{"id":"https://openalex.org/W425173396","doi":null,"title":"TreeHop: a method to improve orthology detection","display_name":"TreeHop: a method to improve orthology detection","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W425173396","mag":"425173396"},"language":"en","primary_location":{"id":"pmh:oai:repositorio.ulisboa.pt:10451/9921","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10451/9921","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"master thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/10451/9921","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074097483","display_name":"Beatriz Margarida Mo\u00e7o Ferreira Gomes","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Beatriz Margarida Mo\u00e7o Ferreira Gomes","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5074097483"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976000189781189,"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":0.9976000189781189,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.000699999975040555,"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":0.0003000000142492354,"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/paralogy","display_name":"paralogy","score":0.7749999761581421},{"id":"https://openalex.org/keywords/homology","display_name":"homology","score":0.6000000238418579},{"id":"https://openalex.org/keywords/gene-tree-reconstruction","display_name":"gene tree reconstruction","score":0.3569999933242798},{"id":"https://openalex.org/keywords/species-tree","display_name":"species tree","score":0.4659999907016754},{"id":"https://openalex.org/keywords/graph-based-methods","display_name":"graph-based methods","score":0.5740000009536743},{"id":"https://openalex.org/keywords/tree-based-models","display_name":"tree-based models","score":0.9150000214576721},{"id":"https://openalex.org/keywords/coiled-coil-proteins","display_name":"coiled-coil proteins","score":0.4690000116825104},{"id":"https://openalex.org/keywords/protein-domain-composition","display_name":"protein domain composition","score":0.35600000619888306},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.35499998927116394},{"id":"https://openalex.org/keywords/genome-annotation","display_name":"genome annotation","score":0.4339999854564667},{"id":"https://openalex.org/keywords/horizontal-gene-transfer","display_name":"horizontal gene transfer","score":0.6439999938011169},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"gene duplication","score":0.5619999766349792},{"id":"https://openalex.org/keywords/gene-loss","display_name":"gene loss","score":0.39800000190734863},{"id":"https://openalex.org/keywords/computational-cost-reduction","display_name":"computational complexity reduction","score":0.38600000739097595},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"parallel computing","score":0.335999995470047}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45111894607543945},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34193864464759827},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3010481297969818}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:repositorio.ulisboa.pt:10451/9921","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10451/9921","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"master thesis"},{"id":"mag:425173396","doi":null,"is_oa":false,"landing_page_url":"http://repositorio.ul.pt/bitstream/10451/9921/1/ulfc105763_tm_Beatriz_Gomes.pdf","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":{"id":"pmh:oai:repositorio.ulisboa.pt:10451/9921","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10451/9921","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"master thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1981791726","https://openalex.org/W1986367828","https://openalex.org/W1990453950","https://openalex.org/W1995117714","https://openalex.org/W1997130867","https://openalex.org/W2002568105","https://openalex.org/W2027745562","https://openalex.org/W2028265997","https://openalex.org/W2029833898","https://openalex.org/W2030317329","https://openalex.org/W2048448217","https://openalex.org/W2082202339","https://openalex.org/W2099321785","https://openalex.org/W2099946731","https://openalex.org/W2109368213","https://openalex.org/W2116494281","https://openalex.org/W2117709367","https://openalex.org/W2124908487","https://openalex.org/W2125531604","https://openalex.org/W2137084536","https://openalex.org/W2137529106","https://openalex.org/W2143335572","https://openalex.org/W2145100181","https://openalex.org/W2151859071","https://openalex.org/W2154044807","https://openalex.org/W2154364831","https://openalex.org/W2159266221","https://openalex.org/W2162327194","https://openalex.org/W2167188257","https://openalex.org/W2315376284","https://openalex.org/W3188783681","https://openalex.org/W7098320409"],"related_works":["https://openalex.org/W7095875234","https://openalex.org/W2571621700","https://openalex.org/W2964089768","https://openalex.org/W4320352502","https://openalex.org/W2510379","https://openalex.org/W1680595618","https://openalex.org/W7096800484","https://openalex.org/W4394792608","https://openalex.org/W2285510792","https://openalex.org/W2752837628"],"abstract_inverted_index":{"Com":[0,232],"as":[1,425],"novas":[2],"t\u00e9cnicas":[3],"de":[4,6,10,30,47,54,63,78,83,86,98,103,106,118,135,139,144,165,169,188,192,213,224,235,247,253,268,281,288,339,351,367,372,374,395,413,489,504,508,520,525,528,547,573,577,615,639,645,647,662,665,678,722,727,731,733,740,763,774,779],"sequencia\u00e7\u00e3o":[5],"genomas,":[7],"a":[8,12,20,27,33,45,114,126,133,163,178,199,206,245,328,337,349,468,470,477,502,585,600,622,671,686,692,698,704,754,788,802],"quantidade":[9],"informa\u00e7\u00e3o":[11],"n\u00edvel":[13,672],"molecular":[14],"tem":[15,42,138,333,417,527],"crescido":[16],"exponencialmente.":[17],"Para":[18,308,442],"perceber":[19,745],"origem":[21],"da":[22,472,706],"diversidade":[23],"biol\u00f3gica":[24],"assim":[25,702],"como":[26,210,334,364,418,439,495,542,691,703],"hist\u00f3ria":[28],"evolutiva":[29],"um":[31,55,79,84,99,104,219,318,325,368,393,403,410,458,482,530,616,629,658,728,761],"gene,":[32],"compara\u00e7\u00e3o":[34,41,606],"entre":[35,116,181,286],"genomas":[36],"tornou-se":[37],"indispens\u00e1vel.":[38],"Normalmente,":[39],"esta":[40,583],"por":[43,131,159],"base":[44,401,429,496,544,638,696,794],"an\u00e1lise":[46],"sequ\u00eancias":[48,51],"hom\u00f3logas":[49],"{":[50],"que":[52,76,96,124,218,329,332,380,522,551,599,635,784],"derivaram":[53,77,97],"ancestral":[56,80,100],"comum.":[57],"H\u00e1":[58],"pelo":[59,399],"menos":[60,291,478],"dois":[61,563],"sub-tipos":[62],"homologia:":[64],"ortologia":[65],"e":[66,130,186,190,271,406,434,497,545,674,736,772,776,790,795],"paralogia.":[67],"Genes":[68,88,108],"ort\u00f3logos":[69,109,151,171,248,282,375,397,421,506,554],"(ortho":[70],"=":[71,91],"exacto)":[72],"s\u00e3o":[73,93,110,121,295,510,553],"genes":[74,94,117,150,170,396,552],"hom\u00f3logos":[75,95],"comum":[81,101],"atrav\u00e9s":[82,102],"evento":[85,105],"especia\u00e7\u00e3o.":[87],"par\u00e1logos":[89],"(para":[90],"paralelo)":[92],"duplica\u00e7\u00e3o.":[107],"importantes":[111],"para":[112,162,244,362,402,409,424,456,476,501,642,684,752,800],"estabelecer":[113],"correspond\u00eancia":[115],"esp\u00e9cies":[119,129,423,440,488],"diferentes;":[120],"os":[122,431],"\u00fanicos":[123],"reflectem":[125],"\u00e1rvore":[127,408,471,707],"das":[128,201,566,588,708],"isso":[132,160],"reconstru\u00e7\u00e3o":[134],"\u00e1rvores":[136],"filogen\u00e9ticas":[137],"ser":[140,259,382,513,529,574,586,750],"baseada":[141],"neste":[142],"tipo":[143],"genes;":[145],"na":[146,266,284,452],"maioria":[147],"dos":[148,700],"casos,":[149],"t\u00eam":[152,300],"fun\u00e7\u00f5es":[153],"equivalentes":[154],"em":[155,261,274,310,342,345,355,384,387,562,605,619,632,654,719],"diferentes":[156],"organismos":[157],"sendo":[158],"utilizados":[161],"anota\u00e7\u00e3o":[164],"fun\u00e7\u00f5es.":[166],"A":[167],"detec\u00e7\u00e3o":[168,207,246,373,503,677],"n\u00e3o":[172,430,464,485],"\u00e9":[173,392,519,570,603,636],"uma":[174,365,407,587,637,652,716],"tarefa":[175],"f\u00e1cil":[176],"devido":[177,592],"v\u00e1rios":[179],"factores,":[180],"eles:":[182],"perda,":[183],"duplica\u00e7\u00e3o,":[184],"fus\u00e3o":[185],"fiss\u00e3o":[187],"genes,":[189,209],"eventos":[191,197],"transfer\u00eancia":[193],"horizontal.":[194],"Al\u00e9m":[195],"destes":[196,208,238],"biol\u00f3gicos,":[198],"composi\u00e7\u00e3o":[200,668],"prote\u00ednas":[202,214,229,666,723,732,737],"pode":[203,381],"tamb\u00e9m":[204,650,711,744,797],"afectar":[205],"no":[211],"caso":[212],"com":[215,222,348,607,725,738],"mais":[216,252,296,301,454,474,487,505,590,610,726],"do":[217,624,688,694,756,768,770,792],"dom\u00ednio":[220],"ou":[221,386,484,516],"dom\u00ednios":[223],"pouca":[225],"complexidade":[226],"(por":[227],"exemplo,":[228],"coiled":[230],"coil).":[231],"o":[233,313,427,446,449,465,498,514,523,537,557,571,713,766,785],"intuito":[234],"ultrapassar":[236],"alguns":[237,608],"obst\u00e1culos,":[239],"foram":[240],"criados":[241],"diversos":[242],"m\u00e9todos":[243,264,272,340,352,609],"(at\u00e9":[249],"\u00e1":[250],"data":[251],"30).":[254],"Em":[255],"geral,":[256],"estes":[257],"podem":[258,512],"divididos":[260],"duas":[262],"categorias:":[263],"baseados":[265,273,283,341],"forma\u00e7\u00e3o":[267],"grafos":[269,343,385],"(graph-based)":[270],"filogenia":[275],"(tree-based).":[276],"Os":[277,298],"primeiros":[278],"formam":[279],"\\clusters\"":[280],"semelhan\u00e7a":[285],"pares":[287],"sequ\u00eancias,":[289],"distinguem":[290],"rela\u00e7\u00f5es":[292,579],"evolutivas":[293],"mas":[294,303],"eficientes.":[297],"segundos":[299],"precis\u00e3o":[302,350,791],"requerem":[304],"maior":[305],"poder":[306],"computacional.":[307],"estudos":[309],"grande":[311,346,734],"escala,":[312,621,656],"custo":[314],"computacional":[315],"poder\u00e1":[316],"tornar-se":[317],"factor":[319],"limitante.":[320],"Neste":[321],"estudo,":[322],"n\u00f3s":[323,535],"propomos":[324,796],"novo":[326],"m\u00e9todo":[327,371,400,428,493,499,524,531,538,543,546,569,630,695,762,793],"cham\u00e1mos":[330],"TreeHop":[331,359,416,447,714,786],"objectivo":[335,419],"combinar":[336],"efici\u00eancia":[338],"usados":[344,354],"escala":[347],"filogen\u00e9ticos":[353],"pequena":[356,655],"escala.":[357],"O":[358,389,415,492],"foi":[360,597,626],"pensado":[361],"funcionar":[363],"extens\u00e3o":[366],"qualquer":[369],"outro":[370],"j\u00e1":[376],"existente":[377],"(m\u00e9todo":[378,507],"base),":[379],"baseado":[383,631],"filogenia.":[388],"seu":[390],"input":[391],"perfil":[394],"detectados":[398],"dado":[404],"gene":[405],"determinado":[411],"conjunto":[412,659],"esp\u00e9cies.":[414],"inferir":[420,578],"nas":[422],"quais":[426,436],"conseguiu":[432],"detectar,":[433],"\u00e0s":[435],"nos":[437],"referimos":[438],"gap.":[441],"cada":[443],"esp\u00e9cie":[444,453,473],"gap,":[445],"utiliza":[448],"ort\u00f3logo":[450,460,483],"detectado":[451],"pr\u00f3xima":[455,475],"procurar":[457],"poss\u00edvel":[459],"nesta":[461],"esp\u00e9cie.":[462],"Se":[463],"encontrar":[466,481],"continua":[467,584],"percorrer":[469],"pr\u00f3xima,":[479],"at\u00e9":[480],"haver":[486],"onde":[490],"saltar.":[491],"usado":[494,500],"salto)":[509],"independentes:":[511],"mesmo":[515],"diferentes.":[517],"Mas":[518],"notar":[521],"salto":[526,764],"pairwise.":[532],"Nesta":[533],"tese,":[534],"utiliz\u00e1mos":[536],"Bi-directional":[539],"Best":[540],"Hit":[541],"salto.":[548,780],"Este":[549],"assume":[550],"se":[555,712,746],"forem":[556],"primeiro":[558],"hit":[559],"(BLAST),":[560],"reciprocamente":[561],"genomas.":[564],"Uma":[565],"desvantagens":[567],"deste":[568],"facto":[572],"apenas":[575],"capaz":[576],"um-para-um.":[580],"Mesmo":[581],"assim,":[582],"metodologias":[589],"usadas":[591],"\u00e0":[593,613,676],"sua":[594,601,803],"efic\u00e1cia.":[595],"Tamb\u00e9m":[596],"mostrado":[598],"performance":[602,717,755],"melhor":[604],"complexos.":[611],"Devido":[612],"falta":[614],"gold":[617],"standard":[618],"larga":[620],"valida\u00e7\u00e3o":[623],"algoritmo":[625],"realizada":[627],"contra":[628,657],"filogenias":[633,646],"PhylomeDB,":[634],"dados":[640],"p\u00fablica":[641],"colec\u00e7\u00f5es":[643],"completas":[644],"genes.":[648],"Foi":[649],"feita":[651],"valida\u00e7\u00e3o,":[653],"manualmente":[660],"curado":[661],"70":[663],"fam\u00edlias":[664],"cuja":[667],"apresenta":[669],"desafios":[670],"biol\u00f3gico":[673],"t\u00e9cnico,":[675],"ortologia.":[679],"Foram":[680],"feitas":[681],"diversas":[682,777],"an\u00e1lises":[683],"testar":[685],"robustez":[687],"algoritmo:":[689],"analisou-se":[690],"escolha":[693],"afecta":[697],"qualidade":[699,705],"resultados;":[701],"esp\u00e9cies;":[709],"testou-se":[710,760],"tinha":[715],"inferior":[718],"certas":[720],"classes":[721],"(prote\u00ednas":[724],"dom\u00ednio,":[729],"fam\u00edlia":[730],"n\u00famero":[735],"regi\u00f5es":[739],"baixa":[741],"complexidade).":[742],"Tentou-se":[743],"determinados":[747],"par\u00e2metros":[748],"poderiam":[749],"mudados":[751],"melhorar":[753],"TreeHop.":[757],"Entre":[758],"eles":[759],"diferente,":[765],"efeito":[767],"e-value":[769],"alinhamento":[771],"tamanho":[773],"prote\u00ednas,":[775],"estrat\u00e9gias":[778],"No":[781],"final,":[782],"conclu\u00edmos":[783],"aumenta":[787],"sensibilidade":[789],"algumas":[798],"heur\u00edsticas":[799],"modular":[801],"performance.":[804]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2016-06-24T00:00:00"}
