{"id":"https://openalex.org/W2024200859","doi":"https://doi.org/10.1089/cmb.2010.0044","title":"Markov Logic Networks in the Analysis of Genetic Data","display_name":"Markov Logic Networks in the Analysis of Genetic Data","publication_year":2010,"publication_date":"2010-10-20","ids":{"openalex":"https://openalex.org/W2024200859","doi":"https://doi.org/10.1089/cmb.2010.0044","mag":"2024200859","pmid":"https://pubmed.ncbi.nlm.nih.gov/20958249"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2010.0044","is_oa":true,"landing_page_url":"https://doi.org/10.1089/cmb.2010.0044","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1089/cmb.2010.0044","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089368584","display_name":"Nikita A. Sakhanenko","orcid":"https://orcid.org/0000-0001-6256-4643"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I4210099575","display_name":"InSysBio (Russia)","ror":"https://ror.org/011fdmv87","country_code":"RU","type":"company","lineage":["https://openalex.org/I4210099575"]}],"countries":["RU","US"],"is_corresponding":true,"raw_author_name":"Nikita A. Sakhanenko","raw_affiliation_strings":["Institute for Systems Biology","Institute for Systems Biology, Seattle, Washington 98103, USA"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology","institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I4210099575"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, Washington 98103, USA","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055985023","display_name":"David J. Galas","orcid":"https://orcid.org/0000-0001-8248-8617"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I4210099575","display_name":"InSysBio (Russia)","ror":"https://ror.org/011fdmv87","country_code":"RU","type":"company","lineage":["https://openalex.org/I4210099575"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"David J. Galas","raw_affiliation_strings":["Institute for Systems Biology","Institute for Systems Biology, Seattle, Washington"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology","institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I4210099575"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, Washington","institution_ids":["https://openalex.org/I3148997608"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5089368584"],"corresponding_institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I4210099575"],"apc_list":null,"apc_paid":null,"fwci":0.2711,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.58692272,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"17","issue":"11","first_page":"1491","last_page":"1508"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9980000257492065,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9962999820709229,"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/inference","display_name":"Inference","score":0.6353808641433716},{"id":"https://openalex.org/keywords/statistical-inference","display_name":"Statistical inference","score":0.5246986150741577},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49368080496788025},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49277999997138977},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.47528472542762756},{"id":"https://openalex.org/keywords/genome-wide-association-study","display_name":"Genome-wide association study","score":0.4374787211418152},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.4219316244125366},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.418138325214386},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41793692111968994},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3664706349372864},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35853925347328186},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3203553855419159},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.21430239081382751},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.21214213967323303},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.16288471221923828},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16191774606704712}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6353808641433716},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.5246986150741577},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49368080496788025},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49277999997138977},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.47528472542762756},{"id":"https://openalex.org/C106208931","wikidata":"https://www.wikidata.org/wiki/Q1098876","display_name":"Genome-wide association study","level":5,"score":0.4374787211418152},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.4219316244125366},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.418138325214386},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41793692111968994},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3664706349372864},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35853925347328186},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3203553855419159},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.21430239081382751},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.21214213967323303},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.16288471221923828},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16191774606704712}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008128","descriptor_name":"Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013172","descriptor_name":"Spores, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013172","descriptor_name":"Spores, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013172","descriptor_name":"Spores, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1089/cmb.2010.0044","is_oa":true,"landing_page_url":"https://doi.org/10.1089/cmb.2010.0044","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:20958249","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20958249","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 computational biology : a journal of computational molecular cell biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3122930","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3122930","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1089/cmb.2010.0044","is_oa":true,"landing_page_url":"https://doi.org/10.1089/cmb.2010.0044","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310700","display_name":"Universit\u00e9 du Luxembourg","ror":"https://ror.org/036x5ad56"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W55914417","https://openalex.org/W1518562958","https://openalex.org/W1561457335","https://openalex.org/W1723714545","https://openalex.org/W1824971879","https://openalex.org/W1960379494","https://openalex.org/W1965426129","https://openalex.org/W1975130368","https://openalex.org/W1977970897","https://openalex.org/W1980991473","https://openalex.org/W1981704956","https://openalex.org/W1984862819","https://openalex.org/W2000805332","https://openalex.org/W2012979684","https://openalex.org/W2039279598","https://openalex.org/W2041467022","https://openalex.org/W2044134419","https://openalex.org/W2066669827","https://openalex.org/W2094945089","https://openalex.org/W2126185296","https://openalex.org/W2159080219","https://openalex.org/W2160842254","https://openalex.org/W2404266688"],"related_works":["https://openalex.org/W3000984192","https://openalex.org/W137830373","https://openalex.org/W4286952477","https://openalex.org/W2134368299","https://openalex.org/W4321348134","https://openalex.org/W2103073163","https://openalex.org/W3202526960","https://openalex.org/W3017020030","https://openalex.org/W2795206833","https://openalex.org/W3183730129"],"abstract_inverted_index":{"Complex,":[0],"non-additive":[1],"genetic":[2,104,171],"interactions":[3,30,234],"are":[4,146],"common":[5],"and":[6,17,57],"can":[7,96,132,235,243],"be":[8,97,236,244],"critical":[9],"in":[10,31,103],"determining":[11],"phenotypes.":[12],"Genome-wide":[13],"association":[14],"studies":[15,20],"(GWAS)":[16],"similar":[18],"statistical":[19,37,94,124,138],"of":[21,28,43,52,54,63,136,187],"linkage":[22],"data,":[23],"however,":[24],"assume":[25],"additive":[26],"models":[27,91],"gene":[29,56,180,228,233],"looking":[32],"for":[33,119,222,250],"genotype-phenotype":[34],"associations.":[35],"These":[36],"methods":[38,68,217],"view":[39],"the":[40,64,81,110,134,188],"compound":[41],"effects":[42],"multiple":[44],"genes":[45],"on":[46,173,206],"a":[47,50,60,156,176,247],"phenotype":[48,157,178],"as":[49,246],"sum":[51],"influences":[53],"each":[55],"often":[58],"miss":[59],"substantial":[61],"part":[62],"heritable":[65],"effect.":[66],"Such":[67],"do":[69,219],"not":[70,214,220],"use":[71,109],"any":[72],"biological":[73],"knowledge":[74,89,102,122],"about":[75],"underlying":[76],"mechanisms.":[77],"Modeling":[78],"approaches":[79],"from":[80],"artificial":[82],"intelligence":[83],"(AI)":[84],"field":[85],"that":[86,144,218],"incorporate":[87],"deterministic":[88,121],"into":[90],"to":[92,99,108,148,155,170,184,227],"perform":[93],"analysis":[95],"applied":[98,169],"include":[100],"prior":[101],"analysis.":[105,125],"We":[106,230],"chose":[107],"most":[111],"general":[112,248],"such":[113],"approach,":[114],"Markov":[115],"Logic":[116],"Networks":[117],"(MLNs),":[118],"combining":[120],"with":[123,179,193,200,216,254],"Using":[126],"simple,":[127],"logistic":[128],"regression-type":[129],"MLNs":[130],"we":[131,141,145],"replicate":[133],"results":[135],"traditional":[137],"methods,":[139],"but":[140],"also":[142],"show":[143,231],"able":[147],"go":[149],"beyond":[150],"finding":[151],"independent":[152],"markers":[153,225],"linked":[154],"by":[158],"using":[159,238],"joint":[160],"inference":[161],"without":[162],"an":[163],"independence":[164],"assumption.":[165],"The":[166],"method":[167,196],"is":[168,208],"data":[172],"yeast":[174],"sporulation,":[175,194],"complex":[177,240],"interactions.":[181,229],"In":[182],"addition":[183],"detecting":[185],"all":[186],"previously":[189],"identified":[190],"loci":[191,199,212],"associated":[192],"our":[195],"identifies":[197],"four":[198,211],"smaller":[201],"effects.":[202],"Since":[203],"their":[204],"effect":[205],"sporulation":[207],"small,":[209],"these":[210],"were":[213],"detected":[215,237],"account":[221],"dependence":[223],"between":[224],"due":[226],"how":[232],"more":[239],"models,":[241],"which":[242],"used":[245],"framework":[249],"incorporating":[251],"systems":[252],"biology":[253],"genetics.":[255]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}