{"id":"https://openalex.org/W3015563293","doi":"https://doi.org/10.1101/2020.04.11.036871","title":"An Algorithm to Build a Multi-genome Reference","display_name":"An Algorithm to Build a Multi-genome Reference","publication_year":2020,"publication_date":"2020-04-13","ids":{"openalex":"https://openalex.org/W3015563293","doi":"https://doi.org/10.1101/2020.04.11.036871","mag":"3015563293"},"language":"en","primary_location":{"id":"doi:10.1101/2020.04.11.036871","doi":"https://doi.org/10.1101/2020.04.11.036871","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.04.11.036871","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/04/13/2020.04.11.036871.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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2020/04/13/2020.04.11.036871.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032084468","display_name":"Leily Rabbani","orcid":"https://orcid.org/0009-0007-0755-3643","observed_orcids":["https://orcid.org/0009-0007-0755-3643"]},"institutions":[{"id":"https://openalex.org/I4210112458","display_name":"Max Planck Institute for Developmental Biology","ror":"https://ror.org/022jc0g24","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210112458"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Leily Rabbani","raw_affiliation_strings":["Max Planck Institute for Developmental Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Developmental Biology","institution_ids":["https://openalex.org/I4210112458"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103215234","display_name":"Jonas M\u00fcller","orcid":"https://orcid.org/0000-0003-3211-3096","observed_orcids":["https://orcid.org/0000-0003-3211-3096"]},"institutions":[{"id":"https://openalex.org/I4210112458","display_name":"Max Planck Institute for Developmental Biology","ror":"https://ror.org/022jc0g24","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210112458"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jonas M\u00fcller","raw_affiliation_strings":["Max Planck Institute for Developmental Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Developmental Biology","institution_ids":["https://openalex.org/I4210112458"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003440649","display_name":"Detlef Weigel","orcid":"https://orcid.org/0000-0002-2114-7963","observed_orcids":["https://orcid.org/0000-0002-2114-7963"]},"institutions":[{"id":"https://openalex.org/I4210112458","display_name":"Max Planck Institute for Developmental Biology","ror":"https://ror.org/022jc0g24","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210112458"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Detlef Weigel","raw_affiliation_strings":["Max Planck Institute for Developmental Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Developmental Biology","institution_ids":["https://openalex.org/I4210112458"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5003440649"],"corresponding_institution_ids":["https://openalex.org/I4210112458"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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":0.9980000257492065,"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/T11269","display_name":"Algorithms and Data Compression","score":0.000699999975040555,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.0003000000142492354,"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/reference-graphs","display_name":"reference graphs","score":0.5040000081062317},{"id":"https://openalex.org/keywords/genome-compression","display_name":"genome compression","score":0.753000020980835}],"concepts":[{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.8655248880386353},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8325238227844238},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5510349273681641},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5066724419593811},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.45810532569885254},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4542177617549896},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3950656056404114},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3312162756919861},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30360156297683716},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18269535899162292},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12505951523780823}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2020.04.11.036871","doi":"https://doi.org/10.1101/2020.04.11.036871","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.04.11.036871","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/04/13/2020.04.11.036871.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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2020.04.11.036871","doi":"https://doi.org/10.1101/2020.04.11.036871","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.04.11.036871","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/04/13/2020.04.11.036871.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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3015563293.pdf","grobid_xml":"https://content.openalex.org/works/W3015563293.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1548134937","https://openalex.org/W1575413654","https://openalex.org/W1777016212","https://openalex.org/W1842847600","https://openalex.org/W1850890413","https://openalex.org/W1978981589","https://openalex.org/W1995875735","https://openalex.org/W2000466469","https://openalex.org/W2001261225","https://openalex.org/W2010361633","https://openalex.org/W2029195137","https://openalex.org/W2037219729","https://openalex.org/W2041404167","https://openalex.org/W2111044311","https://openalex.org/W2111451722","https://openalex.org/W2115252128","https://openalex.org/W2127901812","https://openalex.org/W2129264270","https://openalex.org/W2137351413","https://openalex.org/W2140698423","https://openalex.org/W2142003566","https://openalex.org/W2156104322","https://openalex.org/W2158678815","https://openalex.org/W2159084616","https://openalex.org/W2160969485","https://openalex.org/W2161048357","https://openalex.org/W2162758337","https://openalex.org/W2165232124","https://openalex.org/W2166588423","https://openalex.org/W2167673155","https://openalex.org/W2172527508","https://openalex.org/W2345970915","https://openalex.org/W2474973645","https://openalex.org/W2587659983","https://openalex.org/W2603734366","https://openalex.org/W2786984148","https://openalex.org/W2888300707","https://openalex.org/W2952379406","https://openalex.org/W4235690512"],"related_works":["https://openalex.org/W2921547862","https://openalex.org/W2129264270","https://openalex.org/W2912906340","https://openalex.org/W7099711995","https://openalex.org/W2981501586","https://openalex.org/W3120923229","https://openalex.org/W2553566324","https://openalex.org/W2289922653","https://openalex.org/W3012333907","https://openalex.org/W2146067967"],"abstract_inverted_index":{"1":[0,151],"Abstract":[1],"Motivation":[2],"New":[3],"DNA":[4],"sequencing":[5,30],"technologies":[6],"have":[7,86,172],"enabled":[8],"the":[9,22,25,51,65,88,104,124,140,145,166,184],"rapid":[10],"analysis":[11],"of":[12,15,28,144,168,186],"many":[13],"thousands":[14],"genomes":[16,48],"from":[17,59,108],"a":[18,33,73,111,129,135,174],"single":[19,34,74],"species.":[20],"At":[21],"same":[23],"time,":[24],"conventional":[26],"approach":[27],"mapping":[29,69,79],"reads":[31,71],"against":[32,72,81,95],"reference":[35,47,75,83,98,113],"genome":[36,175],"sequence":[37,70],"is":[38],"no":[39],"longer":[40],"adequate.":[41],"However,":[42],"even":[43],"where":[44],"multiple":[45,82,96],"high-quality":[46,97],"are":[49,156,162],"available,":[50],"problem":[52],"remains":[53],"how":[54],"one":[55],"would":[56],"integrate":[57],"results":[58],"pairwise":[60],"analyses.":[61,118],"Result":[62],"To":[63,119,138,164],"overcome":[64],"limits":[66],"imposed":[67],"by":[68],"genome,":[76],"or":[77],"serially":[78],"them":[80],"genomes,":[84,99],"we":[85,122,171],"developed":[87,173],"MGR":[89,125,132],"method":[90],"that":[91,106,127],"allows":[92],"simultaneous":[93],"comparison":[94],"in":[100],"order":[101],"to":[102,115,182],"remove":[103],"bias":[105],"comes":[107],"using":[109],"only":[110],"single-genome":[112],"and":[114,142,152],"simplify":[116],"downstream":[117],"this":[120],"end,":[121],"present":[123],"algorithm":[126],"creates":[128],"graph":[130],"(":[131],"graph)":[133],"as":[134],"multi-genome":[136,146],"reference.":[137],"reduce":[139],"size":[141],"complexity":[143],"reference,":[147],"highly":[148],"similar":[149],"orthologous":[150],"paralogous":[153],"2":[154],"regions":[155],"collapsed":[157],"while":[158],"more":[159],"substantial":[160],"differences":[161],"retained.":[163],"evaluate":[165],"performance":[167],"our":[169],"model,":[170],"compression":[176],"tool,":[177],"which":[178],"can":[179],"be":[180],"used":[181],"estimate":[183],"amount":[185],"shared":[187],"information":[188],"between":[189],"genomes.":[190],"Availability":[191],"https://github.com/LeilyR/Multi-genome-Reference.git":[192],"Contact":[193],"weigel@tue.mpg.de":[194]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2020-04-17T00:00:00"}