{"id":"https://openalex.org/W1972006187","doi":"https://doi.org/10.1371/journal.pcbi.1003626","title":"Inferring Host Gene Subnetworks Involved in Viral Replication","display_name":"Inferring Host Gene Subnetworks Involved in Viral Replication","publication_year":2014,"publication_date":"2014-05-29","ids":{"openalex":"https://openalex.org/W1972006187","doi":"https://doi.org/10.1371/journal.pcbi.1003626","mag":"1972006187","pmid":"https://pubmed.ncbi.nlm.nih.gov/24874113"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003626","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003626","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003626&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.1003626&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/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":false,"raw_author_name":"Deborah Chasman","raw_affiliation_strings":["Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020730620","display_name":"Brandi Gancarz","orcid":null},"institutions":[{"id":"https://openalex.org/I100162341","display_name":"Luminex (United States)","ror":"https://ror.org/03fef0h61","country_code":"US","type":"company","lineage":["https://openalex.org/I100162341"]},{"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":false,"raw_author_name":"Brandi Gancarz","raw_affiliation_strings":["Luminex Corporation, Madison, Wisconsin, United States of America; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Luminex Corporation, Madison, Wisconsin, United States of America","Institute for Molecular Virology, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Luminex Corporation, Madison, Wisconsin, United States of America; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":[]},{"raw_affiliation_string":"Luminex Corporation, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I100162341"]},{"raw_affiliation_string":"Institute for Molecular Virology, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001069528","display_name":"Linhui Hao","orcid":"https://orcid.org/0000-0002-7325-1009"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"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":false,"raw_author_name":"Linhui Hao","raw_affiliation_strings":["Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Howard Hughes Medical Institute, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","Institute for Molecular Virology, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":[]},{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I135310074"]},{"raw_affiliation_string":"Institute for Molecular Virology, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088455558","display_name":"Michael C. Ferris","orcid":"https://orcid.org/0000-0002-7652-6776"},"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":false,"raw_author_name":"Michael Ferris","raw_affiliation_strings":["Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"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":"Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026899432","display_name":"Paul Ahlquist","orcid":"https://orcid.org/0000-0003-4584-9318"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"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/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Ahlquist","raw_affiliation_strings":["Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Howard Hughes Medical Institute, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","Institute for Molecular Virology, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","Morgridge Institute for Research, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":[]},{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I135310074"]},{"raw_affiliation_string":"Institute for Molecular Virology, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Morgridge Institute for Research, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I29680605","https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071722704","display_name":"Mark Craven","orcid":"https://orcid.org/0000-0002-8917-7464"},"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":"Mark Craven","raw_affiliation_strings":["Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5071722704"],"corresponding_institution_ids":["https://openalex.org/I135310074"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.2852,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.58437591,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"10","issue":"5","first_page":"e1003626","last_page":"e1003626"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9970999956130981,"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":0.9970999956130981,"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":0.9955000281333923,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9919000267982483,"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":0.684238076210022},{"id":"https://openalex.org/keywords/viral-replication","display_name":"Viral replication","score":0.6501894593238831},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6094111204147339},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.6003093719482422},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5431427955627441},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.524057149887085},{"id":"https://openalex.org/keywords/replication","display_name":"Replication (statistics)","score":0.5153176784515381},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4815859794616699},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.39879393577575684},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.21850451827049255}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.684238076210022},{"id":"https://openalex.org/C140704245","wikidata":"https://www.wikidata.org/wiki/Q3933202","display_name":"Viral replication","level":3,"score":0.6501894593238831},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6094111204147339},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.6003093719482422},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5431427955627441},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.524057149887085},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.5153176784515381},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4815859794616699},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.39879393577575684},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.21850451827049255}],"mesh":[{"descriptor_ui":"D002472","descriptor_name":"Cell Transformation, Viral","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D002472","descriptor_name":"Cell Transformation, Viral","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D002472","descriptor_name":"Cell Transformation, Viral","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D002472","descriptor_name":"Cell Transformation, Viral","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005814","descriptor_name":"Genes, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014779","descriptor_name":"Virus Replication","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014779","descriptor_name":"Virus Replication","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014779","descriptor_name":"Virus Replication","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014779","descriptor_name":"Virus Replication","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1003626","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003626","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003626&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:24874113","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24874113","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:CiteSeerX.psu:10.1.1.699.3334","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.699.3334","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://www.biostat.wisc.edu/%7Ecraven/papers/chasman-plos14.pdf","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003626","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003626","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:d852343791f34e5c8da5c1724131d88e","is_oa":true,"landing_page_url":"https://doaj.org/article/d852343791f34e5c8da5c1724131d88e","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 10, Iss 5, p e1003626 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3021945","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4038467","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/1040119","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Inferring_Host_Gene_Subnetworks_Involved_in_Viral_Replication_/1040119","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.1003626","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003626","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003626&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/G1110428745","display_name":null,"funder_award_id":"CMMI-0928023","funder_id":"https://openalex.org/F4320337391","funder_display_name":"Division of Civil, Mechanical and Manufacturing Innovation"},{"id":"https://openalex.org/G2890725500","display_name":"RI: Small: Active Learning with Rich Query Types on Networks and Trees","funder_award_id":"1218880","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3034790953","display_name":null,"funder_award_id":"CMMI-0928023","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3415150707","display_name":"Extended Mathematical Programs: Hierarchical Models and Solution","funder_award_id":"0928023","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G526666672","display_name":null,"funder_award_id":"GM35072","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5954070948","display_name":null,"funder_award_id":"CMMI-","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6939691498","display_name":null,"funder_award_id":"T15-LM007359","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7939070741","display_name":null,"funder_award_id":"LM007359","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337391","display_name":"Division of Civil, Mechanical and Manufacturing Innovation","ror":"https://ror.org/028yd4c30"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1972006187.pdf","grobid_xml":"https://content.openalex.org/works/W1972006187.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W788272009","https://openalex.org/W1520083411","https://openalex.org/W1556027526","https://openalex.org/W1577731219","https://openalex.org/W1644724366","https://openalex.org/W1774304772","https://openalex.org/W1885159080","https://openalex.org/W1905257993","https://openalex.org/W1937721715","https://openalex.org/W1969941684","https://openalex.org/W1972129511","https://openalex.org/W1974220691","https://openalex.org/W1979039733","https://openalex.org/W1980798766","https://openalex.org/W1997714902","https://openalex.org/W1998767819","https://openalex.org/W1999084705","https://openalex.org/W2000805168","https://openalex.org/W2003652380","https://openalex.org/W2007912759","https://openalex.org/W2014011735","https://openalex.org/W2019136808","https://openalex.org/W2021663275","https://openalex.org/W2030317825","https://openalex.org/W2034276590","https://openalex.org/W2038122249","https://openalex.org/W2043698583","https://openalex.org/W2055243119","https://openalex.org/W2057012490","https://openalex.org/W2057160277","https://openalex.org/W2069898971","https://openalex.org/W2075294344","https://openalex.org/W2084175909","https://openalex.org/W2086005597","https://openalex.org/W2098707910","https://openalex.org/W2102221598","https://openalex.org/W2103017472","https://openalex.org/W2103354569","https://openalex.org/W2107067224","https://openalex.org/W2110095004","https://openalex.org/W2114629592","https://openalex.org/W2115143618","https://openalex.org/W2115559271","https://openalex.org/W2116552744","https://openalex.org/W2117555142","https://openalex.org/W2119418518","https://openalex.org/W2120826041","https://openalex.org/W2127712903","https://openalex.org/W2127743304","https://openalex.org/W2133313261","https://openalex.org/W2133465414","https://openalex.org/W2136303131","https://openalex.org/W2136850043","https://openalex.org/W2137804845","https://openalex.org/W2137896695","https://openalex.org/W2139119391","https://openalex.org/W2140502208","https://openalex.org/W2140556695","https://openalex.org/W2140948740","https://openalex.org/W2141152663","https://openalex.org/W2141374568","https://openalex.org/W2142382737","https://openalex.org/W2143341850","https://openalex.org/W2143353745","https://openalex.org/W2145848202","https://openalex.org/W2150158737","https://openalex.org/W2151543932","https://openalex.org/W2155142785","https://openalex.org/W2163485494","https://openalex.org/W2166606182","https://openalex.org/W2171662214","https://openalex.org/W2905461916","https://openalex.org/W4230455772","https://openalex.org/W4252829132"],"related_works":["https://openalex.org/W4205713785","https://openalex.org/W3016766501","https://openalex.org/W2901033488","https://openalex.org/W4393448312","https://openalex.org/W4394142100","https://openalex.org/W3086458689","https://openalex.org/W2031325922","https://openalex.org/W4287666211","https://openalex.org/W2025865172","https://openalex.org/W2312175987"],"abstract_inverted_index":{"Systematic,":[0],"genome-wide":[1],"loss-of-function":[2],"experiments":[3,126],"can":[4],"be":[5,235],"used":[6],"to":[7,42,56,180,219,234],"identify":[8],"host":[9,25,49,78,100,108,215,230],"factors":[10,50,101,109,216],"that":[11,31,88],"directly":[12],"or":[13,16,249,252,259],"indirectly":[14],"facilitate":[15],"inhibit":[17],"the":[18,44,57,94,103,111,116,128,134,148,194],"replication":[19,135],"of":[20,62,74,77,86,136,208,255],"a":[21,24,38,60,70,75,90,141,159,220,224],"virus":[22],"in":[23,66,162,237],"cell.":[26],"We":[27,118,157,203],"present":[28],"an":[29,33,84,171],"approach":[30,177],"combines":[32],"integer":[34],"linear":[35],"program":[36,262],"and":[37,69,105,154,189,227,267],"diffusion":[39],"kernel":[40],"method":[41,58],"infer":[43,119,200],"pathways":[45],"through":[46],"which":[47,98,107,163,197,214,228],"those":[48],"modulate":[51,102],"viral":[52,63,174,225,238],"replication.":[53,175,239],"The":[54,81],"inputs":[55],"are":[59,110,217,232,242,250,271],"set":[61],"phenotypes":[64],"observed":[65],"single-host-gene":[67],"mutants":[68],"background":[71,264],"network":[72,143,265],"consisting":[73],"variety":[76],"intracellular":[79],"interactions.":[80],"output":[82],"is":[83,144,178],"ensemble":[85],"subnetworks":[87,122,150,270],"provides":[89],"consistent":[91],"explanation":[92],"for":[93,131],"measured":[95],"phenotypes,":[96],"predicts":[97,106],"unassayed":[99,229],"virus,":[104],"most":[112],"direct":[113,221],"interfaces":[114],"with":[115,223],"virus.":[117],"host-virus":[120,269],"interaction":[121,222],"using":[123,151],"data":[124],"from":[125],"screening":[127],"yeast":[129],"genome":[130],"genes":[132,169,231],"modulating":[133],"two":[137,206],"RNA":[138],"viruses.":[139],"Because":[140],"gold-standard":[142],"unavailable,":[145],"we":[146,164],"assess":[147],"predicted":[149],"both":[152],"computational":[153],"qualitative":[155],"analyses.":[156],"conduct":[158],"cross-validation":[160],"experiment":[161],"predict":[165],"whether":[166],"held-aside":[167],"test":[168],"have":[170],"effect":[172],"on":[173],"Our":[176],"able":[179],"make":[181],"high-confidence":[182],"predictions":[183,209,241],"more":[184],"accurately":[185],"than":[186],"several":[187],"baselines,":[188],"about":[190],"as":[191,193],"well":[192],"best":[195],"baseline,":[196],"does":[198],"not":[199],"mechanistic":[201],"pathways.":[202,260],"also":[204],"examine":[205],"kinds":[207],"made":[210],"by":[211,244],"our":[212],"method:":[213],"nearest":[218],"component,":[226],"likely":[233],"involved":[236],"Multiple":[240],"supported":[243],"recent":[245],"independent":[246],"experimental":[247],"data,":[248,266],"components":[251],"functional":[253],"partners":[254],"confirmed":[256],"relevant":[257],"complexes":[258],"Integer":[261],"code,":[263],"inferred":[268],"available":[272],"at":[273],"http://www.biostat.wisc.edu/~craven/chasman_host_virus/.":[274]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
