{"id":"https://openalex.org/W2912317892","doi":null,"title":"Genome graphs","display_name":"Genome graphs","publication_year":2010,"publication_date":"2010-01-01","ids":{"openalex":"https://openalex.org/W2912317892","mag":"2912317892"},"language":"en","primary_location":{"id":"mag:2912317892","doi":null,"is_oa":false,"landing_page_url":"http://dl.acm.org/citation.cfm?id=2231598","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"volume":null,"type":"article","indexed_in":[],"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/A5066909672","display_name":"Paul Medvedev","orcid":"https://orcid.org/0000-0003-3143-594X","observed_orcids":["https://orcid.org/0000-0003-3143-594X"]},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Paul Medvedev","raw_affiliation_strings":["(University of Toronto, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"(University of Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5066909672"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.31996834,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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":0.8999000191688538,"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":0.8999000191688538,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.05009999871253967,"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"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.03700000047683716,"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/genome-graphs","display_name":"genome graphs","score":0.9940000176429749},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"copy number variation","score":0.8349999785423279},{"id":"https://openalex.org/keywords/cnv-detection","display_name":"CNV detection","score":0.8939999938011169},{"id":"https://openalex.org/keywords/genome-assembly","display_name":"genome assembly","score":0.9909999966621399},{"id":"https://openalex.org/keywords/whole-genome-shotgun-sequencing","display_name":"whole genome shotgun sequencing","score":0.9440000057220459},{"id":"https://openalex.org/keywords/maximum-likelihood-estimation","display_name":"maximum likelihood estimation","score":0.6159999966621399},{"id":"https://openalex.org/keywords/maximum-parsimony","display_name":"maximum parsimony","score":0.6850000023841858},{"id":"https://openalex.org/keywords/human-genetic-variation","display_name":"human genetic variation","score":0.5070000290870667}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8426038026809692},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.6524541974067688},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.5857619643211365},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5636922717094421},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5040668249130249},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4742783010005951},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.46677225828170776},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.46236565709114075},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.4391424357891083},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.439035564661026},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4369671642780304},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.4293777346611023},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.425849586725235},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2858763337135315},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:2912317892","doi":null,"is_oa":false,"landing_page_url":"http://dl.acm.org/citation.cfm?id=2231598","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4237520300","https://openalex.org/W2889065999","https://openalex.org/W4416722745","https://openalex.org/W7140312793","https://openalex.org/W2329846793","https://openalex.org/W4391004651","https://openalex.org/W2851426844","https://openalex.org/W4392130139","https://openalex.org/W4366316890","https://openalex.org/W4206362576"],"abstract_inverted_index":{"Whole-genome":[0],"shotgun":[1],"sequencing":[2,36,59,164],"is":[3,18,29,37,119,155,184],"an":[4,49],"experimental":[5],"technique":[6,211],"used":[7,140,225],"for":[8,57,84,125,141,180,226,253,271],"obtaining":[9],"in-":[10],"formation":[11],"about":[12],"a":[13,54,105,149,178,187,257,269,278,283],"genome's":[14],"sequence,":[15],"whereby":[16],"it":[17],"broken":[19],"up":[20],"into":[21,205,268],"many":[22],"short":[23],"(possibly":[24],"overlapping)":[25],"segments":[26,102],"whose":[27],"sequence":[28,47,154],"then":[30],"determined.":[31],"A":[32,90],"long-standing":[33],"use":[34,121,276],"of":[35,44,48,60,71,93,108,116,122,148,163,199,212,233,286],"in":[38,88,110,173,177],"genome":[39,123,130,150,189,206,220,248],"assembly":[40,131],"\u2013":[41],"the":[42,46,58,66,69,85,120,146,161,196,210,231,234,239,261],"problem":[43],"determining":[45],"unknown":[50],"genome,":[51],"which":[52,103,135,274],"plays":[53],"central":[55],"role":[56],"novel":[61,188,258],"species.":[62],"However,":[63],"even":[64,151],"within":[65],"same":[67],"species,":[68],"genomes":[70],"two":[72],"individuals":[73],"differ,":[74],"and":[75,129,143,288],"though":[76],"these":[77,94],"variations":[78],"are":[79,95,266],"relatively":[80],"small,":[81],"they":[82],"account":[83],"observed":[86],"variation":[87],"phenotypes.":[89],"large":[91],"portion":[92],"copy":[96],"number":[97,107],"variants":[98],"(CNVs),":[99],"or":[100],"genomic":[101],"appear":[104],"different":[106,111],"times":[109],"individuals.":[112],"\r\nThe":[113],"unifying":[114],"theme":[115],"this":[117,167],"thesis":[118],"graphs":[124,207,221,249],"both":[126],"CNV":[127,181,254],"detection":[128,182,255],"problems.":[132],"Genome":[133],"graphs,":[134],"have":[136],"already":[137],"been":[138],"successfully":[139],"alignment":[142],"assembly,":[144],"capture":[145],"structure":[147],"when":[152],"its":[153],"not":[156],"fully":[157],"known,":[158],"as":[159,236],"with":[160],"case":[162],"data.":[165],"In":[166],"thesis,":[168],"we":[169,193,217,245,275],"extend":[170],"their":[171],"uses":[172],"several":[174],"ways,":[175],"culminating":[176],"method":[179,270],"that":[183,229],"based":[185],"on":[186,277],"graph":[190],"model.":[191],"First,":[192],"demonstrate":[194],"how":[195,219,247],"double-stranded":[197],"nature":[198],"DNA":[200],"can":[201,222,250],"be":[202,223,251],"efficiently":[203,224],"incorporated":[204],"by":[208],"using":[209],"bidirected":[213],"network":[214],"flow.":[215],"Furthermore,":[216],"show":[218,246],"finding":[227],"solutions":[228],"maximize":[230],"likelihood":[232],"data,":[235],"opposed":[237],"to":[238],"usual":[240],"maximum":[241],"parsimony":[242],"approach.":[243],"Finally,":[244],"useful":[252],"through":[256],"construction":[259],"called":[260],"donor":[262],"graph.":[263],"These":[264],"extensions":[265],"combined":[267],"detecting":[272],"CNVs,":[273],"Yoruban":[279],"human":[280],"individual,":[281],"showing":[282],"high":[284],"degree":[285],"accuracy":[287],"improvement":[289],"over":[290],"previous":[291],"methods.":[292]},"counts_by_year":[],"updated_date":"2025-11-06T04:12:42.849631","created_date":"2019-02-21T00:00:00"}