{"id":"https://openalex.org/W2472943510","doi":"https://doi.org/10.1371/journal.pcbi.1005013","title":"Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens","display_name":"Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens","publication_year":2016,"publication_date":"2016-07-12","ids":{"openalex":"https://openalex.org/W2472943510","doi":"https://doi.org/10.1371/journal.pcbi.1005013","mag":"2472943510","pmid":"https://pubmed.ncbi.nlm.nih.gov/27403523"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005013","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005013","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005013&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.1005013&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088715947","display_name":"Deborah Chasman","orcid":"https://orcid.org/0000-0002-7324-0131"},"institutions":[{"id":"https://openalex.org/I2802999273","display_name":"Wisconsin Institutes for Discovery","ror":"https://ror.org/05gbven85","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802999273"]},{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Deborah Chasman","raw_affiliation_strings":["Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Wisconsin Institute for Discovery, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I2802999273","https://openalex.org/I135310074"]},{"raw_affiliation_string":"Wisconsin Institute for Discovery, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I2802999273","https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030602853","display_name":"Kevin Walters","orcid":"https://orcid.org/0000-0002-1541-4447"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kevin B. Walters","raw_affiliation_strings":["Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037557478","display_name":"Tiago J. S. Lopes","orcid":"https://orcid.org/0000-0001-9605-5177"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tiago J. S. Lopes","raw_affiliation_strings":["Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033752290","display_name":"Amie J. Eisfeld","orcid":"https://orcid.org/0000-0003-2231-3107"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Amie J. Eisfeld","raw_affiliation_strings":["Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076363097","display_name":"Yoshihiro Kawaoka","orcid":"https://orcid.org/0000-0001-5061-8296"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I4210086300","display_name":"National Institute of Infectious Diseases","ror":"https://ror.org/001ggbx22","country_code":"JP","type":"government","lineage":["https://openalex.org/I1333985979","https://openalex.org/I4210086300"]}],"countries":["JP","US"],"is_corresponding":true,"raw_author_name":"Yoshihiro Kawaoka","raw_affiliation_strings":["Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan","Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan","Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Laboratory of Bioresponses Regulation, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto, Japan","Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I4210086300"]},{"raw_affiliation_string":"Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan","institution_ids":[]},{"raw_affiliation_string":"Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Laboratory of Bioresponses Regulation, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082616445","display_name":"Sushmita Roy","orcid":"https://orcid.org/0000-0002-3694-1705"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I2802999273","display_name":"Wisconsin Institutes for Discovery","ror":"https://ror.org/05gbven85","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802999273"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sushmita Roy","raw_affiliation_strings":["Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Department of Biostatistics and Medical Informatics, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","Wisconsin Institute for Discovery, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","Department of Computer Sciences, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I2802999273","https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Wisconsin Institute for Discovery, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I2802999273","https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin\u2014Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5030602853","https://openalex.org/A5033752290","https://openalex.org/A5037557478","https://openalex.org/A5076363097","https://openalex.org/A5082616445","https://openalex.org/A5088715947"],"corresponding_institution_ids":["https://openalex.org/I135310074","https://openalex.org/I22299242","https://openalex.org/I2802999273","https://openalex.org/I4210086300"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.8681,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.84996935,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"12","issue":"7","first_page":"e1005013","last_page":"e1005013"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11668","display_name":"interferon and immune responses","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11668","display_name":"interferon and immune responses","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983000159263611,"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":0.9972000122070312,"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/biology","display_name":"Biology","score":0.7715722918510437},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6681661605834961},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6448683142662048},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5753359198570251},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5012478828430176},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.4790124297142029},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.4762594699859619},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.43003910779953003},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.42166393995285034},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.41058409214019775},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3597407937049866},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2800064980983734}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7715722918510437},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6681661605834961},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6448683142662048},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5753359198570251},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5012478828430176},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.4790124297142029},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.4762594699859619},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.43003910779953003},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42166393995285034},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.41058409214019775},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3597407937049866},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2800064980983734}],"mesh":[{"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":"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":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1005013","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005013","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005013&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:27403523","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27403523","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:irdb.nii.ac.jp:01221:0000174479","is_oa":true,"landing_page_url":"http://hdl.handle.net/2433/218703","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal article"},{"id":"pmh:oai:doaj.org/article:3da5b50f2ff249d388e6b11d7390b3b2","is_oa":true,"landing_page_url":"https://doaj.org/article/3da5b50f2ff249d388e6b11d7390b3b2","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 12, Iss 7, p e1005013 (2016)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3931180","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4942116","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:figshare.com:article/3902958","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Integrating_Transcriptomic_and_Proteomic_Data_Using_Predictive_Regulatory_Network_Models_of_Host_Response_to_Pathogens/3902958","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005013","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005013","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005013&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":[{"score":0.5099999904632568,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1942845908","display_name":null,"funder_award_id":"10677","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2299009608","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320306107","funder_display_name":"U.S. Environmental Protection Agency"},{"id":"https://openalex.org/G5326879115","display_name":null,"funder_award_id":"U19AI106772","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5391555051","display_name":null,"funder_award_id":"U19AI106772","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6598064177","display_name":null,"funder_award_id":"Startup funds","funder_id":"https://openalex.org/F4320309434","funder_display_name":"University of Wisconsin-Madison"},{"id":"https://openalex.org/G7577140921","display_name":null,"funder_award_id":"AI106772","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8275688536","display_name":null,"funder_award_id":"83573701","funder_id":"https://openalex.org/F4320306107","funder_display_name":"U.S. Environmental Protection Agency"}],"funders":[{"id":"https://openalex.org/F4320306107","display_name":"U.S. Environmental Protection Agency","ror":"https://ror.org/03tns0030"},{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320309434","display_name":"University of Wisconsin-Madison","ror":"https://ror.org/01y2jtd41"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2472943510.pdf","grobid_xml":"https://content.openalex.org/works/W2472943510.grobid-xml"},"referenced_works_count":113,"referenced_works":["https://openalex.org/W162770707","https://openalex.org/W630322457","https://openalex.org/W1504590764","https://openalex.org/W1842896948","https://openalex.org/W1850224498","https://openalex.org/W1964733653","https://openalex.org/W1966231010","https://openalex.org/W1966327575","https://openalex.org/W1970308473","https://openalex.org/W1976209715","https://openalex.org/W1976286254","https://openalex.org/W1976555683","https://openalex.org/W1977105782","https://openalex.org/W1979513695","https://openalex.org/W1980042862","https://openalex.org/W1981409633","https://openalex.org/W1986567779","https://openalex.org/W1988476050","https://openalex.org/W1992806088","https://openalex.org/W1993217079","https://openalex.org/W1997536991","https://openalex.org/W2000403772","https://openalex.org/W2001294950","https://openalex.org/W2002709996","https://openalex.org/W2003821560","https://openalex.org/W2003988251","https://openalex.org/W2004586645","https://openalex.org/W2007219269","https://openalex.org/W2007222211","https://openalex.org/W2007732647","https://openalex.org/W2009543464","https://openalex.org/W2010457001","https://openalex.org/W2011226251","https://openalex.org/W2011340259","https://openalex.org/W2012896813","https://openalex.org/W2014699371","https://openalex.org/W2028080448","https://openalex.org/W2028133290","https://openalex.org/W2029811552","https://openalex.org/W2031603236","https://openalex.org/W2034946767","https://openalex.org/W2043698583","https://openalex.org/W2049762266","https://openalex.org/W2051871263","https://openalex.org/W2052685738","https://openalex.org/W2055554325","https://openalex.org/W2058904528","https://openalex.org/W2065533930","https://openalex.org/W2068260663","https://openalex.org/W2068859304","https://openalex.org/W2070218828","https://openalex.org/W2070924692","https://openalex.org/W2071688420","https://openalex.org/W2074410038","https://openalex.org/W2076415360","https://openalex.org/W2076513103","https://openalex.org/W2077848026","https://openalex.org/W2078950112","https://openalex.org/W2082127599","https://openalex.org/W2084426569","https://openalex.org/W2085442947","https://openalex.org/W2086383073","https://openalex.org/W2089691349","https://openalex.org/W2090247362","https://openalex.org/W2090441668","https://openalex.org/W2091279668","https://openalex.org/W2093953283","https://openalex.org/W2102158172","https://openalex.org/W2102231637","https://openalex.org/W2103017472","https://openalex.org/W2103208261","https://openalex.org/W2104877015","https://openalex.org/W2105597591","https://openalex.org/W2105681004","https://openalex.org/W2105924489","https://openalex.org/W2106555403","https://openalex.org/W2107513655","https://openalex.org/W2114334846","https://openalex.org/W2114610169","https://openalex.org/W2114782912","https://openalex.org/W2115162652","https://openalex.org/W2116376819","https://openalex.org/W2119862467","https://openalex.org/W2120826041","https://openalex.org/W2127096557","https://openalex.org/W2129265801","https://openalex.org/W2130410032","https://openalex.org/W2130879922","https://openalex.org/W2131649910","https://openalex.org/W2131848047","https://openalex.org/W2138019504","https://openalex.org/W2140327386","https://openalex.org/W2140502208","https://openalex.org/W2140952049","https://openalex.org/W2141152663","https://openalex.org/W2142382737","https://openalex.org/W2143991512","https://openalex.org/W2146053439","https://openalex.org/W2146469651","https://openalex.org/W2150892663","https://openalex.org/W2153398022","https://openalex.org/W2159675211","https://openalex.org/W2160103276","https://openalex.org/W2161666019","https://openalex.org/W2164223927","https://openalex.org/W2165745669","https://openalex.org/W2284189835","https://openalex.org/W2739999456","https://openalex.org/W2784041867","https://openalex.org/W2915975108","https://openalex.org/W2951920373","https://openalex.org/W4244738544","https://openalex.org/W6676167818"],"related_works":["https://openalex.org/W2158714033","https://openalex.org/W78967844","https://openalex.org/W3213185671","https://openalex.org/W4210989272","https://openalex.org/W4386628104","https://openalex.org/W4206945140","https://openalex.org/W2130939068","https://openalex.org/W3163717165","https://openalex.org/W2114466827","https://openalex.org/W2509687359"],"abstract_inverted_index":{"Mammalian":[0],"host":[1,42,61,83,91,135,230],"response":[2,43,62,84,136,155,167,231],"to":[3,23,34,44,63,85,113,126,137,179,232],"pathogenic":[4],"infections":[5,170],"is":[6,33],"controlled":[7],"by":[8],"a":[9,75,96],"complex":[10],"regulatory":[11,14,80,103,117,128,143],"network":[12,81,104,110,144,178],"connecting":[13],"proteins":[15,22],"such":[16,66],"as":[17,67],"transcription":[18],"factors":[19],"and":[20,38,93,109,131,145,156,160,182,185,200,219,224],"signaling":[21,162],"target":[24],"genes.":[25],"An":[26],"important":[27,227],"challenge":[28],"in":[29,40,164],"infectious":[30,64,87],"disease":[31],"research":[32],"understand":[35],"molecular":[36],"similarities":[37],"differences":[39],"mammalian":[41],"diverse":[45],"sets":[46],"of":[47,57,78,153,168,171,191,222,229],"pathogens.":[48],"Recently,":[49],"systems":[50],"biology":[51],"studies":[52],"have":[53],"produced":[54],"rich":[55],"collections":[56],"omic":[58],"profiles":[59],"measuring":[60],"agents":[65],"influenza":[68,139,233],"viruses":[69],"at":[70],"multiple":[71,86,138],"levels.":[72],"To":[73],"gain":[74],"comprehensive":[76],"understanding":[77],"the":[79,165,176],"driving":[82],"agents,":[88],"we":[89],"integrated":[90,209],"transcriptomes":[92],"proteomes":[94],"using":[95],"network-based":[97],"approach.":[98],"Our":[99],"approach":[100,125],"combines":[101],"expression-based":[102],"inference,":[105],"structured-sparsity":[106],"based":[107],"regression,":[108],"information":[111],"flow":[112],"infer":[114],"putative":[115],"physical":[116],"programs":[118],"for":[119,150],"expression":[120,223],"modules.":[121],"We":[122,174],"applied":[123],"our":[124,208],"identify":[127,226],"networks,":[129],"modules":[130,146],"subnetworks":[132],"that":[133,216],"drive":[134],"infections.":[140],"The":[141],"inferred":[142],"are":[147],"significantly":[148],"enriched":[149],"known":[151],"pathways":[152],"immune":[154],"implicate":[157],"apoptosis,":[158],"splicing,":[159],"interferon":[161],"processes":[163],"differential":[166],"viral":[169,198],"different":[172],"pathogenicities.":[173],"used":[175],"learned":[177],"prioritize":[180],"regulators":[181,193,228],"study":[183],"virus":[184],"time-point":[186],"specific":[187],"networks.":[188],"RNAi-based":[189],"knockdown":[190],"predicted":[192],"had":[194],"significant":[195],"impact":[196],"on":[197],"replication":[199],"include":[201],"several":[202],"previously":[203],"unknown":[204],"regulators.":[205],"Taken":[206],"together,":[207],"analysis":[210],"identified":[211],"novel":[212],"module":[213],"level":[214],"patterns":[215,221],"capture":[217],"strain":[218],"pathogenicity-specific":[220],"helped":[225],"infection.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
