{"id":"https://openalex.org/W2105634079","doi":"https://doi.org/10.1142/s0219720008003242","title":"TWO PLUS TWO DOES NOT EQUAL THREE: STATISTICAL TESTS FOR MULTIPLE GENOME COMPARISON","display_name":"TWO PLUS TWO DOES NOT EQUAL THREE: STATISTICAL TESTS FOR MULTIPLE GENOME COMPARISON","publication_year":2008,"publication_date":"2008-02-01","ids":{"openalex":"https://openalex.org/W2105634079","doi":"https://doi.org/10.1142/s0219720008003242","mag":"2105634079","pmid":"https://pubmed.ncbi.nlm.nih.gov/18324742"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720008003242","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003242","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5073910134","display_name":"Narayanan Raghupathy","orcid":"https://orcid.org/0000-0002-2275-3674"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"NARAYANAN RAGHUPATHY","raw_affiliation_strings":["Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085732629","display_name":"Rose Hoberman","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"ROSE HOBERMAN","raw_affiliation_strings":["Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030066238","display_name":"Dannie Durand","orcid":"https://orcid.org/0000-0002-3505-6640"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"DANNIE DURAND","raw_affiliation_strings":["Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA","Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5073910134"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":null,"apc_paid":null,"fwci":1.2761,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.84616074,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"06","issue":"01","first_page":"1","last_page":"22"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9994999766349792,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9976000189781189,"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":0.9947999715805054,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.7504796981811523},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.684970498085022},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.627282977104187},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5677510499954224},{"id":"https://openalex.org/keywords/linkage","display_name":"Linkage (software)","score":0.5540899634361267},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.5475127696990967},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5450520515441895},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5149481892585754},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5089585781097412},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.4885445535182953},{"id":"https://openalex.org/keywords/multiple-comparisons-problem","display_name":"Multiple comparisons problem","score":0.4309065639972687},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.42241716384887695},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4092422425746918},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2577674686908722},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19289055466651917},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15786296129226685},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.1533414125442505}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7504796981811523},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.684970498085022},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.627282977104187},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5677510499954224},{"id":"https://openalex.org/C31266012","wikidata":"https://www.wikidata.org/wiki/Q6554340","display_name":"Linkage (software)","level":3,"score":0.5540899634361267},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.5475127696990967},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5450520515441895},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5149481892585754},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5089585781097412},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.4885445535182953},{"id":"https://openalex.org/C183905921","wikidata":"https://www.wikidata.org/wiki/Q1038757","display_name":"Multiple comparisons problem","level":2,"score":0.4309065639972687},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.42241716384887695},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4092422425746918},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2577674686908722},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19289055466651917},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15786296129226685},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1533414125442505},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1142/s0219720008003242","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003242","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:18324742","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18324742","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:repository.cmu.edu:biology-1029","is_oa":false,"landing_page_url":"http://repository.cmu.edu/biology/18","pdf_url":null,"source":{"id":"https://openalex.org/S4306400668","display_name":"Research Showcase @ Carnegie Mellon University (Carnegie Mellon University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I74973139","host_organization_name":"Carnegie Mellon University","host_organization_lineage":["https://openalex.org/I74973139"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Department of Biological Sciences","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.44999998807907104,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306079","display_name":"David and Lucile Packard Foundation","ror":"https://ror.org/032atxq54"},{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1490427808","https://openalex.org/W1964612763","https://openalex.org/W1966794959","https://openalex.org/W1969260677","https://openalex.org/W1976245710","https://openalex.org/W1990453950","https://openalex.org/W2011889195","https://openalex.org/W2022846158","https://openalex.org/W2029230311","https://openalex.org/W2045385587","https://openalex.org/W2047405437","https://openalex.org/W2047839385","https://openalex.org/W2048009853","https://openalex.org/W2064912476","https://openalex.org/W2077237181","https://openalex.org/W2081933515","https://openalex.org/W2095891619","https://openalex.org/W2098070331","https://openalex.org/W2103733317","https://openalex.org/W2104761612","https://openalex.org/W2127230663","https://openalex.org/W2128119325","https://openalex.org/W2137285541","https://openalex.org/W2143157299","https://openalex.org/W2151302772","https://openalex.org/W2166589098"],"related_works":["https://openalex.org/W2055598935","https://openalex.org/W401943522","https://openalex.org/W2752491143","https://openalex.org/W2330107134","https://openalex.org/W1986765826","https://openalex.org/W154531455","https://openalex.org/W1976797354","https://openalex.org/W2088387197","https://openalex.org/W3174861742","https://openalex.org/W2949905298"],"abstract_inverted_index":{"Gene":[0],"clusters":[1,19,53,108],"that":[2,38,104],"span":[3],"three":[4,56,93,110],"or":[5,31],"more":[6,113,125],"chromosomal":[7],"regions":[8,57,94,111],"are":[9,20,82,112],"of":[10,36,42,62,69,77,100,107],"increasing":[11],"importance,":[12],"yet":[13],"statistical":[14,50],"tests":[15,51,81,106],"to":[16,85,123],"validate":[17],"such":[18],"in":[21,40],"their":[22],"infancy.":[23],"Current":[24],"approaches":[25],"either":[26],"conduct":[27],"several":[28],"pairwise":[29],"comparisons":[30],"consider":[32],"only":[33],"the":[34,43,83],"number":[35],"genes":[37,89,96],"occur":[39],"all":[41,92],"regions.":[44,101,128],"In":[45],"this":[46],"paper,":[47],"we":[48],"provide":[49],"for":[52],"spanning":[54,109],"exactly":[55],"based":[58],"on":[59],"genome":[60],"models":[61],"typical":[63],"comparative":[64],"genomics":[65],"problems,":[66],"including":[67],"analysis":[68],"conserved":[70],"linkage":[71],"within":[72],"multiple":[73],"species":[74],"and":[75,95,118],"identification":[76],"large-scale":[78],"duplications.":[79],"Our":[80],"first":[84],"combine":[86],"evidence":[87],"from":[88],"shared":[90,97],"among":[91],"between":[98],"pairs":[99],"We":[102],"show":[103],"our":[105],"sensitive":[114],"than":[115],"existing":[116],"approaches,":[117],"can":[119],"thus":[120],"be":[121],"used":[122],"identify":[124],"diverged":[126],"homologous":[127]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}