乐胖代购免代理版

{"id":"https://openalex.org/W3164324624","doi":"https://doi.org/10.1093/bioinformatics/btab396","title":"LevioSAM: fast lift-over of variant-aware reference alignments","display_name":"LevioSAM: fast lift-over of variant-aware reference alignments","publication_year":2021,"publication_date":"2021-05-24","ids":{"openalex":"https://openalex.org/W3164324624","doi":"https://doi.org/10.1093/bioinformatics/btab396","mag":"3164324624","pmid":"https://pubmed.ncbi.nlm.nih.gov/34037690"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab396","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/22/4243/41183824/btab396.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/22/4243/41183824/btab396.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000946526","display_name":"Taher Mun","orcid":"https://orcid.org/0000-0002-3588-0883"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Taher Mun","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053574168","display_name":"Nae-Chyun Chen","orcid":"https://orcid.org/0000-0002-4140-4568"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nae-Chyun Chen","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009556658","display_name":"Ben Langmead","orcid":"https://orcid.org/0000-0003-2437-1976"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ben Langmead","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000946526","https://openalex.org/A5009556658"],"corresponding_institution_ids":["https://openalex.org/I145311948","https://openalex.org/I145311948"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618,"provenance":"doaj"},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618,"provenance":"doaj"},"fwci":0.638,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.638317,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":84,"max":86},"biblio":{"volume":"37","issue":"22","first_page":"4243","last_page":"4245"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9996,"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":0.9996,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9816,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9752,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/lift","display_name":"Lift (data mining)","score":0.7205204},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.43280256}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8404991},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.8330072},{"id":"https://openalex.org/C139002025","wikidata":"https://www.wikidata.org/wiki/Q3001212","display_name":"Lift (data mining)","level":2,"score":0.7205204},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5680812},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5484562},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5266319},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.43280256},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40223873},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3051974},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.07341173},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab396","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/22/4243/41183824/btab396.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9502237","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://doi.org/10.1101/2021.02.05.429867","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2021/02/05/2021.02.05.429867.full.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34037690","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab396","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/22/4243/41183824/btab396.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[],"grants":[{"funder":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health","award_id":"R01HG011392"}],"datasets":[],"versions":[],"referenced_works_count":10,"referenced_works":["https://openalex.org/W2101071606","https://openalex.org/W2104549677","https://openalex.org/W2108234281","https://openalex.org/W2127640118","https://openalex.org/W2134199796","https://openalex.org/W2149992227","https://openalex.org/W2150933237","https://openalex.org/W2170551349","https://openalex.org/W2921895833","https://openalex.org/W3120923229"],"related_works":["https://openalex.org/W4382618745","https://openalex.org/W2885125400","https://openalex.org/W2748922771","https://openalex.org/W2595172197","https://openalex.org/W2127970246","https://openalex.org/W2084856301","https://openalex.org/W1989889224","https://openalex.org/W1987128138","https://openalex.org/W1657880117","https://openalex.org/W1001352512"],"abstract_inverted_index":{"As":[0],"more":[1,26,40,99],"population":[2,77],"genetics":[3],"datasets":[4],"and":[5,84],"population-specific":[6],"references":[7],"become":[8],"available,":[9],"the":[10,39],"task":[11],"of":[12,54,93],"translating":[13],"('lifting')":[14],"read":[15,95],"alignments":[16,66],"from":[17,67],"one":[18,68],"reference":[19,69],"coordinate":[20],"system":[21],"to":[22,43,70,87],"another":[23,71],"is":[24,60,98],"becoming":[25],"common.":[27],"Existing":[28,46],"tools":[29,47],"generally":[30],"require":[31],"a":[32,57,61,73,94],"chain":[33],"file,":[34],"whereas":[35],"VCF":[36,74],"files":[37],"are":[38,109,119],"common":[41],"way":[42],"represent":[44],"variation.":[45],"also":[48],"do":[49],"not":[50],"make":[51],"effective":[52],"use":[53],"threads,":[55],"creating":[56],"post-alignment":[58],"bottleneck.LevioSAM":[59],"tool":[62],"for":[63],"lifting":[64],"SAM/BAM":[65],"using":[72],"file":[75],"containing":[76],"variants.":[78],"LevioSAM":[79],"uses":[80],"succinct":[81],"data":[82,118],"structures":[83],"scales":[85],"efficiently":[86],"many":[88],"threads.":[89],"When":[90],"run":[91,110],"downstream":[92],"aligner,":[96],"levioSAM":[97],"than":[100,104],"7":[101],"times":[102],"faster":[103],"an":[105],"aligner":[106],"when":[107],"both":[108],"with":[111],"16":[112],"threads.Software":[113],"Package:":[114],"https://github.com/alshai/levioSAM,":[115],"Experiments:":[116],"https://github.com/langmead-lab/levioSAM-experiments.Supplementary":[117],"available":[120],"at":[121],"Bioinformatics":[122],"online.":[123]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W3164324624","counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2}],"updated_date":"2025-01-05T11:23:13.454838","created_date":"2021-06-07"}