{"id":"https://openalex.org/W2519532642","doi":"https://doi.org/10.1186/s13637-017-0063-3","title":"Learning directed acyclic graphs from large-scale genomics data","display_name":"Learning directed acyclic graphs from large-scale genomics data","publication_year":2017,"publication_date":"2017-09-20","ids":{"openalex":"https://openalex.org/W2519532642","doi":"https://doi.org/10.1186/s13637-017-0063-3","mag":"2519532642","pmid":"https://pubmed.ncbi.nlm.nih.gov/28933027"},"language":"en","primary_location":{"id":"doi:10.1186/s13637-017-0063-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-017-0063-3","pdf_url":"https://bsb-eurasipjournals.springeropen.com/counter/pdf/10.1186/s13637-017-0063-3","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://bsb-eurasipjournals.springeropen.com/counter/pdf/10.1186/s13637-017-0063-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008217140","display_name":"Fabio Nikolay","orcid":"https://orcid.org/0000-0002-6719-9822"},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck KGaA, Darmstadt (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]},{"id":"https://openalex.org/I31512782","display_name":"Technische Universit\u00e4t Darmstadt","ror":"https://ror.org/05n911h24","country_code":"DE","type":"education","lineage":["https://openalex.org/I31512782"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Fabio Nikolay","raw_affiliation_strings":["Communication Systems Group, TU Darmstadt, Merckstr. 25, Darmstadt, Germany. nikolay@nt.tu-darmstadt.de","Communication Systems Group, TU Darmstadt, Merckstr. 25, Darmstadt, Germany"],"raw_orcid":"https://orcid.org/0000-0002-6719-9822","affiliations":[{"raw_affiliation_string":"Communication Systems Group, TU Darmstadt, Merckstr. 25, Darmstadt, Germany. nikolay@nt.tu-darmstadt.de","institution_ids":["https://openalex.org/I31512782"]},{"raw_affiliation_string":"Communication Systems Group, TU Darmstadt, Merckstr. 25, Darmstadt, Germany","institution_ids":["https://openalex.org/I31512782","https://openalex.org/I164928964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001481378","display_name":"Marius Pesavento","orcid":"https://orcid.org/0000-0003-3395-2588"},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck KGaA, Darmstadt (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]},{"id":"https://openalex.org/I31512782","display_name":"Technische Universit\u00e4t Darmstadt","ror":"https://ror.org/05n911h24","country_code":"DE","type":"education","lineage":["https://openalex.org/I31512782"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marius Pesavento","raw_affiliation_strings":["Communication Systems Group, TU Darmstadt, Merckstr. 25, Darmstadt, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Communication Systems Group, TU Darmstadt, Merckstr. 25, Darmstadt, Germany","institution_ids":["https://openalex.org/I31512782","https://openalex.org/I164928964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072675361","display_name":"George Kritikos","orcid":"https://orcid.org/0000-0003-1434-5176"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"George Kritikos","raw_affiliation_strings":["European Molecular Biology Laboratory, Heidelberg, Meyerhofstra\u00dfe 1, Heidelberg, 69117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, Heidelberg, Meyerhofstra\u00dfe 1, Heidelberg, 69117, Germany","institution_ids":["https://openalex.org/I4210153543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046202832","display_name":"Nassos Typas","orcid":null},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nassos Typas","raw_affiliation_strings":["European Molecular Biology Laboratory, Heidelberg, Meyerhofstra\u00dfe 1, Heidelberg, 69117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, Heidelberg, Meyerhofstra\u00dfe 1, Heidelberg, 69117, Germany","institution_ids":["https://openalex.org/I4210153543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5008217140"],"corresponding_institution_ids":["https://openalex.org/I164928964","https://openalex.org/I31512782"],"apc_list":null,"apc_paid":{"value":880,"currency":"EUR","value_usd":949},"fwci":0.4372,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.61114552,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"2017","issue":"1","first_page":"10","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9993000030517578,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9970999956130981,"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/scalability","display_name":"Scalability","score":0.8319138884544373},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7819348573684692},{"id":"https://openalex.org/keywords/directed-acyclic-graph","display_name":"Directed acyclic graph","score":0.7727514505386353},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5296199917793274},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47332295775413513},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4517197608947754},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4144817292690277},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.41306784749031067},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39255648851394653},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2818908989429474},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17928540706634521},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1146460473537445}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.8319138884544373},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7819348573684692},{"id":"https://openalex.org/C74197172","wikidata":"https://www.wikidata.org/wiki/Q1195339","display_name":"Directed acyclic graph","level":2,"score":0.7727514505386353},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5296199917793274},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47332295775413513},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4517197608947754},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4144817292690277},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.41306784749031067},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39255648851394653},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2818908989429474},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17928540706634521},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1146460473537445},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13637-017-0063-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-017-0063-3","pdf_url":"https://bsb-eurasipjournals.springeropen.com/counter/pdf/10.1186/s13637-017-0063-3","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},{"id":"pmid:28933027","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28933027","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":"EURASIP journal on bioinformatics & systems biology","raw_type":null},{"id":"pmh:oai:europepmc.org:4555504","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5607220","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:tubiblio.ulb.tu-darmstadt.de:147014","is_oa":false,"landing_page_url":"http://tubiblio.ulb.tu-darmstadt.de/147014/","pdf_url":null,"source":{"id":"https://openalex.org/S4377196390","display_name":"TUbilio (Technical University of Darmstadt)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I31512782","host_organization_name":"Technische Universit\u00e4t Darmstadt","host_organization_lineage":["https://openalex.org/I31512782"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Artikel"},{"id":"pmh:oai:tubiblio.ulb.tu-darmstadt.de:89553","is_oa":false,"landing_page_url":"http://tubiblio.ulb.tu-darmstadt.de/89553/","pdf_url":null,"source":{"id":"https://openalex.org/S4377196390","display_name":"TUbilio (Technical University of Darmstadt)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I31512782","host_organization_name":"Technische Universit\u00e4t Darmstadt","host_organization_lineage":["https://openalex.org/I31512782"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Artikel"}],"best_oa_location":{"id":"doi:10.1186/s13637-017-0063-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-017-0063-3","pdf_url":"https://bsb-eurasipjournals.springeropen.com/counter/pdf/10.1186/s13637-017-0063-3","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2519532642.pdf","grobid_xml":"https://content.openalex.org/works/W2519532642.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1590472748","https://openalex.org/W1608335442","https://openalex.org/W1967220526","https://openalex.org/W1979422419","https://openalex.org/W1980305675","https://openalex.org/W1986634396","https://openalex.org/W1992325964","https://openalex.org/W2006631099","https://openalex.org/W2008854410","https://openalex.org/W2033839136","https://openalex.org/W2045312029","https://openalex.org/W2053913299","https://openalex.org/W2061004320","https://openalex.org/W2066216023","https://openalex.org/W2069323107","https://openalex.org/W2093631020","https://openalex.org/W2099329054","https://openalex.org/W2105638592","https://openalex.org/W2109630925","https://openalex.org/W2115021853","https://openalex.org/W2117033519","https://openalex.org/W2127073167","https://openalex.org/W2130515279","https://openalex.org/W2133102806","https://openalex.org/W2138470019","https://openalex.org/W2144931885","https://openalex.org/W2162891889","https://openalex.org/W2212314648","https://openalex.org/W2219324110","https://openalex.org/W2478687516","https://openalex.org/W2482939865","https://openalex.org/W2490027396","https://openalex.org/W2492421876","https://openalex.org/W2494664569","https://openalex.org/W2889375751","https://openalex.org/W4249908340","https://openalex.org/W4255329848"],"related_works":["https://openalex.org/W4302345037","https://openalex.org/W2731094954","https://openalex.org/W2789273959","https://openalex.org/W1998712144","https://openalex.org/W2952978498","https://openalex.org/W4292730466","https://openalex.org/W2951616510","https://openalex.org/W3122467582","https://openalex.org/W2728444714","https://openalex.org/W2914790213"],"abstract_inverted_index":{"In":[0,98],"this":[1],"paper,":[2],"we":[3,39,80,100,125],"consider":[4],"the":[5,9,14,43,56,61,70,75,82,95,131,135,144],"problem":[6],"of":[7,16,22,34,109],"learning":[8],"genetic":[10,23,87],"interaction":[11,37,88],"map,":[12],"i.e.,":[13],"topology":[15,72],"a":[17,32,49,102],"directed":[18],"acyclic":[19],"graph":[20],"(DAG)":[21],"interactions":[24,44],"from":[25],"noisy":[26],"double-knockout":[27],"(DK)":[28],"data.":[29,123],"Based":[30],"on":[31],"set":[33],"well-established":[35],"biological":[36,63],"models,":[38],"detect":[40],"and":[41,67,134,147],"classify":[42],"between":[45],"genes.":[46],"We":[47],"propose":[48,101],"novel":[50],"linear":[51],"integer":[52],"optimization":[53],"program":[54,84,133,141],"called":[55],"Genetic-Interactions-Detector":[57],"(GENIE)":[58],"to":[59,68,92,115],"identify":[60],"complex":[62],"dependencies":[64],"among":[65],"genes":[66,110],"compute":[69],"DAG":[71],"that":[73,130],"matches":[74],"DK":[76],"measurements":[77],"best.":[78],"Furthermore,":[79],"extend":[81],"GENIE":[83,132,139],"by":[85],"incorporating":[86],"profile":[89],"(GI-profile)":[90],"data":[91,137,150],"further":[93],"enhance":[94],"detection":[96],"performance.":[97],"addition,":[99],"sequential":[103,155],"scalability":[104,156],"technique":[105],"for":[106,120,152],"large":[107],"sets":[108],"under":[111],"study,":[112],"in":[113],"order":[114],"provide":[116],"statistically":[117],"significant":[118],"results":[119,151],"real":[121,149],"measurement":[122],"Finally,":[124],"show":[126],"via":[127],"numeric":[128],"simulations":[129],"GI-profile":[136],"extended":[138],"(GI-GENIE)":[140],"clearly":[142],"outperform":[143],"conventional":[145],"techniques":[146],"present":[148],"our":[153],"proposed":[154],"technique.":[157]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
