{"id":"https://openalex.org/W2482802595","doi":"https://doi.org/10.1186/s12918-016-0301-4","title":"Identifying the topology of signaling networks from partial RNAi data","display_name":"Identifying the topology of signaling networks from partial RNAi data","publication_year":2016,"publication_date":"2016-08-01","ids":{"openalex":"https://openalex.org/W2482802595","doi":"https://doi.org/10.1186/s12918-016-0301-4","mag":"2482802595","pmid":"https://pubmed.ncbi.nlm.nih.gov/27490106"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-016-0301-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0301-4","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0301-4","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0301-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073900873","display_name":"Yuanfang Ren","orcid":"https://orcid.org/0000-0002-4716-2408"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuanfang Ren","raw_affiliation_strings":["Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA. yuanfang@cise.ufl.edu","Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA. yuanfang@cise.ufl.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088303206","display_name":"Qiyao Wang","orcid":"https://orcid.org/0000-0002-7494-0869"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qiyao Wang","raw_affiliation_strings":["Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA","Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100326701","display_name":"Md Mahmudul Hasan","orcid":"https://orcid.org/0000-0002-2061-6641"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Md Mahmudul Hasan","raw_affiliation_strings":["Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA","Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033580922","display_name":"Ahmet Ay","orcid":"https://orcid.org/0000-0002-0726-5461"},"institutions":[{"id":"https://openalex.org/I39660569","display_name":"Colgate University","ror":"https://ror.org/05d23ve83","country_code":"US","type":"education","lineage":["https://openalex.org/I39660569"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ahmet Ay","raw_affiliation_strings":["Department of Biology & Mathematics, Colgate University, Hamilton, 13346, NY, USA","Department of Biology & Mathematics, Colgate University, Hamilton, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology & Mathematics, Colgate University, Hamilton, 13346, NY, USA","institution_ids":["https://openalex.org/I39660569"]},{"raw_affiliation_string":"Department of Biology & Mathematics, Colgate University, Hamilton, USA","institution_ids":["https://openalex.org/I39660569"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091769289","display_name":"Tamer Kahveci","orcid":"https://orcid.org/0000-0002-4403-8612"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tamer Kahveci","raw_affiliation_strings":["Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA","Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer & Information Science & Engineering, University of Florida, Gainesville, 32611, FL, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Computer & Information Science & Engineering, University of Florida, Gainesville, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5073900873"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04743734,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"10","issue":"S2","first_page":"53","last_page":"53"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"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":0.9987999796867371,"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":0.9973999857902527,"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/T10604","display_name":"RNA Research and Splicing","score":0.9958000183105469,"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/systems-biology","display_name":"Systems biology","score":0.683152437210083},{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.6763531565666199},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6156115531921387},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4724683463573456},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4613367021083832},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.44731152057647705},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.4316951036453247},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.2308371365070343},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21516647934913635},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19346654415130615},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19217431545257568},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.11766090989112854}],"concepts":[{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.683152437210083},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.6763531565666199},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6156115531921387},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4724683463573456},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4613367021083832},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.44731152057647705},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4316951036453247},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.2308371365070343},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21516647934913635},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19346654415130615},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19217431545257568},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.11766090989112854},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","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":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060449","descriptor_name":"Wnt Signaling Pathway","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060449","descriptor_name":"Wnt Signaling Pathway","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060449","descriptor_name":"Wnt Signaling Pathway","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12918-016-0301-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0301-4","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0301-4","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:27490106","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27490106","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 systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4977480","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4977480","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":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-016-0301-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0301-4","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0301-4","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1583951694","display_name":"ABI Innovation: Querying Massive Dynamic Biological Network Databases","funder_award_id":"1262451","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2482802595.pdf","grobid_xml":"https://content.openalex.org/works/W2482802595.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1499476884","https://openalex.org/W1588133965","https://openalex.org/W1647075334","https://openalex.org/W1972129511","https://openalex.org/W1976441097","https://openalex.org/W1984222668","https://openalex.org/W1989129192","https://openalex.org/W1993324235","https://openalex.org/W2027439534","https://openalex.org/W2038863154","https://openalex.org/W2042629507","https://openalex.org/W2046675213","https://openalex.org/W2053087839","https://openalex.org/W2055396579","https://openalex.org/W2061505806","https://openalex.org/W2066113694","https://openalex.org/W2067803871","https://openalex.org/W2068010171","https://openalex.org/W2119740363","https://openalex.org/W2124637492","https://openalex.org/W2137315132","https://openalex.org/W2137412574","https://openalex.org/W2146812359","https://openalex.org/W2161623098","https://openalex.org/W2165940375","https://openalex.org/W2481258410","https://openalex.org/W2494863456","https://openalex.org/W2752573522","https://openalex.org/W3145128584"],"related_works":["https://openalex.org/W2387630553","https://openalex.org/W1572871015","https://openalex.org/W2411232599","https://openalex.org/W3156756868","https://openalex.org/W1998876971","https://openalex.org/W1976394015","https://openalex.org/W2030262874","https://openalex.org/W2885524011","https://openalex.org/W5284979","https://openalex.org/W4245853730"],"abstract_inverted_index":{"Application":[0],"of":[1,42],"our":[2,12],"methods":[3,13,33],"to":[4,17],"Wnt":[5],"signal":[6],"transduction":[7],"pathway":[8],"has":[9],"shown":[10],"that":[11,34],"can":[14],"be":[15],"used":[16],"construct":[18],"highly":[19],"accurate":[20,36],"signaling":[21,45],"networks":[22],"from":[23],"experimental":[24],"data":[25],"in":[26],"less":[27],"than":[28],"100":[29],"ms.":[30],"The":[31],"two":[32],"produce":[35],"results":[37],"efficiently":[38],"show":[39],"great":[40],"promise":[41],"constructing":[43],"real":[44],"networks.":[46]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}