{"id":"https://openalex.org/W2071344383","doi":"https://doi.org/10.1186/1471-2105-12-291","title":"Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'","display_name":"Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'","publication_year":2011,"publication_date":"2011-07-19","ids":{"openalex":"https://openalex.org/W2071344383","doi":"https://doi.org/10.1186/1471-2105-12-291","mag":"2071344383","pmid":"https://pubmed.ncbi.nlm.nih.gov/21771315"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-291","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-291","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-291","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-291","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058699275","display_name":"Christian Bender","orcid":"https://orcid.org/0000-0003-2630-1453"},"institutions":[{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]},{"id":"https://openalex.org/I4210151100","display_name":"DKFZ-ZMBH Alliance","ror":"https://ror.org/05x8b4491","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529","https://openalex.org/I223822909","https://openalex.org/I4210151100"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Christian Bender","raw_affiliation_strings":["German Cancer Research Center (DKFZ), Division of Molecular Genome Analysis, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. c.bender@dkfz-heidelberg.de","Division of Molecular Genome Analysis German Cancer Research Center (DKFZ), Heidelberg Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"German Cancer Research Center (DKFZ), Division of Molecular Genome Analysis, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. c.bender@dkfz-heidelberg.de","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I4210151100","https://openalex.org/I223822909"]},{"raw_affiliation_string":"Division of Molecular Genome Analysis German Cancer Research Center (DKFZ), Heidelberg Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105803257","display_name":"Silvia vd Heyde","orcid":null},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Silvia vd Heyde","raw_affiliation_strings":["Department of Medical Statistics, University of G\u00f6ttingen, Humboldtallee 32, 37073, G\u00f6ttingen, Germany","University of G\u00f3ttingen"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Statistics, University of G\u00f6ttingen, Humboldtallee 32, 37073, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]},{"raw_affiliation_string":"University of G\u00f3ttingen","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057849725","display_name":"Frauke Henjes","orcid":null},"institutions":[{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Frauke Henjes","raw_affiliation_strings":["Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany","Division of Molecular Genome Analysis German Cancer Research Center (DKFZ), Heidelberg Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]},{"raw_affiliation_string":"Division of Molecular Genome Analysis German Cancer Research Center (DKFZ), Heidelberg Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016727101","display_name":"Stefan Wiemann","orcid":"https://orcid.org/0000-0003-4683-3174"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stefan Wiemann","raw_affiliation_strings":["Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany","Division of Molecular Genome Analysis German Cancer Research Center (DKFZ), Heidelberg Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]},{"raw_affiliation_string":"Division of Molecular Genome Analysis German Cancer Research Center (DKFZ), Heidelberg Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059498724","display_name":"Ulrike Korf","orcid":null},"institutions":[{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ulrike Korf","raw_affiliation_strings":["Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany","Division of Molecular Genome Analysis German Cancer Research Center (DKFZ), Heidelberg Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]},{"raw_affiliation_string":"Division of Molecular Genome Analysis German Cancer Research Center (DKFZ), Heidelberg Germany","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017944645","display_name":"Tim Bei\u00dfbarth","orcid":"https://orcid.org/0000-0001-6509-2143"},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tim Bei\u00dfbarth","raw_affiliation_strings":["Department of Medical Statistics, University of G\u00f6ttingen, Humboldtallee 32, 37073, G\u00f6ttingen, Germany","University of G\u00f3ttingen"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Statistics, University of G\u00f6ttingen, Humboldtallee 32, 37073, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]},{"raw_affiliation_string":"University of G\u00f3ttingen","institution_ids":["https://openalex.org/I74656192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5058699275"],"corresponding_institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909","https://openalex.org/I4210151100"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7981,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.71404764,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"12","issue":"1","first_page":"291","last_page":"291"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6913999915122986,"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":0.6913999915122986,"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/T13283","display_name":"Mental Health Research Topics","score":0.0649000033736229,"subfield":{"id":"https://openalex.org/subfields/3205","display_name":"Experimental and Cognitive Psychology"},"field":{"id":"https://openalex.org/fields/32","display_name":"Psychology"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.059300001710653305,"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":0.7173320055007935},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7075120210647583},{"id":"https://openalex.org/keywords/signalling","display_name":"Signalling","score":0.6715689897537231},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5531538724899292},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4783417880535126},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.46369943022727966},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.46339184045791626},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.45125022530555725},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4384724199771881},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.42471349239349365},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.29410073161125183},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2614727020263672},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1404321789741516}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7173320055007935},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7075120210647583},{"id":"https://openalex.org/C39743133","wikidata":"https://www.wikidata.org/wiki/Q3262595","display_name":"Signalling","level":2,"score":0.6715689897537231},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5531538724899292},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4783417880535126},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.46369943022727966},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.46339184045791626},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.45125022530555725},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4384724199771881},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.42471349239349365},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.29410073161125183},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2614727020263672},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1404321789741516},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"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":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008137","descriptor_name":"Longitudinal Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008137","descriptor_name":"Longitudinal Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008137","descriptor_name":"Longitudinal Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-12-291","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-291","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-291","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21771315","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21771315","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:14e0e399e92445c28d62f0cd6da63f76","is_oa":true,"landing_page_url":"https://doaj.org/article/14e0e399e92445c28d62f0cd6da63f76","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 291 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2150872","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3146886","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:goescholar:1/6850","is_oa":true,"landing_page_url":"http://resolver.sub.uni-goettingen.de/purl?gs-1/6850","pdf_url":null,"source":{"id":"https://openalex.org/S4306401634","display_name":"GoeScholar  The Publication Server of the Georg-August-Universit\u00e4t G\u00f6ttingen (Georg-August-Universit\u00e4t G\u00f6ttingen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210122495","host_organization_name":"Asklepios Klinik St. Georg","host_organization_lineage":["https://openalex.org/I4210122495"],"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":"","raw_type":"journalArticle"},{"id":"pmh:oai:publications.goettingen-research-online.de:2/22631","is_oa":true,"landing_page_url":"https://resolver.sub.uni-goettingen.de/purl?gs-1/6850","pdf_url":null,"source":{"id":"https://openalex.org/S4306401634","display_name":"GoeScholar  The Publication Server of the Georg-August-Universit\u00e4t G\u00f6ttingen (Georg-August-Universit\u00e4t G\u00f6ttingen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210122495","host_organization_name":"Asklepios Klinik St. Georg","host_organization_lineage":["https://openalex.org/I4210122495"],"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":"","raw_type":"journal_article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-291","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-291","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-291","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5199999809265137}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320325391","display_name":"Federalno Ministarstvo Obrazovanja i Nauke","ror":"https://ror.org/0355d0s55"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2071344383.pdf","grobid_xml":"https://content.openalex.org/works/W2071344383.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W89551800","https://openalex.org/W263239518","https://openalex.org/W1857467473","https://openalex.org/W1977876909","https://openalex.org/W2025803032","https://openalex.org/W2073307618","https://openalex.org/W2076417436","https://openalex.org/W2079829409","https://openalex.org/W2102862543","https://openalex.org/W2115620023","https://openalex.org/W2116566535","https://openalex.org/W2120018526","https://openalex.org/W2123060905","https://openalex.org/W2140116490","https://openalex.org/W2144791939","https://openalex.org/W2155087336","https://openalex.org/W2160533336"],"related_works":["https://openalex.org/W2901655697","https://openalex.org/W118100147","https://openalex.org/W2727283706","https://openalex.org/W1525985997","https://openalex.org/W108107911","https://openalex.org/W2161626927","https://openalex.org/W2952963846","https://openalex.org/W2135602072","https://openalex.org/W2023465156","https://openalex.org/W2013286793"],"abstract_inverted_index":{"BACKGROUND:":[0],"Network":[1],"inference":[2,199],"from":[3,107,152,200],"high-throughput":[4,202],"data":[5,109,203],"has":[6],"become":[7],"an":[8,143],"important":[9],"means":[10],"of":[11,14,25,34,40,71,114,145,162],"current":[12],"analysis":[13],"biological":[15],"systems.":[16],"For":[17],"instance,":[18],"in":[19,63,90],"cancer":[20,26],"research,":[21],"the":[22,38,57,76,91,96,177],"functional":[23],"relationships":[24,78],"related":[27],"proteins,":[28],"summarised":[29],"into":[30],"signalling":[31,77,174],"networks":[32,175],"are":[33,79],"central":[35],"interest":[36],"for":[37,75,131],"identification":[39],"pathways":[41],"that":[42,81,99,149,172],"influence":[43],"tumour":[44],"development.":[45],"Cancer":[46],"cell":[47],"lines":[48],"can":[49],"be":[50],"used":[51],"as":[52,165],"model":[53,148,171],"systems":[54],"to":[55,60,83,195],"study":[56],"cellular":[58],"response":[59],"drug":[61],"treatments":[62],"a":[64,125,146,153,170],"time-resolved":[65],"way.":[66],"Based":[67],"on":[68,86,104,187],"these":[69,159],"kind":[70],"data,":[72],"modelling":[73],"approaches":[74],"needed,":[80],"allow":[82],"generate":[84],"hypotheses":[85],"potential":[87],"interference":[88],"points":[89],"networks.":[92],"RESULTS:":[93],"We":[94,117],"present":[95],"R-package":[97],"'ddepn'":[98,183],"implements":[100],"our":[101,119],"recent":[102],"approach":[103,120],"network":[105,115,133,156,198,209],"reconstruction":[106],"longitudinal":[108,201],"generated":[110],"after":[111],"external":[112],"perturbation":[113],"components.":[116],"extend":[118],"by":[121],"two":[122,136,160,205],"novel":[123],"methods:":[124],"Markov":[126],"Chain":[127],"Monte":[128],"Carlo":[129],"method":[130],"sampling":[132,207],"structures":[134],"with":[135,176],"edge":[137],"types":[138,161],"(activation":[139],"and":[140,142,189],"inhibition)":[141],"extension":[144],"prior":[147,167],"penalises":[150],"deviances":[151],"given":[154],"reference":[155],"while":[157],"incorporating":[158],"edges.":[163],"Further,":[164],"alternative":[166],"we":[168],"include":[169],"learns":[173],"scale-free":[178],"property.":[179],"CONCLUSIONS:":[180],"The":[181],"package":[182],"is":[184],"freely":[185],"available":[186],"R-Forge":[188],"CRAN":[190],"http://ddepn.r-forge.r-project.org,":[191],"http://cran.r-project.org.":[192],"It":[193],"allows":[194],"conveniently":[196],"perform":[197],"using":[204],"different":[206],"based":[208],"structure":[210],"search":[211],"algorithms.":[212]},"counts_by_year":[{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}