{"id":"https://openalex.org/W2134151735","doi":"https://doi.org/10.1109/bibm.2010.5706648","title":"PSI-RA: A parallel sparse index for read alignment on genomes","display_name":"PSI-RA: A parallel sparse index for read alignment on genomes","publication_year":2010,"publication_date":"2010-12-01","ids":{"openalex":"https://openalex.org/W2134151735","doi":"https://doi.org/10.1109/bibm.2010.5706648","mag":"2134151735"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2010.5706648","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2010.5706648","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5024416450","display_name":"M. O\u011fuzhan K\u00fclek\u00e7i","orcid":"https://orcid.org/0000-0002-4583-6261"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Oguzhan Kulekci","raw_affiliation_strings":["National Research Institute of Electronics and Cryptology, Turkey","National Research Institute of Electronics & Cryptology, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Research Institute of Electronics and Cryptology, Turkey","institution_ids":[]},{"raw_affiliation_string":"National Research Institute of Electronics & Cryptology, Turkey","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013112058","display_name":"Wing-Kai Hon","orcid":"https://orcid.org/0000-0002-0570-2904"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Wing-Kai Hon","raw_affiliation_strings":["Department of Computer Science, National Tsing Hua University, Taiwan","Department of Computer Science, National Tsing Hua University, , Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National Tsing Hua University, Taiwan","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"Department of Computer Science, National Tsing Hua University, , Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105778361","display_name":"Rahul Shah","orcid":"https://orcid.org/0000-0002-0605-5681"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rahul Shah","raw_affiliation_strings":["Department of Computer Science, Louisiana State University, USA","[Department of Computer Science, Louisiana State University, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Louisiana State University, USA","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"[Department of Computer Science, Louisiana State University, USA]","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003340402","display_name":"Jeffrey Scott Vitter","orcid":"https://orcid.org/0000-0001-7970-6118"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey Scott Vitter","raw_affiliation_strings":["Information and Telecommunication Technology Center, University of Kansas, USA","Information and Telecomunication Technology Center, University of Kansas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Telecommunication Technology Center, University of Kansas, USA","institution_ids":["https://openalex.org/I146416000"]},{"raw_affiliation_string":"Information and Telecomunication Technology Center, University of Kansas, USA","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058084642","display_name":"Bojian Xu","orcid":"https://orcid.org/0000-0001-5642-6826"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bojian Xu","raw_affiliation_strings":["Information and Telecommunication Technology Center, University of Kansas, USA","Information and Telecomunication Technology Center, University of Kansas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Telecommunication Technology Center, University of Kansas, USA","institution_ids":["https://openalex.org/I146416000"]},{"raw_affiliation_string":"Information and Telecomunication Technology Center, University of Kansas, USA","institution_ids":["https://openalex.org/I146416000"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.8174,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.73038332,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"663","last_page":"668"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9986000061035156,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9670000076293945,"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/search-engine-indexing","display_name":"Search engine indexing","score":0.8219519853591919},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7775272130966187},{"id":"https://openalex.org/keywords/suffix-array","display_name":"Suffix array","score":0.7303783297538757},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.5868648290634155},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5368697047233582},{"id":"https://openalex.org/keywords/compressed-suffix-array","display_name":"Compressed suffix array","score":0.521088719367981},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4794275164604187},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.47072163224220276},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.4415777623653412},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.42482441663742065},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3907809555530548},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.3483082056045532},{"id":"https://openalex.org/keywords/string-searching-algorithm","display_name":"String searching algorithm","score":0.324138879776001},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22924575209617615},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1802314817905426}],"concepts":[{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.8219519853591919},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7775272130966187},{"id":"https://openalex.org/C2779259728","wikidata":"https://www.wikidata.org/wiki/Q281472","display_name":"Suffix array","level":3,"score":0.7303783297538757},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.5868648290634155},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5368697047233582},{"id":"https://openalex.org/C100903775","wikidata":"https://www.wikidata.org/wiki/Q5157028","display_name":"Compressed suffix array","level":4,"score":0.521088719367981},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4794275164604187},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.47072163224220276},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.4415777623653412},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.42482441663742065},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3907809555530548},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.3483082056045532},{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.324138879776001},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22924575209617615},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1802314817905426},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"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/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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm.2010.5706648","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2010.5706648","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:repository.lsu.edu:eecs_pubs-3675","is_oa":false,"landing_page_url":"https://repository.lsu.edu/eecs_pubs/2673","pdf_url":null,"source":{"id":"https://openalex.org/S4210169993","display_name":"Civil War Book Review","issn_l":"1528-6592","issn":["1528-6592"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310315936","host_organization_name":"Louisiana State University","host_organization_lineage":["https://openalex.org/P4310315936"],"host_organization_lineage_names":["Louisiana State University"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1788916882","https://openalex.org/W1969173824","https://openalex.org/W1972924519","https://openalex.org/W2037953066","https://openalex.org/W2061680337","https://openalex.org/W2088386938","https://openalex.org/W2093931624","https://openalex.org/W2103441770","https://openalex.org/W2104132688","https://openalex.org/W2104822159","https://openalex.org/W2115872073","https://openalex.org/W2118526609","https://openalex.org/W2124985265","https://openalex.org/W2139747296","https://openalex.org/W2139749722","https://openalex.org/W2139760555","https://openalex.org/W2158322625","https://openalex.org/W2158874082","https://openalex.org/W2161488606","https://openalex.org/W2170899819","https://openalex.org/W2171196697","https://openalex.org/W6621160150","https://openalex.org/W6683504902"],"related_works":["https://openalex.org/W2576782855","https://openalex.org/W2359436045","https://openalex.org/W153119118","https://openalex.org/W2005977804","https://openalex.org/W2143531254","https://openalex.org/W2608759984","https://openalex.org/W363060408","https://openalex.org/W2003608043","https://openalex.org/W2355168454","https://openalex.org/W2045266738"],"abstract_inverted_index":{"We":[0,87,128],"concentrate":[1],"on":[2,50,72],"indexing":[3,143],"DNA":[4],"sequences":[5],"via":[6],"sparse":[7,21],"suffix":[8],"arrays":[9],"(SSAs)":[10],"and":[11,57,140],"propose":[12],"a":[13,148],"new":[14],"short":[15,76,137],"read":[16,23,138],"aligner":[17],"named":[18],"PSI-RA":[19,119],"(parallel":[20],"index":[22,48],"aligner).":[24],"The":[25],"motivation":[26],"in":[27,125],"using":[28],"SSAs":[29,67],"is":[30,39,108,147],"the":[31,43,47,51,55,58,62,92,98,101,104,111,134],"ability":[32],"to":[33,41,151],"trade":[34],"memory":[35,53],"against":[36],"time.":[37],"It":[38],"possible":[40],"tune":[42],"space":[44],"consumption":[45],"of":[46,54,61,75,81,103,123,133],"based":[49,156],"available":[52],"machine":[56],"minimum":[59],"length":[60],"arriving":[63],"pattern":[64],"queries.":[65],"Although":[66],"have":[68],"been":[69],"studied":[70],"before":[71],"exact":[73],"matching":[74,83],"reads,":[77],"an":[78],"elegant":[79],"way":[80],"approximate":[82],"capability":[84],"was":[85],"missing.":[86],"provide":[88],"this":[89],"by":[90],"defining":[91],"right-most":[93],"mismatch":[94],"criteria":[95],"that":[96,110,117,142],"prioritizes":[97],"errors":[99,112],"towards":[100],"end":[102],"reads":[105],"since":[106],"it":[107],"known":[109,136],"are":[113],"more":[114],"probable":[115],"at":[116],"area.":[118],"supports":[120],"any":[121],"number":[122],"mismatches":[124],"aligning":[126],"reads.":[127],"give":[129],"comparisons":[130],"with":[131,145],"some":[132],"well":[135],"aligners,":[139],"show":[141],"genome":[144],"SSA":[146],"good":[149],"alternative":[150],"Burrows-Wheeler":[152],"transform":[153],"or":[154],"seed":[155],"solutions.":[157]},"counts_by_year":[{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
