{"id":"https://openalex.org/W2149681234","doi":"https://doi.org/10.1186/1471-2105-10-s1-s61","title":"On optimal comparability editing with applications to molecular diagnostics","display_name":"On optimal comparability editing with applications to molecular diagnostics","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W2149681234","doi":"https://doi.org/10.1186/1471-2105-10-s1-s61","mag":"2149681234","pmid":"https://pubmed.ncbi.nlm.nih.gov/19208165"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-s1-s61","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s1-s61","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S1-S61","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S1-S61","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033025664","display_name":"Sebastian B\u00f6cker","orcid":"https://orcid.org/0000-0002-9304-8091"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sebastian B\u00f6cker","raw_affiliation_strings":["Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t, Jena, Germany. boecker@minet.uni-jena.de","Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t, Jena, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t, Jena, Germany. boecker@minet.uni-jena.de","institution_ids":["https://openalex.org/I76198965"]},{"raw_affiliation_string":"Institut f\u00fcr Informatik, Friedrich-Schiller-Universit\u00e4t, Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026295810","display_name":"Sebastian Briesemeister","orcid":null},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sebastian Briesemeister","raw_affiliation_strings":["Div. for Simulation of Biological Systems, ZBIT/WSI, Eberhard Karls Universit\u00e4t T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Div. for Simulation of Biological Systems, ZBIT/WSI, Eberhard Karls Universit\u00e4t T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029642674","display_name":"Gunnar W. Klau","orcid":"https://orcid.org/0000-0002-6340-0090"},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832","https://openalex.org/I4405262988"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Gunnar W Klau","raw_affiliation_strings":["CWI, P.O. Box 94079, 1090, GB, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CWI, P.O. Box 94079, 1090, GB, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5029642674"],"corresponding_institution_ids":["https://openalex.org/I1341640284"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.2519,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58342832,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"10","issue":"S1","first_page":"S61","last_page":"S61"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.3928999900817871,"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/T10885","display_name":"Gene expression and cancer classification","score":0.3928999900817871,"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":0.10260000079870224,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.053199999034404755,"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/heuristics","display_name":"Heuristics","score":0.7125668525695801},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6017873883247375},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.5618208646774292},{"id":"https://openalex.org/keywords/comparability","display_name":"Comparability","score":0.5365216135978699},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5085560083389282},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.48508086800575256},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.44539761543273926},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43182891607284546},{"id":"https://openalex.org/keywords/linear-programming","display_name":"Linear programming","score":0.41671112179756165},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.407988578081131},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2965199947357178},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.19911187887191772},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17798098921775818},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08261910080909729}],"concepts":[{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.7125668525695801},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6017873883247375},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.5618208646774292},{"id":"https://openalex.org/C197947376","wikidata":"https://www.wikidata.org/wiki/Q5155608","display_name":"Comparability","level":2,"score":0.5365216135978699},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5085560083389282},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.48508086800575256},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.44539761543273926},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43182891607284546},{"id":"https://openalex.org/C41045048","wikidata":"https://www.wikidata.org/wiki/Q202843","display_name":"Linear programming","level":2,"score":0.41671112179756165},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.407988578081131},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2965199947357178},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.19911187887191772},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17798098921775818},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08261910080909729},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025202","descriptor_name":"Molecular Diagnostic Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025202","descriptor_name":"Molecular Diagnostic Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025202","descriptor_name":"Molecular Diagnostic Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025202","descriptor_name":"Molecular Diagnostic Techniques","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D025202","descriptor_name":"Molecular Diagnostic Techniques","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D025202","descriptor_name":"Molecular Diagnostic Techniques","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-10-s1-s61","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s1-s61","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S1-S61","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19208165","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19208165","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:cwi:oai:cwi.nl:14845","is_oa":true,"landing_page_url":"https://ir.cwi.nl/pub/14845","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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":"BMC Bioinformatics, 10(suppl 1)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.364.2454","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.364.2454","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.biomedcentral.com/content/pdf/1471-2105-10-S1-S61.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:93eb7c46537245eb91e96bf643906702","is_oa":true,"landing_page_url":"https://doaj.org/article/93eb7c46537245eb91e96bf643906702","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss Suppl 1, p S61 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2648753","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2648753","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-s1-s61","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s1-s61","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S1-S61","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321112","display_name":"Eberhard Karls Universit\u00e4t T\u00fcbingen","ror":"https://ror.org/03a1kwz48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149681234.pdf","grobid_xml":"https://content.openalex.org/works/W2149681234.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1517036688","https://openalex.org/W1586744224","https://openalex.org/W1975023024","https://openalex.org/W2015480586","https://openalex.org/W2037306276","https://openalex.org/W2050470778","https://openalex.org/W2055747219","https://openalex.org/W2055764977","https://openalex.org/W2133131759","https://openalex.org/W2135798380","https://openalex.org/W2137745608","https://openalex.org/W2152729085","https://openalex.org/W4255284090"],"related_works":["https://openalex.org/W2788438366","https://openalex.org/W2115618655","https://openalex.org/W2470895000","https://openalex.org/W2483226803","https://openalex.org/W1968110187","https://openalex.org/W4311991594","https://openalex.org/W4377249757","https://openalex.org/W15582532","https://openalex.org/W2087409062","https://openalex.org/W2801711508"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,30],"COMPARABILITY":[2],"EDITING":[3],"problem":[4,77],"appears":[5],"in":[6,112],"the":[7,35,76,123,140,144],"context":[8],"of":[9,38,132,143],"hierarchical":[10,25],"disease":[11],"classification":[12],"based":[13,78],"on":[14,79],"noisy":[15],"data.":[16],"We":[17,70],"are":[18,59,107,130],"given":[19],"a":[20,47,115],"directed":[21],"graph":[22],"G":[23,45],"representing":[24],"relationships":[26],"between":[27],"patient":[28],"subgroups.":[29],"task":[31],"is":[32],"to":[33,43,88,122],"identify":[34],"minimum":[36],"number":[37],"edge":[39,62],"insertions":[40],"or":[41],"deletions":[42],"transform":[44],"into":[46],"transitive":[48],"graph,":[49],"that":[50,103],"is,":[51],"if":[52],"edges":[53],"(u,":[54,63],"v)":[55],"and":[56,82,137],"(v,":[57],"w)":[58,64],"present":[60,71],"then":[61],"must":[65],"be":[66],"present,":[67],"too.":[68],"RESULTS:":[69],"two":[72],"new":[73],"approaches":[74,93],"for":[75],"fixed-parameter":[80],"algorithmics":[81],"integer":[83],"linear":[84],"programming.":[85],"In":[86,120],"contrast":[87],"previously":[89,116],"used":[90,117],"heuristics,":[91],"our":[92,104,128],"compute":[94],"provably":[95],"optimal":[96,135],"solutions.":[97],"CONCLUSION:":[98],"Our":[99],"computational":[100],"results":[101],"demonstrate":[102],"exact":[105],"algorithms":[106,129],"by":[108],"far":[109],"more":[110],"efficient":[111],"practice":[113],"than":[114],"heuristic":[118],"approach.":[119],"addition":[121],"superior":[124],"running":[125],"time":[126],"performance,":[127],"capable":[131],"enumerating":[133],"all":[134],"solutions,":[136],"naturally":[138],"solve":[139],"weighted":[141],"version":[142],"problem.":[145]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
