{"id":"https://openalex.org/W2097147218","doi":"https://doi.org/10.1371/journal.pcbi.1000828","title":"Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows","display_name":"Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows","publication_year":2010,"publication_date":"2010-06-24","ids":{"openalex":"https://openalex.org/W2097147218","doi":"https://doi.org/10.1371/journal.pcbi.1000828","mag":"2097147218","pmid":"https://pubmed.ncbi.nlm.nih.gov/20585619"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000828","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000828","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000828&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000828&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017091352","display_name":"Yishai Shimoni","orcid":"https://orcid.org/0000-0002-4364-4207"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yishai Shimoni","raw_affiliation_strings":["Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104273375","display_name":"Marc Fink","orcid":null},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marc Y. Fink","raw_affiliation_strings":["Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075749836","display_name":"Soon Gang Choi","orcid":"https://orcid.org/0000-0003-0314-3958"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Soon-gang Choi","raw_affiliation_strings":["Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058017696","display_name":"Stuart C. Sealfon","orcid":"https://orcid.org/0000-0001-5791-1217"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stuart C. Sealfon","raw_affiliation_strings":["Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America","institution_ids":["https://openalex.org/I98704320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5058017696"],"corresponding_institution_ids":["https://openalex.org/I98704320"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6808,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.69733751,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"6","issue":"6","first_page":"e1000828","last_page":"e1000828"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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":0.9997000098228455,"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":0.998199999332428,"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":"Gene expression and cancer classification","score":0.9927999973297119,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6490161418914795},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6182417273521423},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5352969765663147},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5285131931304932},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5098490118980408},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.49386483430862427},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.46566155552864075},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.45320984721183777},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4338003993034363},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.4281439781188965},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.42596709728240967},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.41274118423461914},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40574097633361816},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3528093099594116},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.25335049629211426},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23601824045181274}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6490161418914795},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6182417273521423},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5352969765663147},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5285131931304932},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5098490118980408},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.49386483430862427},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46566155552864075},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.45320984721183777},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4338003993034363},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.4281439781188965},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.42596709728240967},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.41274118423461914},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40574097633361816},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3528093099594116},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.25335049629211426},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23601824045181274},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004815","descriptor_name":"Epidermal Growth Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004815","descriptor_name":"Epidermal Growth Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004815","descriptor_name":"Epidermal Growth Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004815","descriptor_name":"Epidermal Growth Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004815","descriptor_name":"Epidermal Growth Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004815","descriptor_name":"Epidermal Growth Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"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":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","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},{"descriptor_ui":"D048031","descriptor_name":"JNK Mitogen-Activated Protein Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048031","descriptor_name":"JNK Mitogen-Activated Protein Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048031","descriptor_name":"JNK Mitogen-Activated Protein Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048031","descriptor_name":"JNK Mitogen-Activated Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048031","descriptor_name":"JNK Mitogen-Activated Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048031","descriptor_name":"JNK Mitogen-Activated Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1000828","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000828","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000828&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:20585619","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20585619","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1000828","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000828","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:b1b652f6d60c4a7aafb8189bc7f47a3e","is_oa":true,"landing_page_url":"https://doaj.org/article/b1b652f6d60c4a7aafb8189bc7f47a3e","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":"PLoS Computational Biology, Vol 6, Iss 6, p e1000828 (2010)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/142910","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Plato_s_Cave_Algorithm_Inferring_Functional_Signaling_Networks_from_Early_Gene_Expression_Shadows/142910","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2891706","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2891706","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000828","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000828","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000828&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2150262284","display_name":null,"funder_award_id":"HHSN266200500021C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G2410259943","display_name":null,"funder_award_id":"HHSN266200500021C","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"},{"id":"https://openalex.org/G3422883332","display_name":null,"funder_award_id":"R01 DK046943","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G4795566888","display_name":null,"funder_award_id":"R01 DK 46943.","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332505","display_name":"U.S. Public Health Service","ror":"https://ror.org/05xf94514"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2097147218.pdf","grobid_xml":"https://content.openalex.org/works/W2097147218.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W291356173","https://openalex.org/W1528206681","https://openalex.org/W1599207601","https://openalex.org/W1729034583","https://openalex.org/W1968421512","https://openalex.org/W1971564731","https://openalex.org/W1972764318","https://openalex.org/W1975499170","https://openalex.org/W1979683683","https://openalex.org/W1989053944","https://openalex.org/W1989712725","https://openalex.org/W1996993801","https://openalex.org/W2009134620","https://openalex.org/W2012482128","https://openalex.org/W2021429824","https://openalex.org/W2033104002","https://openalex.org/W2035334007","https://openalex.org/W2036258710","https://openalex.org/W2036924431","https://openalex.org/W2038012561","https://openalex.org/W2050141745","https://openalex.org/W2051390567","https://openalex.org/W2076350564","https://openalex.org/W2077245462","https://openalex.org/W2078287614","https://openalex.org/W2079145130","https://openalex.org/W2091879895","https://openalex.org/W2097057782","https://openalex.org/W2098045561","https://openalex.org/W2104499761","https://openalex.org/W2110070747","https://openalex.org/W2110699703","https://openalex.org/W2116075981","https://openalex.org/W2116566535","https://openalex.org/W2117625122","https://openalex.org/W2121604817","https://openalex.org/W2125631472","https://openalex.org/W2126602684","https://openalex.org/W2137727595","https://openalex.org/W2139025111","https://openalex.org/W2139439234","https://openalex.org/W2140116490","https://openalex.org/W2149310258","https://openalex.org/W2152164604","https://openalex.org/W2152227081","https://openalex.org/W2153624566","https://openalex.org/W2156061761","https://openalex.org/W2160508724","https://openalex.org/W2161297153","https://openalex.org/W2171104921","https://openalex.org/W2434605070","https://openalex.org/W4242836717","https://openalex.org/W6610472406"],"related_works":["https://openalex.org/W2158714033","https://openalex.org/W4386628104","https://openalex.org/W78967844","https://openalex.org/W3213185671","https://openalex.org/W2509687359","https://openalex.org/W4206945140","https://openalex.org/W2130939068","https://openalex.org/W3163717165","https://openalex.org/W2114466827","https://openalex.org/W2156421048"],"abstract_inverted_index":{"Improving":[0],"the":[1,33,36,50,64,86,90,93,101,106,137,148,190,195,202,205,212,219,238,265,278,282],"ability":[2],"to":[3,20,158,223,226,276,285],"reverse":[4,159,166,196,236],"engineer":[5,160],"biochemical":[6,133],"networks":[7,18],"is":[8,47,221],"a":[9,80],"major":[10],"goal":[11],"of":[12,39,52,57,83,109,123,140,185,211,241,267,281],"systems":[13],"biology.":[14],"Lesions":[15],"in":[16,22,26,43,85,92,100,105],"signaling":[17,40,98,142,162,186,191,244,274],"lead":[19],"alterations":[21],"gene":[23,45,53,178],"expression,":[24],"which":[25],"principle":[27],"should":[28],"allow":[29],"network":[30,59,102,240,247,275,283],"reconstruction.":[31],"However,":[32],"information":[34],"about":[35],"activity":[37,138],"levels":[38,139],"proteins":[41],"conveyed":[42],"overall":[44],"expression":[46,54,121,145,179],"limited":[48],"by":[49,260],"complexity":[51],"dynamics":[55],"and":[56,252,284],"regulatory":[58],"topology.":[60],"Two":[61],"observations":[62],"provide":[63,131,147],"basis":[65,149],"for":[66,150,272],"overcoming":[67],"this":[68],"limitation:":[69],"a.":[70],"genes":[71,116,125,203],"induced":[72],"without":[73,188],"de-novo":[74],"protein":[75],"synthesis":[76],"(early":[77],"genes)":[78],"show":[79],"linear":[81,107],"accumulation":[82],"product":[84],"first":[87],"hour":[88],"after":[89],"change":[91],"cell's":[94],"state;":[95],"b.":[96],"The":[97,246],"components":[99,192],"largely":[103],"function":[104],"range":[108],"their":[110],"stimulus-response":[111],"curves.":[112],"Therefore,":[113],"unlike":[114],"most":[115,118],"or":[117],"time":[119,129],"points,":[120],"profiles":[122],"early":[124,128,177],"at":[126],"an":[127,151],"point":[130],"direct":[132],"assays":[134],"that":[135,169,257,269],"represent":[136],"upstream":[141],"components.":[143,245],"Such":[144],"data":[146,231],"efficient":[152],"algorithm":[153,220],"(Plato's":[154],"Cave":[155],"algorithm;":[156],"PLACA)":[157],"functional":[161,206,214,255,279],"networks.":[163],"Unlike":[164],"conventional":[165],"engineering":[167],"algorithms":[168],"use":[170],"steady":[171],"state":[172],"values,":[173],"PLACA":[174,199,235,263],"uses":[175,264],"stimulated":[176],"measurements":[180],"associated":[181],"with":[182],"systematic":[183],"perturbations":[184],"components,":[187],"measuring":[189],"themselves.":[193],"Besides":[194],"engineered":[197,237],"network,":[198],"also":[200],"identifies":[201],"detecting":[204],"interaction,":[207],"thereby":[208],"facilitating":[209],"validation":[210],"predicted":[213],"network.":[215],"Using":[216,229],"simulated":[217],"datasets,":[218],"shown":[222],"be":[224],"robust":[225],"experimental":[227,230],"noise.":[228],"obtained":[232],"from":[233],"gonadotropes,":[234],"interaction":[239],"six":[242],"perturbed":[243],"recapitulated":[248],"many":[249],"known":[250],"interactions":[251,256],"identified":[253],"novel":[254,287],"were":[258],"validated":[259],"further":[261],"experiment.":[262],"results":[266],"experiments":[268],"are":[270],"feasible":[271],"any":[273],"predict":[277],"topology":[280],"identify":[286],"relationships.":[288]},"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2012,"cited_by_count":4}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}