iBet uBet web content aggregator. Adding the entire web to your favor.
iBet uBet web content aggregator. Adding the entire web to your favor.



Link to original content: https://api.openalex.org/works/doi:10.1109/TCBB.2017.2688355
{"id":"https://openalex.org/W2949816873","doi":"https://doi.org/10.1109/tcbb.2017.2688355","title":"BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement","display_name":"BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement","publication_year":2017,"publication_date":"2017-03-28","ids":{"openalex":"https://openalex.org/W2949816873","doi":"https://doi.org/10.1109/tcbb.2017.2688355","mag":"2949816873","pmid":"https://pubmed.ncbi.nlm.nih.gov/28368827"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2017.2688355","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://ifp.hal.science/hal-01330638/file/Pirayre_A_2016_j-ieee-tcbb_BRANEClust-HAL.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043991938","display_name":"Aur\u00e9lie Pirayre","orcid":"https://orcid.org/0000-0003-0112-3689"},"institutions":[{"id":"https://openalex.org/I265217849","display_name":"IFP \u00c9nergies nouvelles","ror":"https://ror.org/03gcbhc33","country_code":"FR","type":"facility","lineage":["https://openalex.org/I265217849"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Aurelie Pirayre","raw_affiliation_strings":["IFP Energies nouvelles, 1 et 4 avenue de Bois-Pr\u00e9au, Rueil-Malmaison, France"],"affiliations":[{"raw_affiliation_string":"IFP Energies nouvelles, 1 et 4 avenue de Bois-Pr\u00e9au, Rueil-Malmaison, France","institution_ids":["https://openalex.org/I265217849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004095177","display_name":"Camille Couprie","orcid":"https://orcid.org/0000-0002-2549-3038"},"institutions":[],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Camille Couprie","raw_affiliation_strings":["Facebook AI Research, Paris, France"],"affiliations":[{"raw_affiliation_string":"Facebook AI Research, Paris, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005435241","display_name":"Laurent Duval","orcid":"https://orcid.org/0000-0002-7732-4666"},"institutions":[{"id":"https://openalex.org/I265217849","display_name":"IFP \u00c9nergies nouvelles","ror":"https://ror.org/03gcbhc33","country_code":"FR","type":"facility","lineage":["https://openalex.org/I265217849"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurent Duval","raw_affiliation_strings":["IFP Energies nouvelles, 1 et 4 avenue de Bois-Pr\u00e9au, Rueil-Malmaison, France"],"affiliations":[{"raw_affiliation_string":"IFP Energies nouvelles, 1 et 4 avenue de Bois-Pr\u00e9au, Rueil-Malmaison, France","institution_ids":["https://openalex.org/I265217849"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062845079","display_name":"Jean\u2010Christophe Pesquet","orcid":"https://orcid.org/0000-0002-5943-8061"},"institutions":[{"id":"https://openalex.org/I216852786","display_name":"\u00c9cole Centrale Paris","ror":"https://ror.org/00v0y5771","country_code":"FR","type":"education","lineage":["https://openalex.org/I216852786"]},{"id":"https://openalex.org/I4210107720","display_name":"CentraleSup\u00e9lec","ror":"https://ror.org/019tcpt25","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210107720"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jean-Christophe Pesquet","raw_affiliation_strings":["CentraleSup\u00e9lec, Ch\u00e2tenay-Malabry, F-92295, France"],"affiliations":[{"raw_affiliation_string":"CentraleSup\u00e9lec, Ch\u00e2tenay-Malabry, F-92295, France","institution_ids":["https://openalex.org/I216852786","https://openalex.org/I4210107720"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.532,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":24,"citation_normalized_percentile":{"value":0.999983,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":92,"max":93},"biblio":{"volume":"15","issue":"3","first_page":"850","last_page":"860"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Stochasticity in Gene Regulatory Networks","score":0.9998,"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":"Stochasticity in Gene Regulatory Networks","score":0.9998,"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":"Analysis of Gene Interaction Networks","score":0.9997,"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":"Microarray Data Analysis and Gene Expression Profiling","score":0.9973,"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/clustering","display_name":"Clustering","score":0.585987},{"id":"https://openalex.org/keywords/modularity","display_name":"Modularity (biology)","score":0.53569007},{"id":"https://openalex.org/keywords/biological-network-integration","display_name":"Biological Network Integration","score":0.520674},{"id":"https://openalex.org/keywords/network-inference","display_name":"Network Inference","score":0.516126},{"id":"https://openalex.org/keywords/gene-set-enrichment-analysis","display_name":"Gene Set Enrichment Analysis","score":0.509895},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.44012144},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4187858}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.71102583},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.70493454},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5837207},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.57285136},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.53569007},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.49404696},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.465901},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45676044},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.44012144},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.43734658},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4187858},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.31519333},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24517289},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22819749},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19935623},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13772535},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0931426},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2017.2688355","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"https://ifp.hal.science/hal-01330638/file/Pirayre_A_2016_j-ieee-tcbb_BRANEClust-HAL.pdf","pdf_url":"https://ifp.hal.science/hal-01330638/file/Pirayre_A_2016_j-ieee-tcbb_BRANEClust-HAL.pdf","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":["Centre National de la Recherche Scientifique"],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"https://hal-ifp.archives-ouvertes.fr/hal-01330638","pdf_url":"https://ifp.hal.science/hal-01330638/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":["Centre National de la Recherche Scientifique"],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"https://hal-ifp.archives-ouvertes.fr/hal-01330638/file/Pirayre_A_2016_j-ieee-tcbb_BRANEClust-HAL.pdf","pdf_url":"https://hal-ifp.archives-ouvertes.fr/hal-01330638/file/Pirayre_A_2016_j-ieee-tcbb_BRANEClust-HAL.pdf","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":["Centre National de la Recherche Scientifique"],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"https://hal-ifp.archives-ouvertes.fr/hal-01330638/document","pdf_url":"https://hal-ifp.archives-ouvertes.fr/hal-01330638/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":["Centre National de la Recherche Scientifique"],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"https://doi.org/10.1101/114769","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2017/03/24/114769.full.pdf","source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28368827","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://ifp.hal.science/hal-01330638/file/Pirayre_A_2016_j-ieee-tcbb_BRANEClust-HAL.pdf","pdf_url":"https://ifp.hal.science/hal-01330638/file/Pirayre_A_2016_j-ieee-tcbb_BRANEClust-HAL.pdf","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":["Centre National de la Recherche Scientifique"],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false},"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":41,"referenced_works":["https://openalex.org/W1585610988","https://openalex.org/W1966327575","https://openalex.org/W1992570579","https://openalex.org/W2002709996","https://openalex.org/W2023348596","https://openalex.org/W2026368892","https://openalex.org/W2044525257","https://openalex.org/W2064950342","https://openalex.org/W2076513103","https://openalex.org/W2078149659","https://openalex.org/W2083786039","https://openalex.org/W2101580881","https://openalex.org/W2105924489","https://openalex.org/W2109384743","https://openalex.org/W2120324727","https://openalex.org/W2123500593","https://openalex.org/W2124007391","https://openalex.org/W2125631472","https://openalex.org/W2125637308","https://openalex.org/W2127218421","https://openalex.org/W2137788236","https://openalex.org/W2139997707","https://openalex.org/W2145590522","https://openalex.org/W2153467314","https://openalex.org/W2157305458","https://openalex.org/W2157581457","https://openalex.org/W2161868542","https://openalex.org/W2161922735","https://openalex.org/W2161986541","https://openalex.org/W2163296115","https://openalex.org/W2167190345","https://openalex.org/W2175370850","https://openalex.org/W2177920816","https://openalex.org/W2180150046","https://openalex.org/W2205763937","https://openalex.org/W2226059528","https://openalex.org/W2232370058","https://openalex.org/W2323257522","https://openalex.org/W2340796580","https://openalex.org/W2345889914","https://openalex.org/W2583780192"],"related_works":["https://openalex.org/W3109014690","https://openalex.org/W2884798239","https://openalex.org/W2378076731","https://openalex.org/W2366669483","https://openalex.org/W2297768894","https://openalex.org/W2127721729","https://openalex.org/W2122405502","https://openalex.org/W2114254072","https://openalex.org/W1985973698","https://openalex.org/W1531253727"],"abstract_inverted_index":{"Discovering":[0],"meaningful":[1],"gene":[2,59],"interactions":[3],"is":[4,85,106,149,161],"crucial":[5],"for":[6,74],"the":[7,17,24,38,83,88,125,134,141],"identification":[8],"of":[9,27,90,93,127,147],"novel":[10,128],"regulatory":[11,60,129],"processes":[12],"in":[13,133],"cells.":[14],"Building":[15],"accurately":[16],"related":[18],"graphs":[19],"remains":[20],"challenging":[21],"due":[22],"to":[23,65],"large":[25],"number":[26],"possible":[28],"solutions":[29],"from":[30],"available":[31,162],"data.":[32],"Nonetheless,":[33],"enforcing":[34],"a":[35,71,91,97,101],"priori":[36,53],"on":[37,87,108,124],"graph":[39],"structure,":[40],"such":[41],"as":[42,70],"modularity,":[43],"may":[44],"reduce":[45],"network":[46,61,138],"indeterminacy":[47],"issues.":[48],"BRANE":[49,81,158],"Clust":[50,159],"(Biologically-Related":[51],"A":[52],"Network":[54],"Enhancement":[55],"with":[56,113],"Clustering)":[57],"refines":[58],"(GRN)":[62],"inference":[63,75],"thanks":[64],"cluster":[66],"information.":[67],"It":[68],"works":[69],"post-processing":[72],"tool":[73],"methods":[76],"(i.e.,":[77],"CLR,":[78],"GENIE3).":[79],"In":[80],"Clust,":[82],"clustering":[84,148],"based":[86],"inversion":[89],"system":[92],"linear":[94],"equations":[95],"involving":[96],"graph-Laplacian":[98],"matrix":[99],"promoting":[100],"modular":[102],"structure.":[103],"Our":[104],"approach":[105],"validated":[107],"DREAM4":[109],"and":[110,155],"DREAM5":[111],"datasets":[112],"objective":[114],"measures,":[115],"showing":[116],"significant":[117],"comparative":[118,145],"improvements.":[119],"We":[120],"provide":[121],"additional":[122],"insights":[123],"discovery":[126],"or":[130],"co-expressed":[131],"links":[132],"inferred":[135],"Escherichia":[136],"coli":[137],"evaluated":[139],"using":[140],"STRING":[142],"database.":[143],"The":[144],"pertinence":[146],"discussed":[150],"computationally":[151],"(SIMoNe,":[152],"WGCNA,":[153],"X-means)":[154],"biologically":[156],"(RegulonDB).":[157],"software":[160],"at:":[163],"http://www-syscom.univ-mlv.fr/~pirayre/Codes-GRN-BRANE-clust.html.":[164]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2949816873","counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1}],"updated_date":"2024-11-21T05:23:59.435047","created_date":"2019-06-27"}