{"id":"https://openalex.org/W4415295489","doi":"https://doi.org/10.1093/bioinformatics/btag362","title":"Movi 2: fast and space-efficient queries on pangenomes","display_name":"Movi 2: fast and space-efficient queries on pangenomes","publication_year":2026,"publication_date":"2026-06-16","ids":{"openalex":"https://openalex.org/W4415295489","doi":"https://doi.org/10.1093/bioinformatics/btag362","pmid":"https://pubmed.ncbi.nlm.nih.gov/41279150"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag362","pdf_url":null,"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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag362","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028361756","display_name":"Mohsen Zakeri","orcid":"https://orcid.org/0000-0002-9856-719X"},"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"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mohsen Zakeri","raw_affiliation_strings":["Johns Hopkins University Department of Computer Science, , Baltimore, Maryland 21218,","University of Maryland"],"raw_orcid":"https://orcid.org/0000-0002-9856-719X","affiliations":[{"raw_affiliation_string":"Johns Hopkins University Department of Computer Science, , Baltimore, Maryland 21218,","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]},{"raw_affiliation_string":"University of Maryland","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025703951","display_name":"Nathaniel K. Brown","orcid":"https://orcid.org/0000-0002-6201-2301"},"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"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathaniel K Brown","raw_affiliation_strings":["Johns Hopkins University Department of Computer Science, , Baltimore, Maryland 21218,","Johns Hopkins University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johns Hopkins University Department of Computer Science, , Baltimore, Maryland 21218,","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]},{"raw_affiliation_string":"Johns Hopkins University","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013172801","display_name":"Travis Gagie","orcid":"https://orcid.org/0000-0003-3689-327X"},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]},{"id":"https://openalex.org/I911713783","display_name":"Universidad Diego Portales","ror":"https://ror.org/03gtdcg60","country_code":"CL","type":"education","lineage":["https://openalex.org/I911713783"]}],"countries":["CA","CL"],"is_corresponding":false,"raw_author_name":"Travis Gagie","raw_affiliation_strings":["Dalhousie University Faculty of Computer Science, , Halifax, Nova Scotia B3H 4R2,","Diego Portales University"],"raw_orcid":"https://orcid.org/0000-0003-3689-327X","affiliations":[{"raw_affiliation_string":"Dalhousie University Faculty of Computer Science, , Halifax, Nova Scotia B3H 4R2,","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Diego Portales University","institution_ids":["https://openalex.org/I911713783"]}]},{"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"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ben Langmead","raw_affiliation_strings":["Johns Hopkins University Department of Computer Science, , Baltimore, Maryland 21218,","Johns Hopkins University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johns Hopkins University Department of Computer Science, , Baltimore, Maryland 21218,","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]},{"raw_affiliation_string":"Johns Hopkins University","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5028361756"],"corresponding_institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436","https://openalex.org/I66946132"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":19.1439,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.98235978,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"42","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.993399977684021,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.993399977684021,"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/T11719","display_name":"Data Quality and Management","score":0.9896000027656555,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11478","display_name":"Caching and Content Delivery","score":0.9864000082015991,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/memory-footprint","display_name":"Memory footprint","score":0.8361999988555908},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.48069998621940613},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.4255000054836273},{"id":"https://openalex.org/keywords/footprint","display_name":"Footprint","score":0.4147000014781952},{"id":"https://openalex.org/keywords/compression","display_name":"Compression (physics)","score":0.2921999990940094},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.27810001373291016}],"concepts":[{"id":"https://openalex.org/C74912251","wikidata":"https://www.wikidata.org/wiki/Q6815727","display_name":"Memory footprint","level":2,"score":0.8361999988555908},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6365000009536743},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.48069998621940613},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4255000054836273},{"id":"https://openalex.org/C132943942","wikidata":"https://www.wikidata.org/wiki/Q2562511","display_name":"Footprint","level":2,"score":0.4147000014781952},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32710000872612},{"id":"https://openalex.org/C180016635","wikidata":"https://www.wikidata.org/wiki/Q2712821","display_name":"Compression (physics)","level":2,"score":0.2921999990940094},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.27810001373291016},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.2605000138282776},{"id":"https://openalex.org/C176649486","wikidata":"https://www.wikidata.org/wiki/Q2308807","display_name":"Memory management","level":3,"score":0.258899986743927},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.25859999656677246},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.25279998779296875}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btag362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag362","pdf_url":null,"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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/2025.10.16.682873","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.10.16.682873","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/10/17/2025.10.16.682873.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:41279150","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41279150","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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmid:42312341","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42312341","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:11440419","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12632922","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:13379629","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13379629/","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":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag362","pdf_url":null,"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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4711506138","display_name":null,"funder_award_id":"R21HG013433","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W2159647614","https://openalex.org/W2173739051","https://openalex.org/W2765284830","https://openalex.org/W2889833303","https://openalex.org/W2953263404","https://openalex.org/W2967058481","https://openalex.org/W2979531022","https://openalex.org/W3011828211","https://openalex.org/W3012034924","https://openalex.org/W3088711112","https://openalex.org/W3093722121","https://openalex.org/W3109164186","https://openalex.org/W3119507732","https://openalex.org/W3125235775","https://openalex.org/W3171564659","https://openalex.org/W4220999759","https://openalex.org/W4230945265","https://openalex.org/W4283816770","https://openalex.org/W4376133202","https://openalex.org/W4377013047","https://openalex.org/W4394961089","https://openalex.org/W4404770452","https://openalex.org/W4404814486"],"related_works":[],"abstract_inverted_index":{"SUMMARY:":[0],"Space-efficient":[1],"compressed":[2,38,62],"indexing":[3],"methods":[4,48,139,158],"are":[5,164],"critical":[6],"for":[7,10,161],"pangenomics":[8],"and":[9,26,45,53,86,99,112,143,149],"avoiding":[11],"reference":[12],"bias.":[13],"In":[14],"the":[15,20,68,110,116,123],"Movi":[16,29,43,65,69,94,135,162],"study,":[17],"we":[18,41,91,159],"implemented":[19],"move-structure":[21],"index,":[22],"highlighting":[23],"its":[24],"locality-of-reference":[25],"speed.":[27],"However,":[28],"had":[30],"a":[31],"high":[32],"memory":[33,54,144],"footprint":[34,55,72],"compared":[35],"to":[36,104],"other":[37],"indexes.":[39,59],"Here,":[40],"introduce":[42,78],"2":[44,66,95,136,163],"describe":[46],"new":[47],"that":[49,81,93,134],"greatly":[50],"reduce":[51],"size":[52],"of":[56,64,115,125],"move":[57],"structure-based":[58],"The":[60,157],"most":[61],"version":[63],"reduces":[67],"index's":[70],"space":[71,87,100],"more":[73],"than":[74],"five-fold.":[75],"We":[76,132],"also":[77],"sampling":[79],"approaches":[80],"enable":[82],"trade-offs":[83],"between":[84],"query":[85],"efficiency.":[88],"To":[89],"demonstrate,":[90],"show":[92,133],"achieves":[96],"advantageous":[97],"time":[98],"tradeoffs":[101],"when":[102],"applied":[103],"large":[105],"pangenome":[106],"collections,":[107],"including":[108,146],"both":[109,141,147],"first":[111],"second":[113],"releases":[114],"Human":[117],"Pangenome":[118],"Reference":[119],"Consortium":[120],"(HPRC)":[121],"collection,":[122],"latter":[124],"which":[126],"spans":[127],"over":[128],"460":[129],"human":[130],"haplotypes.":[131],"dominates":[137],"prior":[138],"on":[140],"speed":[142],"footprint,":[145],"r-index-based":[148],"our":[150],"previous":[151],"move-structure-based":[152],"method.":[153],"AVAILABILITY":[154],"AND":[155],"IMPLEMENTATION:":[156],"developed":[160],"publicly":[165],"available":[166],"at":[167],"https://github.com/mohsenzakeri/Movi.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-07-25T15:57:00.446498","created_date":"2025-10-18T00:00:00"}
