{"id":"https://openalex.org/W62380669","doi":null,"title":"Mechanistic Bayesian Networks for Integrating Knowledge and Data to Unravel Biological Complexity","display_name":"Mechanistic Bayesian Networks for Integrating Knowledge and Data to Unravel Biological Complexity","publication_year":2011,"publication_date":"2011-01-01","ids":{"openalex":"https://openalex.org/W62380669","mag":"62380669"},"language":"en","primary_location":{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/84502","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/2027.42/84502","pdf_url":"https://hdl.handle.net/2027.42/84502","source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/2027.42/84502","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113841773","display_name":"Abhik Shah","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Abhik Shah","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5113841773"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9160000085830688,"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":0.9160000085830688,"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":0.07349999994039536,"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/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.002199999988079071,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.7940000295639038},{"id":"https://openalex.org/keywords/transcriptome","display_name":"transcriptome","score":0.8960000276565552},{"id":"https://openalex.org/keywords/gene-expression-regulation","display_name":"gene expression regulation","score":0.6990000009536743},{"id":"https://openalex.org/keywords/hidden-variable-models","display_name":"hidden variable models","score":0.7879999876022339},{"id":"https://openalex.org/keywords/sonic-hedgehog-signaling","display_name":"Sonic hedgehog signaling","score":0.8619999885559082},{"id":"https://openalex.org/keywords/epithelial-mesenchymal-transition","display_name":"epithelial-mesenchymal transition","score":0.9309999942779541},{"id":"https://openalex.org/keywords/lung-cancer","display_name":"lung cancer","score":0.7279999852180481},{"id":"https://openalex.org/keywords/upstream-regulators","display_name":"upstream regulators","score":0.5130000114440918},{"id":"https://openalex.org/keywords/mirna-target-interactions","display_name":"miRNA-target interactions","score":0.6740000247955322},{"id":"https://openalex.org/keywords/protein-dna-interactions","display_name":"protein-DNA interactions","score":0.8529999852180481},{"id":"https://openalex.org/keywords/metastasis","display_name":"metastasis","score":0.5839999914169312},{"id":"https://openalex.org/keywords/high-dimensional-data","display_name":"high-dimensional data","score":0.44200000166893005}],"concepts":[{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.8174251914024353},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5726072192192078},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.561455488204956},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5355479717254639},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.49571359157562256},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.45679500699043274},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.4360715448856354},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.43051066994667053},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35167086124420166},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34401848912239075},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34187641739845276},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2095385491847992},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12419629096984863},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11801990866661072}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/84502","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/2027.42/84502","pdf_url":"https://hdl.handle.net/2027.42/84502","source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},{"id":"mag:62380669","doi":null,"is_oa":false,"landing_page_url":"https://deepblue.lib.umich.edu/bitstream/handle/2027.42/84502/shahad_1.pdf;sequence=1","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/84502","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/2027.42/84502","pdf_url":"https://hdl.handle.net/2027.42/84502","source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W62380669.pdf","grobid_xml":"https://content.openalex.org/works/W62380669.grobid-xml"},"referenced_works_count":168,"referenced_works":["https://openalex.org/W1155605805","https://openalex.org/W1501281998","https://openalex.org/W1517993545","https://openalex.org/W1524731504","https://openalex.org/W1535333477","https://openalex.org/W1584637157","https://openalex.org/W1589511079","https://openalex.org/W1593793857","https://openalex.org/W1615454278","https://openalex.org/W1795936879","https://openalex.org/W1809042650","https://openalex.org/W1876024155","https://openalex.org/W1928907742","https://openalex.org/W1931073059","https://openalex.org/W1963754847","https://openalex.org/W1968874378","https://openalex.org/W1974615767","https://openalex.org/W1974886995","https://openalex.org/W1975589376","https://openalex.org/W1984268382","https://openalex.org/W1985695385","https://openalex.org/W1988545801","https://openalex.org/W1988810849","https://openalex.org/W1989090935","https://openalex.org/W1989684700","https://openalex.org/W1991980638","https://openalex.org/W1995449365","https://openalex.org/W1995945562","https://openalex.org/W1996118868","https://openalex.org/W1997063559","https://openalex.org/W1997989529","https://openalex.org/W2001552323","https://openalex.org/W2001717872","https://openalex.org/W2001910980","https://openalex.org/W2008906462","https://openalex.org/W2010507548","https://openalex.org/W2013305240","https://openalex.org/W2017729871","https://openalex.org/W2021239799","https://openalex.org/W2024060531","https://openalex.org/W2025803032","https://openalex.org/W2032383947","https://openalex.org/W2032558547","https://openalex.org/W2032855297","https://openalex.org/W2037021470","https://openalex.org/W2039760291","https://openalex.org/W2041648785","https://openalex.org/W2042351431","https://openalex.org/W2044315923","https://openalex.org/W2044965556","https://openalex.org/W2047161074","https://openalex.org/W2052848609","https://openalex.org/W2053282744","https://openalex.org/W2057380162","https://openalex.org/W2059717396","https://openalex.org/W2061439657","https://openalex.org/W2063011414","https://openalex.org/W2067957566","https://openalex.org/W2068137415","https://openalex.org/W2072516425","https://openalex.org/W2073307618","https://openalex.org/W2076753758","https://openalex.org/W2077802746","https://openalex.org/W2078505529","https://openalex.org/W2080204105","https://openalex.org/W2083249373","https://openalex.org/W2085590348","https://openalex.org/W2086127647","https://openalex.org/W2086580927","https://openalex.org/W2086703813","https://openalex.org/W2087562900","https://openalex.org/W2087859070","https://openalex.org/W2088394753","https://openalex.org/W2090184738","https://openalex.org/W2091914950","https://openalex.org/W2092104789","https://openalex.org/W2094144098","https://openalex.org/W2097803027","https://openalex.org/W2097978324","https://openalex.org/W2098036848","https://openalex.org/W2100603120","https://openalex.org/W2101859789","https://openalex.org/W2102528678","https://openalex.org/W2102560361","https://openalex.org/W2102777101","https://openalex.org/W2104033956","https://openalex.org/W2108022229","https://openalex.org/W2108707301","https://openalex.org/W2109182932","https://openalex.org/W2109623522","https://openalex.org/W2109902738","https://openalex.org/W2110114082","https://openalex.org/W2112811019","https://openalex.org/W2114063979","https://openalex.org/W2116634113","https://openalex.org/W2117625122","https://openalex.org/W2118577784","https://openalex.org/W2118636185","https://openalex.org/W2119028181","https://openalex.org/W2119634636","https://openalex.org/W2120179781","https://openalex.org/W2120702690","https://openalex.org/W2120842170","https://openalex.org/W2120865735","https://openalex.org/W2120954784","https://openalex.org/W2122123241","https://openalex.org/W2125323026","https://openalex.org/W2125631472","https://openalex.org/W2128036243","https://openalex.org/W2128417568","https://openalex.org/W2130410032","https://openalex.org/W2130515775","https://openalex.org/W2131071353","https://openalex.org/W2131291909","https://openalex.org/W2133465414","https://openalex.org/W2133636765","https://openalex.org/W2133747068","https://openalex.org/W2135827569","https://openalex.org/W2136479434","https://openalex.org/W2136482324","https://openalex.org/W2137883630","https://openalex.org/W2142082526","https://openalex.org/W2142750219","https://openalex.org/W2142913541","https://openalex.org/W2142941314","https://openalex.org/W2144175203","https://openalex.org/W2145068337","https://openalex.org/W2145290999","https://openalex.org/W2146045333","https://openalex.org/W2146521249","https://openalex.org/W2148432857","https://openalex.org/W2148866736","https://openalex.org/W2149310258","https://openalex.org/W2151041575","https://openalex.org/W2152983466","https://openalex.org/W2154452346","https://openalex.org/W2154972152","https://openalex.org/W2155829013","https://openalex.org/W2156531916","https://openalex.org/W2158217645","https://openalex.org/W2159080219","https://openalex.org/W2159178453","https://openalex.org/W2159675211","https://openalex.org/W2159725359","https://openalex.org/W2159845262","https://openalex.org/W2161511352","https://openalex.org/W2161566367","https://openalex.org/W2161642932","https://openalex.org/W2162243457","https://openalex.org/W2162408649","https://openalex.org/W2163480486","https://openalex.org/W2163976012","https://openalex.org/W2164889994","https://openalex.org/W2165160727","https://openalex.org/W2165190832","https://openalex.org/W2167119716","https://openalex.org/W2168546553","https://openalex.org/W2169248105","https://openalex.org/W2169528473","https://openalex.org/W2170218772","https://openalex.org/W2170949754","https://openalex.org/W2170989872","https://openalex.org/W2171662214","https://openalex.org/W2566091043","https://openalex.org/W2611370172","https://openalex.org/W2789897293","https://openalex.org/W3189912187","https://openalex.org/W7100847525"],"related_works":["https://openalex.org/W2164889994","https://openalex.org/W7096480184","https://openalex.org/W2001173523","https://openalex.org/W2150627960","https://openalex.org/W2611370172","https://openalex.org/W7100167923","https://openalex.org/W2757839622","https://openalex.org/W2165061932","https://openalex.org/W7096893880","https://openalex.org/W7096184262"],"abstract_inverted_index":{"The":[0,144,179,301],"determination":[1],"of":[2,108,130,146,153,197,207,231,247,252],"how":[3],"protein":[4,233,273],"interactions":[5,248,274,315],"affect":[6],"gene":[7,213],"regulation":[8],"is":[9,137,182,292],"an":[10,92],"important":[11],"problem":[12],"in":[13,25,65,90,139,224,305,313,342],"systems":[14],"biology.":[15],"By":[16,227],"identifying":[17,185,332],"quantitative":[18],"relationships":[19,161,341],"between":[20],"the":[21,128,131,151,208,216,229,245,253,279,288],"interactome":[22,210],"and":[23,37,48,62,82,110,141,150,159,164,172,176,269,275,303,322,326,339],"transcriptome":[24],"complex":[26],"pathologies,":[27],"we":[28],"can":[29],"better":[30],"characterize":[31],"dysfunctional":[32],"pathways,":[33],"generate":[34],"further":[35],"hypotheses":[36],"identify":[38,127,194,205],"potential":[39],"targets":[40,129,166],"for":[41,50,79,95,184,295],"therapeutic":[42],"interventions.":[43],"This":[44,74],"thesis":[45,75,307],"develops":[46],"methods":[47,302,330],"software":[49,304],"elucidating":[51,314],"biological":[52],"networks":[53,60,72],"consistent":[54,334],"with":[55,98,335],"known":[56,163,337],"mechanisms":[57,338],"using":[58,120,318],"Bayesian":[59,71],"(BN)":[61],"high-throughput":[63],"datasets":[64,325],"a":[66,220,232,238,256,262],"novel":[67,165],"methodology":[68],"termed":[69],"Mechanistic":[70],"(MBN).":[73],"contributes":[76],"new":[77],"algorithms":[78],"data":[80],"pre-processing":[81],"evaluating":[83],"hidden":[84,147],"variable":[85,148],"models":[86,149],"that":[87,136,167,211,243,265],"are":[88,124,168,201,308],"implemented":[89],"PEBL,":[91],"open-source":[93],"library":[94],"MBN":[96,123,200],"modeling":[97,228],"features":[99],"unmatched":[100],"by":[101,331],"other":[102,174],"software.":[103],"Due":[104],"to":[105,115,126,155,193,204,249,255,311],"its":[106],"ease":[107],"use":[109,145],"extensibility,":[111],"PEBL":[112],"allows":[113],"one":[114],"run":[116],"large,":[117],"distributed":[118],"analyses":[119],"cloud-computing":[121],"platforms.":[122],"used":[125],"Sonic":[132],"hedgehog":[133],"signaling":[134],"pathway":[135,186],"implicated":[138,223],"development":[140],"cancer":[142,225,259],"progression.":[143],"ability":[152],"BN":[154,175,329],"capture":[156],"nonlinear,":[157],"combinatorial":[158],"stochastic":[160],"identifies":[162,261],"more":[169,191],"biologically":[170],"meaningful":[171],"outperforms":[173],"non-BN":[177],"methods.":[178],"approach":[180],"developed":[181,242],"useful":[183,294],"targets,":[187],"upstream":[188],"regulators":[189],"or,":[190],"generally,":[192],"additional":[195],"components":[196],"partially-characterized":[198],"topologies.":[199],"next":[202],"applied":[203],"subnetworks":[206],"global":[209],"govern":[212],"expression":[214,286],"during":[215],"epithelial-mesenchymal":[217],"transition":[218],"(EMT),":[219],"developmental":[221],"process":[222],"metastasis.":[226],"effects":[230],"interaction":[234],"on":[235,284],"downstream":[236],"genes,":[237],"scoring":[239],"metric":[240],"was":[241],"quantifies":[244],"relevance":[246],"EMT.":[250],"Application":[251],"method":[254,280],"cell-line":[257],"lung":[258],"dataset":[260],"core":[263],"subnetwork":[264],"recapitulates":[266],"EMT":[267],"biology":[268],"makes":[270],"predictions":[271],"about":[272],"their":[276],"targets.":[277],"Because":[278],"does":[281],"not":[282],"rely":[283],"differential":[285],"or":[287,298],"co-regulation":[289],"assumptions,":[290],"it":[291],"equally":[293],"microRNA-target,":[296],"protein-DNA":[297],"mixed-interaction":[299],"networks.":[300],"this":[306],"generally":[309],"applicable":[310],"problems":[312],"among":[316],"variables":[317],"partially":[319],"characterized":[320],"knowledge":[321],"noisy":[323],"high-dimensional":[324],"furthers":[327],"state-of-the-art":[328],"results":[333],"both":[336],"statistical":[340],"data.":[343]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
