org/W2903638214","https://openalex.org/W2951893579","https://openalex.org/W3001630589","https://openalex.org/W3038746171","https://openalex.org/W4205915047","https://openalex.org/W4214559301","https://openalex.org/W4390939384","https://openalex.org/W4391316557","https://openalex.org/W4392747035"],"related_works":[],"abstract_inverted_index":{"The":[0,97],"rapid":[1],"growth":[2],"of":[3],"genomic":[4,46,120,151],"data":[5,152],"has":[6],"created":[7],"a":[8,49,56,71,127,146],"demand":[9],"for":[10,44,91,149],"storage-efficient":[11],"formats":[12],"that":[13,123],"also":[14],"support":[15],"fast":[16],"search.":[17],"Most":[18],"existing":[19],"compressors,":[20],"whether":[21],"general-purpose":[22],"or":[23],"domain-specific,":[24],"require":[25],"full":[26],"decompression":[27],"before":[28],"analysis,":[29],"resulting":[30],"in":[31,88],"substantial":[32],"time":[33],"and":[34,64,105,135,141,154],"memory":[35,133],"costs.":[36],"We":[37],"present":[38],"an":[39,65],"efficient":[40,92],"pattern":[41],"matching":[42,137],"approach":[43],"compressed":[45,89],"sequences,":[47],"combining":[48],"Gene":[50],"Sequence":[51,102],"Bitmap":[52],"Compression":[53],"(GSBC)":[54],"scheme,":[55],"Low-Frequency":[57],"Byte":[58],"Position-Based":[59],"Pattern":[60],"Matching":[61],"(LFBPBPM)":[62],"algorithm,":[63],"optimized":[66],"indexing":[67,98],"method.":[68],"GSBC":[69],"applies":[70],"2-bit":[72],"nucleotide":[73],"encoding":[74],"to":[75,114],"reduce":[76],"storage":[77,153],"while":[78],"preserving":[79],"biological":[80],"semantics.":[81],"LFBPBPM":[82],"exploits":[83],"the":[84],"skewed":[85],"byte-frequency":[86],"distribution":[87],"sequences":[90],"candidate":[93],"filtering,":[94],"avoiding":[95],"decompression.":[96],"strategy,":[99],"based":[100],"on":[101,118],"Indexing":[103],"Triads":[104],"horizontal":[106],"compression,":[107],"further":[108],"reduces":[109],"index":[110],"size":[111],"by":[112],"up":[113],"28":[115],"%.":[116],"Experiments":[117],"large":[119],"datasets":[121],"show":[122],"our":[124],"method":[125],"achieves":[126],"29%":[128],"compression":[129],"ratio":[130],"with":[131],"lower":[132],"usage":[134],"faster":[136],"than":[138],"18":[139],"compressors":[140],"11":[142],"search":[143],"algorithms,":[144],"offering":[145],"promising":[147],"solution":[148],"large-scale":[150],"retrieval.":[155]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-01-30T00:00:00"}
