{"id":"https://openalex.org/W2100352482","doi":"https://doi.org/10.1142/s0219720008003515","title":"USING DIRECTED INFORMATION TO BUILD BIOLOGICALLY RELEVANT INFLUENCE NETWORKS","display_name":"USING DIRECTED INFORMATION TO BUILD BIOLOGICALLY RELEVANT INFLUENCE NETWORKS","publication_year":2008,"publication_date":"2008-06-01","ids":{"openalex":"https://openalex.org/W2100352482","doi":"https://doi.org/10.1142/s0219720008003515","mag":"2100352482","pmid":"https://pubmed.ncbi.nlm.nih.gov/18574860"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720008003515","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003515","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082923675","display_name":"Arvind Rao","orcid":"https://orcid.org/0000-0002-9613-426X"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"ARVIND RAO","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science and Department of Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science and Department of Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077692655","display_name":"Alfred O. Hero","orcid":"https://orcid.org/0000-0002-2531-9670"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"ALFRED O. HERO","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science and Department of Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science and Department of Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111548295","display_name":"David J. States","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"DAVID J. STATES","raw_affiliation_strings":["Department of Bioinformatics and Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024115870","display_name":"James Douglas Engel","orcid":"https://orcid.org/0000-0001-9593-1825"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"JAMES DOUGLAS ENGEL","raw_affiliation_strings":["Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5082923675"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":null,"apc_paid":null,"fwci":2.0746,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.86674015,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"06","issue":"03","first_page":"493","last_page":"519"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.978600025177002,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.978600025177002,"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":0.9369000196456909,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9254999756813049,"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/computer-science","display_name":"Computer science","score":0.4712764620780945},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.45631182193756104},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.21756649017333984},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15568998456001282}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4712764620780945},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.45631182193756104},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.21756649017333984},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15568998456001282}],"mesh":[{"descriptor_ui":"D007255","descriptor_name":"Information Services","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007255","descriptor_name":"Information Services","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007255","descriptor_name":"Information Services","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1142/s0219720008003515","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003515","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:18574860","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18574860","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 bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.115.2062","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.115.2062","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.eecs.umich.edu/~hero/Preprints/csb_0100_jnl_ver_final.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.501.3954","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.501.3954","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.lifesciencessociety.org/CSB2007/toc/PDF/145.2007.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.44999998807907104}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W72967156","https://openalex.org/W589880435","https://openalex.org/W1547789987","https://openalex.org/W1584270973","https://openalex.org/W1964526847","https://openalex.org/W1965979273","https://openalex.org/W1977466966","https://openalex.org/W1981101983","https://openalex.org/W1992711566","https://openalex.org/W1993974403","https://openalex.org/W1995945562","https://openalex.org/W2000674952","https://openalex.org/W2014078900","https://openalex.org/W2025371899","https://openalex.org/W2047698397","https://openalex.org/W2055967751","https://openalex.org/W2066734455","https://openalex.org/W2082484220","https://openalex.org/W2084585676","https://openalex.org/W2091899323","https://openalex.org/W2097173970","https://openalex.org/W2097966523","https://openalex.org/W2099111195","https://openalex.org/W2103353381","https://openalex.org/W2106848313","https://openalex.org/W2107664245","https://openalex.org/W2110065044","https://openalex.org/W2112616936","https://openalex.org/W2113305236","https://openalex.org/W2114011703","https://openalex.org/W2114771311","https://openalex.org/W2117994680","https://openalex.org/W2123270006","https://openalex.org/W2127234432","https://openalex.org/W2130515775","https://openalex.org/W2130917261","https://openalex.org/W2131347386","https://openalex.org/W2134092975","https://openalex.org/W2134392502","https://openalex.org/W2137571953","https://openalex.org/W2139881468","https://openalex.org/W2140911775","https://openalex.org/W2141478391","https://openalex.org/W2143508168","https://openalex.org/W2146180420","https://openalex.org/W2146506956","https://openalex.org/W2151297727","https://openalex.org/W2157076973","https://openalex.org/W2158314946","https://openalex.org/W2163296115","https://openalex.org/W2167057061","https://openalex.org/W2167785315","https://openalex.org/W2344364145","https://openalex.org/W2999905431","https://openalex.org/W3023807737","https://openalex.org/W3099289621","https://openalex.org/W4236758372","https://openalex.org/W4246186327","https://openalex.org/W4293747882","https://openalex.org/W4313331945"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"The":[0],"systematic":[1],"inference":[2,55,100],"of":[3,19,26,34,40,43,68,98,116,130,146],"biologically":[4],"relevant":[5,108],"influence":[6,192],"networks":[7,107,193],"remains":[8],"a":[9,53,160],"challenging":[10],"problem":[11],"in":[12,184],"computational":[13],"biology.":[14],"Even":[15],"though":[16],"the":[17,24,31,41,44,59,66,71,105,117,121,128,140,144,157],"availability":[18],"high-throughput":[20],"data":[21],"has":[22],"enabled":[23],"use":[25,81],"probabilistic":[27],"models":[28],"to":[29,75,90,109,163,189],"infer":[30,190],"plausible":[32],"structure":[33],"such":[35],"networks,":[36],"their":[37],"true":[38],"interpretation":[39],"biology":[42,67],"process":[45],"is":[46,174],"questionable.":[47],"In":[48],"this":[49],"work,":[50],"we":[51,177],"propose":[52],"network":[54,99,138],"methodology,":[56],"based":[57],"on":[58],"directed":[60],"information":[61,188],"(DTI)":[62],"criterion,":[63],"that":[64,179],"incorporates":[65],"transcription":[69,167],"within":[70],"framework":[72,142,162],"so":[73],"as":[74,123,125],"enable":[76],"experimentally":[77],"verifiable":[78],"inference.":[79],"We":[80,94],"publicly":[82],"available":[83],"embryonic":[84],"kidney":[85],"and":[86,103,112,170],"T-cell":[87,113],"microarray":[88],"datasets":[89],"demonstrate":[91],"our":[92],"results.":[93],"present":[95],"two":[96],"variants":[97],"via":[101],"DTI--supervised":[102],"unsupervised--and":[104],"inferred":[106],"mammalian":[110],"nephrogenesis":[111],"activation.":[114],"Conformity":[115],"obtained":[118],"interactions":[119,165],"with":[120,127,186],"literature":[122],"well":[124],"comparison":[126],"coefficient":[129],"determination":[131],"(CoD)":[132],"method":[133],"are":[134],"demonstrated.":[135],"Apart":[136],"from":[137],"inference,":[139],"proposed":[141],"enables":[143],"exploration":[145],"specific":[147],"interactions,":[148],"not":[149],"just":[150],"those":[151],"revealed":[152],"by":[153],"data.":[154],"To":[155],"illustrate":[156],"latter":[158],"point,":[159],"DTI-based":[161],"resolve":[164],"between":[166],"factor":[168],"modules":[169],"target":[171],"coregulated":[172],"genes":[173],"proposed.":[175],"Additionally,":[176],"show":[178],"DTI":[180],"can":[181],"be":[182],"used":[183],"conjunction":[185],"mutual":[187],"higher-order":[191],"involving":[194],"cooperative":[195],"gene":[196],"interactions.":[197]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
