{"id":"https://openalex.org/W2444312726","doi":"https://doi.org/10.1093/bioinformatics/btw692","title":"An integer programming framework for inferring disease complexes from network data","display_name":"An integer programming framework for inferring disease complexes from network data","publication_year":2016,"publication_date":"2016-12-15","ids":{"openalex":"https://openalex.org/W2444312726","doi":"https://doi.org/10.1093/bioinformatics/btw692","mag":"2444312726","pmid":"https://pubmed.ncbi.nlm.nih.gov/27993841"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw692","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw692","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/24/3855/30137892/btw692.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"erratum","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/24/3855/30137892/btw692.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041425450","display_name":"Arnon Mazza","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Arnon Mazza","raw_affiliation_strings":["Blavatnik Sch. of Comput. Sci., Tel Aviv Univ., Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"Blavatnik Sch. of Comput. Sci., Tel Aviv Univ., Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038268195","display_name":"Konrad Klockmeier","orcid":null},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Konrad Klockmeier","raw_affiliation_strings":["Max Delbr\u00fcck Center for Molecular Medicine  Berlin Germany"],"affiliations":[{"raw_affiliation_string":"Max Delbr\u00fcck Center for Molecular Medicine  Berlin Germany","institution_ids":["https://openalex.org/I205582932"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014950513","display_name":"Erich E. Wanker","orcid":"https://orcid.org/0000-0001-8072-1630"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erich Wanker","raw_affiliation_strings":["Max Delbr\u00fcck Center for Molecular Medicine  Berlin Germany"],"affiliations":[{"raw_affiliation_string":"Max Delbr\u00fcck Center for Molecular Medicine  Berlin Germany","institution_ids":["https://openalex.org/I205582932"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046958549","display_name":"Roded Sharan","orcid":"https://orcid.org/0000-0001-8363-4882"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Roded Sharan","raw_affiliation_strings":["Blavatnik Sch. of Comput. Sci., Tel Aviv Univ., Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"Blavatnik Sch. of Comput. Sci., Tel Aviv Univ., Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5041425450"],"corresponding_institution_ids":["https://openalex.org/I16391192"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2202,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.80344313,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"32","issue":"24","first_page":"3855","last_page":"3855"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10086","display_name":"Alzheimer's disease research and treatments","score":0.9926000237464905,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T13127","display_name":"Biotin and Related Studies","score":0.9904999732971191,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/executable","display_name":"Executable","score":0.8668935298919678},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6727253198623657},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6531945466995239},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.6186805367469788},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5959227085113525},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.5576194524765015},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5172796249389648},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.46166661381721497},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4533897042274475},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.44562917947769165},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39728856086730957},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3803468644618988},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32959315180778503},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3150128126144409},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2386678159236908},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.19880729913711548},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1606590449810028},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.12210610508918762}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.8668935298919678},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6727253198623657},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6531945466995239},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.6186805367469788},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5959227085113525},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5576194524765015},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5172796249389648},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.46166661381721497},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4533897042274475},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.44562917947769165},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39728856086730957},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3803468644618988},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32959315180778503},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3150128126144409},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2386678159236908},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.19880729913711548},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1606590449810028},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.12210610508918762},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btw692","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw692","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/24/3855/30137892/btw692.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27993841","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27993841","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":null},{"id":"pmh:oai:edoc.mdc-berlin.de:15923","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/24/3855","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/24/3855","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:7297212","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7297212","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw692","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw692","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/24/3855/30137892/btw692.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332324","display_name":"Edmond J. Safra Center for Ethics, Harvard University","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2444312726.pdf","grobid_xml":"https://content.openalex.org/works/W2444312726.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W584809366","https://openalex.org/W1588318052","https://openalex.org/W2010817599","https://openalex.org/W2011340259","https://openalex.org/W2015123704","https://openalex.org/W2036568936","https://openalex.org/W2038122249","https://openalex.org/W2053039860","https://openalex.org/W2060429763","https://openalex.org/W2063451981","https://openalex.org/W2068537457","https://openalex.org/W2071335594","https://openalex.org/W2083474208","https://openalex.org/W2088891952","https://openalex.org/W2103017472","https://openalex.org/W2104261859","https://openalex.org/W2110065044","https://openalex.org/W2112922820","https://openalex.org/W2119079421","https://openalex.org/W2119220491","https://openalex.org/W2123122813","https://openalex.org/W2124276356","https://openalex.org/W2126101709","https://openalex.org/W2126434293","https://openalex.org/W2127006085","https://openalex.org/W2134699030","https://openalex.org/W2136410628","https://openalex.org/W2145627818","https://openalex.org/W2146495783","https://openalex.org/W2148043260","https://openalex.org/W2156443053","https://openalex.org/W2159092541","https://openalex.org/W2169179075","https://openalex.org/W2170870388","https://openalex.org/W2244718251","https://openalex.org/W2605068739"],"related_works":["https://openalex.org/W2350278424","https://openalex.org/W2071432835","https://openalex.org/W4234371507","https://openalex.org/W4299534542","https://openalex.org/W1925942709","https://openalex.org/W2047683846","https://openalex.org/W2044902158","https://openalex.org/W2082154838","https://openalex.org/W2109912052","https://openalex.org/W1711527768"],"abstract_inverted_index":{"MOTIVATION:":[0],"Unraveling":[1],"the":[2,14,29,70,120,123],"molecular":[3],"mechanisms":[4],"that":[5,11,25,63,86,92,102],"underlie":[6],"disease":[7,30],"calls":[8],"for":[9,40,69],"methods":[10],"go":[12],"beyond":[13],"identification":[15],"of":[16],"single":[17],"causal":[18],"genes":[19],"to":[20,59,66,80,100],"inferring":[21],"larger":[22],"protein":[23,42,84],"assemblies":[24],"take":[26],"part":[27],"in":[28,54],"process.":[31],"RESULTS:":[32],"Here,":[33],"we":[34,118],"develop":[35],"an":[36],"exact,":[37],"integer-programming-based":[38],"method":[39,94],"associating":[41],"complexes":[43,85],"with":[44,77],"disease.":[45,72],"Our":[46],"approach":[47],"scores":[48,74],"proteins":[49],"based":[50],"on":[51],"their":[52],"proximity":[53],"a":[55,60],"protein-protein":[56],"interaction":[57,78],"network":[58],"prior":[61],"set":[62],"is":[64],"known":[65],"be":[67],"relevant":[68],"studied":[71],"These":[73],"are":[75,87,103,125],"combined":[76],"information":[79],"infer":[81],"densely":[82],"interacting":[83],"potentially":[88],"disease-associated.":[89],"We":[90],"show":[91],"our":[93],"outperforms":[95],"previous":[96],"ones":[97],"and":[98,110,122],"leads":[99],"predictions":[101],"well":[104],"supported":[105],"by":[106],"current":[107],"experimental":[108],"data":[109],"literature":[111],"knowledge.":[112],"AVAILABILITY":[113],"AND":[114],"IMPLEMENTATION:":[115],"The":[116],"datasets":[117],"used,":[119],"executables":[121],"results":[124],"available":[126],"at":[127],"www.cs.tau.ac.il/roded/disease_complexes.zip.":[128],"CONTACT:":[129],"roded@post.tau.ac.il.":[130]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
