{"id":"https://openalex.org/W2950825102","doi":"https://doi.org/10.1093/bioinformatics/bty240","title":"Improved pathway reconstruction from RNA interference screens by exploiting off-target effects","display_name":"Improved pathway reconstruction from RNA interference screens by exploiting off-target effects","publication_year":2018,"publication_date":"2018-04-12","ids":{"openalex":"https://openalex.org/W2950825102","doi":"https://doi.org/10.1093/bioinformatics/bty240","mag":"2950825102","pmid":"https://pubmed.ncbi.nlm.nih.gov/29950000"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty240","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty240","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i519/25098482/bty240.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i519/25098482/bty240.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032064550","display_name":"Sumana Srivatsa","orcid":"https://orcid.org/0000-0002-2471-8821"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","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":"Sumana Srivatsa","raw_affiliation_strings":["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","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038666930","display_name":"Jack Kuipers","orcid":"https://orcid.org/0000-0001-5357-2705"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","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":"Jack Kuipers","raw_affiliation_strings":["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","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028827406","display_name":"Fabian Schmich","orcid":"https://orcid.org/0000-0003-1604-4406"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","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":"Fabian Schmich","raw_affiliation_strings":["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","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081376238","display_name":"Simone Eicher","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":"Simone Eicher","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/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/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":"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":"nonprofit","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"],"raw_orcid":null,"affiliations":[{"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":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5035497488"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7421,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.71447753,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"34","issue":"13","first_page":"i519","last_page":"i527"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.259799987077713,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.259799987077713,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.2363000065088272,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.027000000700354576,"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/nanoelectromechanical-systems","display_name":"Nanoelectromechanical systems","score":0.7161806225776672},{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.669362485408783},{"id":"https://openalex.org/keywords/gene-knockdown","display_name":"Gene knockdown","score":0.6367573142051697},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5664228200912476},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5350870490074158},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5021498203277588},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40538114309310913},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24271535873413086},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.21263012290000916},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.203264981508255},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18842005729675293},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.18818959593772888},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.09805917739868164}],"concepts":[{"id":"https://openalex.org/C173409883","wikidata":"https://www.wikidata.org/wiki/Q175593","display_name":"Nanoelectromechanical systems","level":4,"score":0.7161806225776672},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.669362485408783},{"id":"https://openalex.org/C173396325","wikidata":"https://www.wikidata.org/wiki/Q1501275","display_name":"Gene knockdown","level":3,"score":0.6367573142051697},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5664228200912476},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5350870490074158},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5021498203277588},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40538114309310913},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24271535873413086},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.21263012290000916},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.203264981508255},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18842005729675293},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.18818959593772888},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.09805917739868164},{"id":"https://openalex.org/C155672457","wikidata":"https://www.wikidata.org/wiki/Q61231","display_name":"Nanoparticle","level":2,"score":0.0},{"id":"https://openalex.org/C15083742","wikidata":"https://www.wikidata.org/wiki/Q261659","display_name":"Nanomedicine","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055785","descriptor_name":"Gene Knockdown Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055785","descriptor_name":"Gene Knockdown Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055785","descriptor_name":"Gene Knockdown Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty240","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty240","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i519/25098482/bty240.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29950000","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29950000","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:edoc.unibas.ch:66848","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401836","display_name":"edoc (University of Basel)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1850255","host_organization_name":"University of Basel","host_organization_lineage":["https://openalex.org/I1850255"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:4991143","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6022657","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty240","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty240","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i519/25098482/bty240.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2008399308","display_name":null,"funder_award_id":"RTD 2013/152","funder_id":"https://openalex.org/F4320327577","funder_display_name":"SystemsX.ch"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"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/W2950825102.pdf","grobid_xml":"https://content.openalex.org/works/W2950825102.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1516970347","https://openalex.org/W1647075334","https://openalex.org/W1811064827","https://openalex.org/W1973260880","https://openalex.org/W1978472619","https://openalex.org/W1986050428","https://openalex.org/W1992685981","https://openalex.org/W2009275634","https://openalex.org/W2010173075","https://openalex.org/W2011876692","https://openalex.org/W2016631235","https://openalex.org/W2016718526","https://openalex.org/W2044895919","https://openalex.org/W2065973221","https://openalex.org/W2079548558","https://openalex.org/W2083381199","https://openalex.org/W2107554012","https://openalex.org/W2119541898","https://openalex.org/W2126276987","https://openalex.org/W2142901992","https://openalex.org/W2144510218","https://openalex.org/W2144791939","https://openalex.org/W2146264532","https://openalex.org/W2148780239","https://openalex.org/W2150673577","https://openalex.org/W2152054207","https://openalex.org/W2159129586","https://openalex.org/W2159482845","https://openalex.org/W2165586566","https://openalex.org/W2173603050","https://openalex.org/W2295110112","https://openalex.org/W3104952140","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W4285099144","https://openalex.org/W4391126805","https://openalex.org/W2093213574","https://openalex.org/W2076785949","https://openalex.org/W2129321041","https://openalex.org/W2167306613","https://openalex.org/W1963563485","https://openalex.org/W2026561311","https://openalex.org/W2810831330","https://openalex.org/W1974857950"],"abstract_inverted_index":{"Motivation:":[0],"Pathway":[1],"reconstruction":[2,85,115,165],"has":[3,67],"proven":[4],"to":[5,33,58,140,167,171],"be":[6],"an":[7,94,124,179,213],"indispensable":[8],"tool":[9],"for":[10,113,130,206],"analyzing":[11],"the":[12,52,80,108,141,207],"molecular":[13],"mechanisms":[14],"of":[15,28,86,96,133,144,152,194],"signal":[16],"transduction":[17],"underlying":[18],"cell":[19],"function.":[20],"Nested":[21],"effects":[22,102,112,154],"models":[23,31,103],"(NEMs)":[24],"are":[25,62,222],"a":[26],"class":[27],"probabilistic":[29,99],"graphical":[30],"designed":[32,57],"reconstruct":[34],"signalling":[35],"pathways":[36],"from":[37,41,116],"high-dimensional":[38],"observations":[39],"resulting":[40,82],"perturbation":[42],"experiments,":[43],"such":[44],"as":[45,158,160,212],"RNA":[46],"interference":[47],"(RNAi).":[48],"NEMs":[49,97],"assume":[50],"that":[51,70],"short":[53],"interfering":[54],"RNAs":[55],"(siRNAs)":[56],"knockdown":[59,119],"specific":[60],"genes":[61],"always":[63],"on-target.":[64],"However,":[65],"it":[66],"been":[68],"shown":[69],"most":[71],"siRNAs":[72],"exhibit":[73],"strong":[74],"off-target":[75,111],"effects,":[76],"which":[77,105],"further":[78],"confound":[79],"data,":[81],"in":[83,184],"unreliable":[84],"networks":[87],"by":[88],"NEMs.":[89,169],"Results:":[90],"Here,":[91],"we":[92],"present":[93],"extension":[95],"called":[98],"combinatorial":[100,117],"nested":[101],"(pc-NEMs),":[104],"capitalize":[106],"on":[107,146],"ancillary":[109],"siRNA":[110],"network":[114,134,182],"gene":[118],"data.":[120,142],"Our":[121],"model":[122],"employs":[123],"adaptive":[125],"simulated":[126,147],"annealing":[127],"search":[128],"algorithm":[129],"simultaneous":[131],"inference":[132],"structure":[135],"and":[136,155,189,201],"error":[137],"rates":[138],"inherent":[139],"Evaluation":[143],"pc-NEMs":[145],"data":[148,162,177,221],"with":[149,186],"varying":[150],"number":[151],"phenotypic":[153],"noise":[156],"levels":[157],"well":[159],"real":[161],"demonstrates":[163],"improved":[164],"compared":[166],"classical":[168],"Application":[170],"Bartonella":[172],"henselae":[173],"infection":[174],"RNAi":[175],"screening":[176],"yielded":[178],"eight":[180],"node":[181],"largely":[183],"agreement":[185],"previous":[187],"works,":[188],"revealed":[190],"novel":[191],"binary":[192],"interactions":[193],"direct":[195],"impact":[196],"between":[197],"established":[198],"components.":[199],"Availability":[200],"implementation:":[202],"The":[203],"software":[204],"used":[205],"analysis":[208],"is":[209],"freely":[210],"available":[211,223],"R":[214],"package":[215],"at":[216,224],"https://github.com/cbg-ethz/pcNEM.git.":[217],"Supplementary":[218,220],"information:":[219],"Bioinformatics":[225],"online.":[226]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-27T09:02:27.158192","created_date":"2025-10-10T00:00:00"}