{"id":"https://openalex.org/W1607524461","doi":"https://doi.org/10.5075/epfl-thesis-5435","title":"Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference","display_name":"Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W1607524461","doi":"https://doi.org/10.5075/epfl-thesis-5435","mag":"1607524461"},"language":"en","primary_location":{"id":"pmh:oai:infoscience.tind.io:180627","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/84631","pdf_url":"http://infoscience.epfl.ch/record/180627","source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"doctoral thesis"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://infoscience.epfl.ch/record/180627","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079714822","display_name":"Yu Lin","orcid":"https://orcid.org/0000-0001-6339-2644"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Lin, Yu","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5079714822"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9993000030517578,"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"}},"topics":[{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9926000237464905,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7871248722076416},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6679844856262207},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.541100025177002},{"id":"https://openalex.org/keywords/genome-evolution","display_name":"Genome evolution","score":0.5381760001182556},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5260602831840515},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.46629518270492554},{"id":"https://openalex.org/keywords/bootstrapping","display_name":"Bootstrapping (finance)","score":0.46340155601501465},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.45267486572265625},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.437834769487381},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.43639522790908813},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.42479318380355835},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.42404255270957947},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3961929678916931},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2665237486362457},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26222920417785645},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19523078203201294},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15644127130508423},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11388516426086426}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7871248722076416},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6679844856262207},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.541100025177002},{"id":"https://openalex.org/C174600577","wikidata":"https://www.wikidata.org/wiki/Q5533491","display_name":"Genome evolution","level":4,"score":0.5381760001182556},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5260602831840515},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.46629518270492554},{"id":"https://openalex.org/C207609745","wikidata":"https://www.wikidata.org/wiki/Q4944086","display_name":"Bootstrapping (finance)","level":2,"score":0.46340155601501465},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.45267486572265625},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.437834769487381},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.43639522790908813},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.42479318380355835},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.42404255270957947},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3961929678916931},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2665237486362457},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26222920417785645},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19523078203201294},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15644127130508423},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11388516426086426},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:infoscience.tind.io:180627","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/84631","pdf_url":"http://infoscience.epfl.ch/record/180627","source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"doctoral thesis"},{"id":"pmh:oai:infoscience.epfl.ch:180627","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/180627","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"doi:10.5075/epfl-thesis-5435","is_oa":true,"landing_page_url":"https://doi.org/10.5075/epfl-thesis-5435","pdf_url":null,"source":{"id":"https://openalex.org/S4306400488","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"thesis"},{"id":"mag:1607524461","is_oa":false,"landing_page_url":"https://infoscience.epfl.ch/record/180627","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:infoscience.tind.io:180627","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/84631","pdf_url":"http://infoscience.epfl.ch/record/180627","source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"doctoral thesis"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W1607524461.pdf"},"referenced_works_count":118,"referenced_works":["https://openalex.org/W74509308","https://openalex.org/W75871853","https://openalex.org/W152315924","https://openalex.org/W1491688952","https://openalex.org/W1504968226","https://openalex.org/W1507091143","https://openalex.org/W1511771787","https://openalex.org/W1519987066","https://openalex.org/W1525734744","https://openalex.org/W1530804984","https://openalex.org/W1547622250","https://openalex.org/W1554477894","https://openalex.org/W1555623370","https://openalex.org/W1572531572","https://openalex.org/W1585116395","https://openalex.org/W1585881831","https://openalex.org/W1589174490","https://openalex.org/W1592788845","https://openalex.org/W1594983821","https://openalex.org/W1606486549","https://openalex.org/W1656398202","https://openalex.org/W1890701999","https://openalex.org/W1963847479","https://openalex.org/W1972412557","https://openalex.org/W1973186137","https://openalex.org/W1976927254","https://openalex.org/W1981231088","https://openalex.org/W1981492171","https://openalex.org/W1981509964","https://openalex.org/W1982970543","https://openalex.org/W1984347506","https://openalex.org/W1995945562","https://openalex.org/W1996816368","https://openalex.org/W1999269351","https://openalex.org/W2006355424","https://openalex.org/W2006820723","https://openalex.org/W2009596137","https://openalex.org/W2013783433","https://openalex.org/W2015472416","https://openalex.org/W2015800458","https://openalex.org/W2020350008","https://openalex.org/W2020891730","https://openalex.org/W2022394456","https://openalex.org/W2024305671","https://openalex.org/W2025489760","https://openalex.org/W2026452889","https://openalex.org/W2027840499","https://openalex.org/W2029423003","https://openalex.org/W2029943378","https://openalex.org/W2030966943","https://openalex.org/W2041797002","https://openalex.org/W2045017146","https://openalex.org/W2049796549","https://openalex.org/W2051578566","https://openalex.org/W2055257453","https://openalex.org/W2057729471","https://openalex.org/W2060425093","https://openalex.org/W2060973867","https://openalex.org/W2065461553","https://openalex.org/W2065691269","https://openalex.org/W2067249552","https://openalex.org/W2081742431","https://openalex.org/W2082638565","https://openalex.org/W2084215753","https://openalex.org/W2086532189","https://openalex.org/W2090074287","https://openalex.org/W2095815023","https://openalex.org/W2097082463","https://openalex.org/W2097412226","https://openalex.org/W2097706568","https://openalex.org/W2098276108","https://openalex.org/W2098448352","https://openalex.org/W2102424972","https://openalex.org/W2102813451","https://openalex.org/W2103546861","https://openalex.org/W2103849916","https://openalex.org/W2105556779","https://openalex.org/W2106151976","https://openalex.org/W2106179083","https://openalex.org/W2106228995","https://openalex.org/W2108531996","https://openalex.org/W2108998942","https://openalex.org/W2116794821","https://openalex.org/W2117897510","https://openalex.org/W2119500092","https://openalex.org/W2120819924","https://openalex.org/W2122004093","https://openalex.org/W2122112080","https://openalex.org/W2122903088","https://openalex.org/W2124181495","https://openalex.org/W2126769883","https://openalex.org/W2131071295","https://openalex.org/W2131459995","https://openalex.org/W2133090982","https://openalex.org/W2140222156","https://openalex.org/W2143335572","https://openalex.org/W2144958703","https://openalex.org/W2149468371","https://openalex.org/W2149628296","https://openalex.org/W2151229046","https://openalex.org/W2151949784","https://openalex.org/W2153520172","https://openalex.org/W2156434383","https://openalex.org/W2157312689","https://openalex.org/W2158734856","https://openalex.org/W2160045133","https://openalex.org/W2160852880","https://openalex.org/W2161192208","https://openalex.org/W2163165362","https://openalex.org/W2163443324","https://openalex.org/W2168696662","https://openalex.org/W2168777931","https://openalex.org/W2169198329","https://openalex.org/W2171189056","https://openalex.org/W2176286246","https://openalex.org/W2177752687","https://openalex.org/W2944768395","https://openalex.org/W2994240441"],"related_works":["https://openalex.org/W1737192842","https://openalex.org/W2177752687","https://openalex.org/W1965898554","https://openalex.org/W3022126255","https://openalex.org/W1543587915","https://openalex.org/W1492288346","https://openalex.org/W2794335363","https://openalex.org/W2068403678","https://openalex.org/W1574209958","https://openalex.org/W2098994155","https://openalex.org/W1541562473","https://openalex.org/W2122903088","https://openalex.org/W2039592185","https://openalex.org/W1555623370","https://openalex.org/W2531578752","https://openalex.org/W2026452889","https://openalex.org/W2041101954","https://openalex.org/W1515496483","https://openalex.org/W142517115","https://openalex.org/W2143518155"],"abstract_inverted_index":{"The":[0,23,56,246],"rapid":[1],"accumulation":[2],"of":[3,19,21,27,100,185,188,208,220,258,327,333],"sequenced":[4],"genomes":[5,136,209],"offers":[6],"the":[7,14,90,130,150,155,161,256,319,325,331],"chance":[8],"to":[9,45,79,103,120,128,153,159,194,205,255,272,284,303],"resolve":[10],"longstanding":[11],"questions":[12],"about":[13],"evolutionary":[15,29,91,132,151],"histories,":[16],"or":[17],"phylogenies,":[18],"groups":[20],"organisms.":[22],"relatively":[24],"rare":[25],"occurrence":[26],"large-scale":[28,85],"events":[30,35],"in":[31,59,73,115,164,261,268],"a":[32,47,180,237,250,300],"whole":[33],"genome,":[34],"such":[36,291],"as":[37],"genome":[38,138],"rearrangements,":[39,139,143],"duplications":[40],"and":[41,49,65,70,106,118,140,146,170,175,192,210,236,252,264,270],"losses,":[42],"enables":[43],"us":[44],"extract":[46],"strong":[48],"robust":[50],"phylogenetic":[51,74,110,262,285,304,322],"signal":[52],"from":[53,84,199,306],"whole-genome":[54,68,94,123,200,259,296,307,328],"data.":[55,124,277,297,308],"work":[57],"presented":[58],"this":[60,315],"dissertation":[61],"focuses":[62],"on":[63,93,242],"models":[64,92,174],"algorithms":[66,78,127],"for":[67,109,182,275,287,295,324],"evolution":[69,189],"their":[71],"use":[72,99,257],"inference.":[75],"We":[76,88,96,125,148,222,298],"designed":[77,126],"estimate":[80,129],"pairwise":[81],"genomic":[82,86,165,244],"distances":[83],"changes.":[87],"refined":[89,149],"evolution.":[95],"also":[97,141,215],"made":[98],"these":[101],"results":[102,266],"provide":[104,179],"fast":[105],"accurate":[107],"methods":[108,274],"inference,":[111],"that":[112,226],"scales":[113],"up,":[114],"both":[116],"speed":[117],"accuracy,":[119],"modern":[121],"high-resolution":[122],"true":[131],"distance":[133,177,229],"between":[134,167],"two":[135],"under":[137,142],"plus":[144],"gains":[145],"losses.":[147],"model":[152,158],"be":[154],"first":[156,320],"mathematical":[157],"preserve":[160],"structural":[162],"dichotomy":[163],"organization":[166],"most":[168,171],"prokaryotes":[169],"eukaryotes.":[172],"Those":[173],"associated":[176],"estimators":[178],"basis":[181],"studying":[183],"facets":[184],"possible":[186],"mechanisms":[187],"through":[190],"simulation":[191],"application":[193],"real":[195],"genomes.":[196],"Phylogenetic":[197],"analyses":[198],"data":[201,260,329],"have":[202,214,280],"been":[203,281],"limited":[204],"small":[206],"collections":[207],"low-resolution":[211],"data;":[212],"they":[213],"lacked":[216],"an":[217,224],"effective":[218],"assessment":[219],"robustness.":[221],"developed":[223,299],"approach":[225,302,317],"combines":[227],"our":[228,312],"estimator,":[230],"any":[231],"standard":[232],"distance-based":[233,273],"reconstruction":[234],"algorithm,":[235],"novel":[238],"bootstrapping":[239],"method":[240],"based":[241],"resampling":[243],"adjacencies.":[245],"resulting":[247],"tool":[248,323],"overcomes":[249],"serious":[251],"long-standing":[253],"impediment":[254],"inference":[263],"provides":[265],"comparable":[267],"accuracy":[269],"robustness":[271],"sequence":[276],"Maximum-likelihood":[278],"approaches":[279],"successfully":[282],"applied":[283],"inferences":[286],"aligned":[288],"sequences,":[289],"but":[290],"applications":[292],"remain":[293],"primitive":[294],"maximum-likelihood":[301],"analysis":[305,326],"In":[309],"combination":[310],"with":[311],"bootstrap":[313],"scheme,":[314],"new":[316],"yields":[318],"reliable":[321],"at":[330],"level":[332],"syntenic":[334],"blocks.":[335]},"counts_by_year":[],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}
