{"id":"https://openalex.org/W4408068966","doi":"https://doi.org/10.1186/s13015-025-00272-y","title":"Mem-based pangenome indexing for k-mer queries","display_name":"Mem-based pangenome indexing for k-mer queries","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4408068966","doi":"https://doi.org/10.1186/s13015-025-00272-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/40025556"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-025-00272-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-025-00272-y","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-025-00272-y","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-025-00272-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062078487","display_name":"Stephen Hwang","orcid":"https://orcid.org/0000-0003-0299-569X"},"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":"Stephen Hwang","raw_affiliation_strings":["XDBio Program, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"XDBio Program, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathaniel K. Brown","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062095386","display_name":"Omar Ahmed","orcid":"https://orcid.org/0000-0002-9933-8508"},"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":"Omar Y. Ahmed","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067230314","display_name":"Katharine M. Jenike","orcid":"https://orcid.org/0000-0002-7276-8110"},"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":"Katharine M. Jenike","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090348465","display_name":"Sam Kovaka","orcid":"https://orcid.org/0000-0002-4835-8023"},"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":"Sam Kovaka","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058192453","display_name":"Michael C. Schatz","orcid":"https://orcid.org/0000-0002-4118-4446"},"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":"Michael C. Schatz","raw_affiliation_strings":["Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, 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"]},{"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":["Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. langmea@cs.jhu.edu","Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. langmea@cs.jhu.edu","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5062078487"],"corresponding_institution_ids":["https://openalex.org/I145311948"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.6255,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.65104407,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"20","issue":"1","first_page":"3","last_page":"3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9958999752998352,"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":0.9926999807357788,"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":0.7027896642684937},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6378861665725708},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.520779550075531},{"id":"https://openalex.org/keywords/de-bruijn-graph","display_name":"De Bruijn graph","score":0.4980030059814453},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.4439735412597656},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43733859062194824},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.2867286801338196},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.22613811492919922},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.09383466839790344}],"concepts":[{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.7027896642684937},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6378861665725708},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.520779550075531},{"id":"https://openalex.org/C20218877","wikidata":"https://www.wikidata.org/wiki/Q3066095","display_name":"De Bruijn graph","level":3,"score":0.4980030059814453},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.4439735412597656},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43733859062194824},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2867286801338196},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.22613811492919922},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.09383466839790344}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13015-025-00272-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-025-00272-y","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-025-00272-y","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:40025556","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40025556","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:4310431f42514b97992e6abf68d4ba22","is_oa":true,"landing_page_url":"https://doaj.org/article/4310431f42514b97992e6abf68d4ba22","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 20, Iss 1, Pp 1-15 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11871630","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11871630","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":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-025-00272-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-025-00272-y","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-025-00272-y","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.699999988079071,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G2241781793","display_name":null,"funder_award_id":"R01HG011392","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4700650626","display_name":"Assembling and recombining the Arabidopsis centromeres","funder_award_id":"RGP0025/2021","funder_id":"https://openalex.org/F4320307846","funder_display_name":"Human Frontier Science Program"},{"id":"https://openalex.org/G6450098338","display_name":null,"funder_award_id":"2216612","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6723691416","display_name":null,"funder_award_id":"U01CA253481","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320307846","display_name":"Human Frontier Science Program","ror":"https://ror.org/02ebx7v45"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4408068966.pdf"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1985437611","https://openalex.org/W2055417893","https://openalex.org/W2101849110","https://openalex.org/W2142386149","https://openalex.org/W2583363792","https://openalex.org/W2784788330","https://openalex.org/W2897603717","https://openalex.org/W2952139763","https://openalex.org/W3005228641","https://openalex.org/W3109503472","https://openalex.org/W3110395203","https://openalex.org/W3159728495","https://openalex.org/W3171564659","https://openalex.org/W3196896210","https://openalex.org/W4205330988","https://openalex.org/W4220999759","https://openalex.org/W4224278121","https://openalex.org/W4243495532","https://openalex.org/W4312045005","https://openalex.org/W4377013047","https://openalex.org/W4378803010","https://openalex.org/W4385997373","https://openalex.org/W4386113054","https://openalex.org/W4387691790","https://openalex.org/W4394718494"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W3024364549","https://openalex.org/W4206019083","https://openalex.org/W2048865712","https://openalex.org/W1976265003","https://openalex.org/W2370378377","https://openalex.org/W2073681303","https://openalex.org/W2130160813","https://openalex.org/W2054476758","https://openalex.org/W2393932274"],"abstract_inverted_index":{"Abstract":[0],"Pangenomes":[1],"are":[2,55],"growing":[3],"in":[4,118,134,194,231],"number":[5,112],"and":[6,23,51,108,149,217,227],"size,":[7,210],"thanks":[8],"to":[9,57],"the":[10,111,189],"prevalence":[11],"of":[12,113,128,212],"high-quality":[13],"long-read":[14],"assemblies.":[15],"However,":[16],"current":[17],"methods":[18],"for":[19,125,186,225],"studying":[20,226],"sequence":[21],"composition":[22],"conservation":[24,184,230],"within":[25],"pangenomes":[26,33],"have":[27],"limitations.":[28],"Methods":[29],"based":[30,47,78],"on":[31,48,79],"graph":[32],"require":[34],"a":[35,61,74,119,126,145,158,183,222],"computationally":[36],"expensive":[37],"multiple-alignment":[38],"step,":[39],"which":[40],"can":[41,90,163,181],"leave":[42],"out":[43],"some":[44,169],"variation.":[45],"Indexes":[46],"k":[49,65,103,116,213],"-mers":[50,117],"de":[52],"Bruijn":[53],"graphs":[54],"limited":[56],"answering":[58],"questions":[59],"at":[60],"specific":[62],"substring":[63,229],"length":[64,215],".":[66],"We":[67],"present":[68],"Maximal":[69],"Exact":[70],"Match":[71],"Ordered":[72],"(MEMO),":[73],"pangenome":[75,127],"indexing":[76],"method":[77],"maximal":[80],"exact":[81],"matches":[82],"(MEMs)":[83],"between":[84],"sequences.":[85],"A":[86],"single":[87],"MEMO":[88,97,161,180],"index":[89,124,148,176,209],"handle":[91],"arbitrary-length":[92],"queries":[93,100,219],"over":[94,188],"pangenomic":[95],"windows.":[96],"enables":[98],"both":[99],"that":[101,109],"test":[102],"-mer":[104,214],"presence/absence":[105],"(membership":[106],"queries)":[107],"count":[110],"genomes":[114],"containing":[115],"window":[120],"(conservation":[121],"queries).":[122],"MEMO\u2019s":[123,207],"89":[129],"human":[130,190],"autosomal":[131],"haplotypes":[132],"fits":[133],"2.04":[135],"GB,":[136],"8.8":[137],"$$\\times$$":[138,151,198],"<mml:math":[139,152,199],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">":[140,153,200],"<mml:mo>\u00d7</mml:mo>":[141,154,201],"</mml:math>":[142,155,202],"smaller":[143,156,166],"than":[144,157,204],"comparable":[146],"KMC3":[147],"11.4":[150],"PanKmer":[159],"index.":[160],"indexes":[162],"be":[164],"made":[165],"by":[167],"sacrificing":[168],"counting":[170],"resolution,":[171],"with":[172],"our":[173],"decile-resolution":[174],"HPRC":[175],"reaching":[177],"0.67":[178],"GB.":[179],"conduct":[182],"query":[185],"31-mers":[187],"leukocyte":[191],"antigen":[192],"locus":[193],"13.89":[195],"s,":[196],"2.5":[197],"faster":[203],"other":[205],"approaches.":[206],"small":[208],"lack":[211],"dependence,":[216],"efficient":[218],"make":[220],"it":[221],"flexible":[223],"tool":[224],"visualizing":[228],"pangenomes.":[232]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}