{"id":"https://openalex.org/W2011876692","doi":"https://doi.org/10.1371/journal.pcbi.1004078","title":"NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation","display_name":"NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation","publication_year":2015,"publication_date":"2015-04-16","ids":{"openalex":"https://openalex.org/W2011876692","doi":"https://doi.org/10.1371/journal.pcbi.1004078","mag":"2011876692","pmid":"https://pubmed.ncbi.nlm.nih.gov/25879530"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004078","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004078","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004078&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","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004078&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043312189","display_name":"Juliane Siebourg\u2010Polster","orcid":"https://orcid.org/0000-0002-1759-3223"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Juliane Siebourg-Polster","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland","Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025467252","display_name":"Daria Mudrak","orcid":"https://orcid.org/0000-0002-2197-8169"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Daria Mudrak","raw_affiliation_strings":["Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041639548","display_name":"Mario Emmenlauer","orcid":"https://orcid.org/0000-0002-1982-0477"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Mario Emmenlauer","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046495095","display_name":"Pauli R\u00e4m\u00f6","orcid":null},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Pauli R\u00e4m\u00f6","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018962844","display_name":"Christoph Dehio","orcid":"https://orcid.org/0000-0001-7288-1052"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Christoph Dehio","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056886474","display_name":"Urs F. Greber","orcid":"https://orcid.org/0000-0003-2278-120X"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Urs Greber","raw_affiliation_strings":["Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054001409","display_name":"Holger Fr\u00f6hlich","orcid":"https://orcid.org/0000-0002-5328-1243"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Holger Fr\u00f6hlich","raw_affiliation_strings":["Algorithmic Bioinformatics, Bonn-Aachen International Center for IT, University of Bonn, Bonn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Algorithmic Bioinformatics, Bonn-Aachen International Center for IT, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I4210164149","https://openalex.org/I135140700"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035497488","display_name":"Niko Beerenwinkel","orcid":"https://orcid.org/0000-0002-0573-6119"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Niko Beerenwinkel","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland","Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5035497488"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2184,"currency":"EUR","value_usd":2355},"fwci":1.807,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.8487765,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":"4","first_page":"e1004078","last_page":"e1004078"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.992900013923645,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.992900013923645,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9900000095367432,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/bioconductor","display_name":"Bioconductor","score":0.5603228807449341},{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.5478506088256836},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5161110162734985},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4830925464630127},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4770369231700897},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4687143862247467},{"id":"https://openalex.org/keywords/identifiability","display_name":"Identifiability","score":0.4301190674304962},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4163845479488373},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2736329436302185},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19759970903396606},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.19347190856933594},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.17220598459243774},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14667749404907227},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.10163399577140808}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.5603228807449341},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.5478506088256836},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5161110162734985},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4830925464630127},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4770369231700897},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4687143862247467},{"id":"https://openalex.org/C122770356","wikidata":"https://www.wikidata.org/wiki/Q1656753","display_name":"Identifiability","level":2,"score":0.4301190674304962},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4163845479488373},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2736329436302185},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19759970903396606},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.19347190856933594},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.17220598459243774},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14667749404907227},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10163399577140808},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":10,"locations":[{"id":"doi:10.1371/journal.pcbi.1004078","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004078","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004078&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:25879530","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25879530","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:www.zora.uzh.ch:110518","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401281","display_name":"Zurich Open Repository and Archive (University of Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I202697423","host_organization_name":"University of Zurich","host_organization_lineage":["https://openalex.org/I202697423"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Siebourg-Polster, Juliane; Mudrak, Daria; Emmenlauer, Mario; R\u00e4m\u00f6, Pauli; Dehio, Christoph; Greber, Urs; Fr\u00f6hlich, Holger; Beerenwinkel, Niko  (2015). NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation.  PLoS Computational Biology, 11(4):e1004078.","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:RePEc:plo:pcbi00:1004078","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004078","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:49df760292d241b18bc8637c4d08f516","is_oa":true,"landing_page_url":"https://doaj.org/article/49df760292d241b18bc8637c4d08f516","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 11, Iss 4, p e1004078 (2015)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/1382555","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_NEMix_Single_cell_Nested_Effects_Models_for_Probabilistic_Pathway_Stimulation_/1382555","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:4400057","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4400057","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/101826","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/101826","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 11 (4)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000101826","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000101826","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.5167/uzh-110518","is_oa":true,"landing_page_url":"https://doi.org/10.5167/uzh-110518","pdf_url":null,"source":{"id":"https://openalex.org/S7407051291","display_name":"Universit\u00e4t Z\u00fcrich, ZORA","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004078","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004078","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004078&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/G1708250660","display_name":null,"funder_award_id":"51RTP0_151029","funder_id":"https://openalex.org/F4320327577","funder_display_name":"SystemsX.ch"}],"funders":[{"id":"https://openalex.org/F4320327577","display_name":"SystemsX.ch","ror":"https://ror.org/02s09gf16"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2011876692.pdf","grobid_xml":"https://content.openalex.org/works/W2011876692.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1516970347","https://openalex.org/W1611419331","https://openalex.org/W1665914593","https://openalex.org/W1913492903","https://openalex.org/W1978308088","https://openalex.org/W2008109277","https://openalex.org/W2009707997","https://openalex.org/W2019621874","https://openalex.org/W2036145275","https://openalex.org/W2042378638","https://openalex.org/W2047119613","https://openalex.org/W2049633694","https://openalex.org/W2056022845","https://openalex.org/W2062289724","https://openalex.org/W2068707689","https://openalex.org/W2069412330","https://openalex.org/W2069881735","https://openalex.org/W2080805014","https://openalex.org/W2099305058","https://openalex.org/W2099826569","https://openalex.org/W2103290626","https://openalex.org/W2107554012","https://openalex.org/W2116093604","https://openalex.org/W2119541898","https://openalex.org/W2119778725","https://openalex.org/W2123334163","https://openalex.org/W2126276987","https://openalex.org/W2130410032","https://openalex.org/W2134701923","https://openalex.org/W2147356380","https://openalex.org/W2148578992","https://openalex.org/W2148780239","https://openalex.org/W2149228177","https://openalex.org/W2150091347","https://openalex.org/W2152482800","https://openalex.org/W2156568771","https://openalex.org/W2158900785","https://openalex.org/W2159482845","https://openalex.org/W2786258633","https://openalex.org/W3104952140","https://openalex.org/W4211039187","https://openalex.org/W4231704412","https://openalex.org/W4285719527","https://openalex.org/W4292820908","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2724847603","https://openalex.org/W2135678793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W4223449272","https://openalex.org/W2978247079","https://openalex.org/W2166887457","https://openalex.org/W2148708580","https://openalex.org/W2034041141","https://openalex.org/W2800002600"],"abstract_inverted_index":{"Nested":[0],"effects":[1,14,29,73,114,125,227],"models":[2,115],"have":[3],"been":[4],"used":[5],"successfully":[6],"for":[7,130],"learning":[8,162],"subcellular":[9],"networks":[10],"from":[11,17,36,185],"high-dimensional":[12],"perturbation":[13],"that":[15,128,159,214],"result":[16,70],"RNA":[18],"interference":[19],"(RNAi)":[20],"experiments.":[21],"Here,":[22],"we":[23,95,157,212],"further":[24],"develop":[25],"the":[26,83,98,110,136,148,171,197,215,224,239],"basic":[27],"nested":[28,113,124,226],"model":[30,97,127,180,228],"using":[31],"high-content":[32],"single-cell":[33,49,182],"imaging":[34,183],"data":[35,184],"RNAi":[37,46,186],"screens":[38,47,187],"of":[39,65,101,112,138,163,173,196,207,238],"cultured":[40],"cells":[41,75],"infected":[42],"with":[43,48,209],"human":[44,189],"rhinovirus.":[45],"readouts":[50],"are":[51],"becoming":[52],"increasingly":[53],"common,":[54],"and":[55,76,120,140,222,243],"they":[56],"often":[57],"reveal":[58],"high":[59,220],"cell-to-cell":[60],"variation.":[61],"As":[62],"a":[63,102,123,142,205],"consequence":[64],"this":[66,89],"cellular":[67],"heterogeneity,":[68],"knock-downs":[69,119],"in":[71,92,105,170,200],"variable":[72],"among":[74],"lead":[77],"to":[78,116,181],"weak":[79],"average":[80],"phenotypes":[81],"on":[82,147],"cell":[84],"population":[85],"level.":[86],"To":[87],"address":[88],"confounding":[90],"factor":[91],"network":[93,218],"inference,":[94],"explicitly":[96],"stimulation":[99],"status":[100],"signaling":[103],"pathway":[104,132,164,175,202,231],"individual":[106],"cells.":[107],"We":[108,134,177],"extend":[109],"framework":[111],"probabilistic":[117],"combinatorial":[118],"propose":[121],"NEMix,":[122],"mixture":[126],"accounts":[129],"unobserved":[131],"activation.":[133],"analyzed":[135],"identifiability":[137],"NEMix":[139,160,217,233],"developed":[141],"parameter":[143],"inference":[144],"scheme":[145],"based":[146],"Expectation":[149],"Maximization":[150],"algorithm.":[151],"In":[152],"an":[153],"extensive":[154],"simulation":[155],"study,":[156],"show":[158,213],"improves":[161],"structures":[165],"over":[166],"classical":[167,225],"NEMs":[168],"significantly":[169],"presence":[172],"hidden":[174,230],"stimulation.":[176,203],"applied":[178],"our":[179],"monitoring":[188],"rhinovirus":[190],"infection,":[191],"where":[192],"limited":[193],"infection":[194],"efficiency":[195],"assay":[198],"results":[199],"uncertain":[201],"Using":[204],"subset":[206],"genes":[208],"known":[210],"interactions,":[211],"inferred":[216],"has":[219],"accuracy":[221],"outperforms":[223],"without":[229],"activity.":[232],"is":[234],"implemented":[235],"as":[236],"part":[237],"R/Bioconductor":[240],"package":[241],"'nem'":[242],"available":[244],"at":[245],"www.cbg.ethz.ch/software/NEMix.":[246]},"counts_by_year":[{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}