{"id":"https://openalex.org/W2099783690","doi":"https://doi.org/10.1093/bioinformatics/bti107","title":"Theoretical and practical advances in genome halving","display_name":"Theoretical and practical advances in genome halving","publication_year":2004,"publication_date":"2004-10-28","ids":{"openalex":"https://openalex.org/W2099783690","doi":"https://doi.org/10.1093/bioinformatics/bti107","mag":"2099783690","pmid":"https://pubmed.ncbi.nlm.nih.gov/15513986"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti107","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti107","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/869/48972229/bioinformatics_21_7_869.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/869/48972229/bioinformatics_21_7_869.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101675787","display_name":"Peng Yin","orcid":"https://orcid.org/0000-0002-4773-359X"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peng Yin","raw_affiliation_strings":["Department of Computer Science, Duke University Box 90129, Durham, NC 27708-0129, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University Box 90129, Durham, NC 27708-0129, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026273992","display_name":"Alexander J. Hartemink","orcid":"https://orcid.org/0000-0002-1292-2606"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander J. Hartemink","raw_affiliation_strings":["Department of Computer Science, Duke University Box 90129, Durham, NC 27708-0129, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University Box 90129, Durham, NC 27708-0129, USA","institution_ids":["https://openalex.org/I170897317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5101675787"],"corresponding_institution_ids":["https://openalex.org/I170897317"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.8562,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.74771375,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"7","first_page":"869","last_page":"879"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9958999752998352,"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":0.9958999752998352,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.002099999925121665,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.00019999999494757503,"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/genome","display_name":"Genome","score":0.8738234639167786},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.7174296379089355},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6175159811973572},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5712735652923584},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5534986853599548},{"id":"https://openalex.org/keywords/genome-evolution","display_name":"Genome evolution","score":0.46182185411453247},{"id":"https://openalex.org/keywords/segmental-duplication","display_name":"Segmental duplication","score":0.45739755034446716},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4501889646053314},{"id":"https://openalex.org/keywords/gene-family","display_name":"Gene family","score":0.25358617305755615}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8738234639167786},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.7174296379089355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6175159811973572},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5712735652923584},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5534986853599548},{"id":"https://openalex.org/C174600577","wikidata":"https://www.wikidata.org/wiki/Q5533491","display_name":"Genome evolution","level":4,"score":0.46182185411453247},{"id":"https://openalex.org/C57808653","wikidata":"https://www.wikidata.org/wiki/Q7446270","display_name":"Segmental duplication","level":5,"score":0.45739755034446716},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4501889646053314},{"id":"https://openalex.org/C5911399","wikidata":"https://www.wikidata.org/wiki/Q2278983","display_name":"Gene family","level":4,"score":0.25358617305755615}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008040","descriptor_name":"Genetic Linkage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008040","descriptor_name":"Genetic Linkage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008040","descriptor_name":"Genetic Linkage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti107","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti107","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/869/48972229/bioinformatics_21_7_869.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15513986","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15513986","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti107","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti107","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/869/48972229/bioinformatics_21_7_869.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2099783690.pdf","grobid_xml":"https://content.openalex.org/works/W2099783690.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W207054344","https://openalex.org/W602132365","https://openalex.org/W1483189080","https://openalex.org/W1494075612","https://openalex.org/W1541767983","https://openalex.org/W1641544182","https://openalex.org/W1970800531","https://openalex.org/W1972628065","https://openalex.org/W1988591865","https://openalex.org/W2008047531","https://openalex.org/W2008956020","https://openalex.org/W2011889195","https://openalex.org/W2016057692","https://openalex.org/W2019591778","https://openalex.org/W2019915835","https://openalex.org/W2021142940","https://openalex.org/W2026055857","https://openalex.org/W2049896656","https://openalex.org/W2056433290","https://openalex.org/W2070387787","https://openalex.org/W2071262938","https://openalex.org/W2077237181","https://openalex.org/W2080163922","https://openalex.org/W2081840182","https://openalex.org/W2081933515","https://openalex.org/W2091943445","https://openalex.org/W2094780854","https://openalex.org/W2098188415","https://openalex.org/W2107383419","https://openalex.org/W2111839706","https://openalex.org/W2116905253","https://openalex.org/W2135123683","https://openalex.org/W2142627516","https://openalex.org/W2346628768","https://openalex.org/W2401846384","https://openalex.org/W2911804362","https://openalex.org/W3187176588","https://openalex.org/W4211019135","https://openalex.org/W4248536238"],"related_works":["https://openalex.org/W4212827698","https://openalex.org/W2035628732","https://openalex.org/W1573987240","https://openalex.org/W1849892148","https://openalex.org/W2004759596","https://openalex.org/W300962949","https://openalex.org/W3135134858","https://openalex.org/W2149483362","https://openalex.org/W2094844584","https://openalex.org/W2072851287"],"abstract_inverted_index":{"MOTIVATION:":[0],"Duplication":[1],"of":[2,17,27,42,67,80,99,104,159,210],"an":[3,68,105,185],"organism's":[4],"entire":[5],"genome":[6,75,107,113,130,160,176,216],"is":[7,110,134,146,218],"a":[8,61,73,124,141,180,191,208],"rare":[9],"but":[10],"spectacular":[11],"event,":[12],"enabling":[13],"the":[14,24,39,63,78,95,101,129,137,151,157,204,214],"rapid":[15],"emergence":[16],"multiple":[18],"new":[19,125,142,181,198],"gene":[20],"functions.":[21],"Over":[22],"time,":[23],"parallel":[25,85],"linkage":[26,102],"duplicated":[28,187],"genes":[29,43,53],"across":[30],"chromosomes":[31],"may":[32,44,54,76],"be":[33,45,58,77],"disrupted":[34],"by":[35,47],"reciprocal":[36],"translocations,":[37],"while":[38],"intra-chromosomal":[40],"order":[41],"shuffled":[46],"inversions":[48],"and":[49,140,163,167,200],"transpositions.":[50],"Some":[51],"duplicate":[52],"evolve":[55],"unrecognizably":[56],"or":[57],"deleted.":[59],"As":[60],"consequence,":[62],"only":[64],"detectable":[65],"signature":[66],"ancient":[69],"duplication":[70,109],"event":[71],"in":[72,94],"modern":[74],"presence":[79],"various":[81],"chromosomal":[82],"segments":[83],"containing":[84],"paralogous":[86],"genes,":[87],"with":[88,115],"each":[89],"segment":[90],"appearing":[91],"exactly":[92],"twice":[93],"genome.":[96,188],"The":[97],"problem":[98],"reconstructing":[100,184],"structure":[103],"ancestral":[106,186],"before":[108],"known":[111],"as":[112],"halving":[114,131,161,177,213],"unordered":[116],"chromosomes.":[117],"RESULTS:":[118],"In":[119],"this":[120,197],"paper,":[121],"we":[122],"derive":[123],"upper":[126,166],"bound":[127,144],"on":[128,175,196,203],"distance":[132,178],"that":[133,145,217],"tighter":[135,149,173],"than":[136,150,220],"best":[138,152],"known,":[139],"lower":[143,168],"almost":[147],"always":[148],"known.":[153],"We":[154,189],"also":[155],"define":[156],"notion":[158],"diameter,":[162],"obtain":[164],"both":[165],"bounds":[169,174],"for":[170,183,212],"it.":[171],"Our":[172],"yield":[179],"algorithm":[182,199],"create":[190],"software":[192],"package":[193],"GenomeHalving":[194],"based":[195],"test":[201],"it":[202],"yeast":[205,215],"genome,":[206],"identifying":[207],"sequence":[209],"translocations":[211],"shorter":[219],"previously":[221],"conjectured":[222],"possible.":[223]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}