{"id":"https://openalex.org/W2971908266","doi":"https://doi.org/10.1186/s12859-019-3016-x","title":"NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks","display_name":"NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks","publication_year":2019,"publication_date":"2019-09-03","ids":{"openalex":"https://openalex.org/W2971908266","doi":"https://doi.org/10.1186/s12859-019-3016-x","mag":"2971908266","pmid":"https://pubmed.ncbi.nlm.nih.gov/31481014"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3016-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3016-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3016-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3016-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058143169","display_name":"Florian Martin","orcid":"https://orcid.org/0000-0002-5968-5484"},"institutions":[{"id":"https://openalex.org/I2800621710","display_name":"Philip Morris International (Switzerland)","ror":"https://ror.org/03z9zz970","country_code":"CH","type":"company","lineage":["https://openalex.org/I2800621710","https://openalex.org/I4210088192"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Florian Martin","raw_affiliation_strings":["PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland. Florian.Martin@pmi.com","PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland. Florian.Martin@pmi.com","institution_ids":[]},{"raw_affiliation_string":"PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland","institution_ids":["https://openalex.org/I2800621710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040042148","display_name":"Sylvain Gubian","orcid":null},"institutions":[{"id":"https://openalex.org/I2800621710","display_name":"Philip Morris International (Switzerland)","ror":"https://ror.org/03z9zz970","country_code":"CH","type":"company","lineage":["https://openalex.org/I2800621710","https://openalex.org/I4210088192"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Sylvain Gubian","raw_affiliation_strings":["PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland","institution_ids":["https://openalex.org/I2800621710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011233293","display_name":"Marja Talikka","orcid":"https://orcid.org/0000-0001-8105-5756"},"institutions":[{"id":"https://openalex.org/I2800621710","display_name":"Philip Morris International (Switzerland)","ror":"https://ror.org/03z9zz970","country_code":"CH","type":"company","lineage":["https://openalex.org/I2800621710","https://openalex.org/I4210088192"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Marja Talikka","raw_affiliation_strings":["PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland","institution_ids":["https://openalex.org/I2800621710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087038430","display_name":"Julia Hoeng","orcid":"https://orcid.org/0000-0001-5371-6801"},"institutions":[{"id":"https://openalex.org/I2800621710","display_name":"Philip Morris International (Switzerland)","ror":"https://ror.org/03z9zz970","country_code":"CH","type":"company","lineage":["https://openalex.org/I2800621710","https://openalex.org/I4210088192"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Julia Hoeng","raw_affiliation_strings":["PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland","institution_ids":["https://openalex.org/I2800621710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012278670","display_name":"Manuel C. Peitsch","orcid":"https://orcid.org/0000-0001-5324-359X"},"institutions":[{"id":"https://openalex.org/I2800621710","display_name":"Philip Morris International (Switzerland)","ror":"https://ror.org/03z9zz970","country_code":"CH","type":"company","lineage":["https://openalex.org/I2800621710","https://openalex.org/I4210088192"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Manuel C. Peitsch","raw_affiliation_strings":["PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PMI R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, CH-2000, Neuch\u00e2tel, Switzerland","institution_ids":["https://openalex.org/I2800621710"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5058143169"],"corresponding_institution_ids":["https://openalex.org/I2800621710"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5127,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.64973378,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"20","issue":"1","first_page":"451","last_page":"451"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.3391999900341034,"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":0.3391999900341034,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.24809999763965607,"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":0.11789999902248383,"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/computer-science","display_name":"Computer science","score":0.6986817121505737},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6509224772453308},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5312684774398804},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.45990511775016785},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4558213949203491},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4366745948791504},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36999908089637756},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3393590450286865},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.30735477805137634},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.28014785051345825},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23997357487678528},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21110108494758606},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07872173190116882}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6986817121505737},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6509224772453308},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5312684774398804},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.45990511775016785},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4558213949203491},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4366745948791504},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36999908089637756},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3393590450286865},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.30735477805137634},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.28014785051345825},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23997357487678528},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21110108494758606},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07872173190116882},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008810","descriptor_name":"Mice, Inbred C57BL","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008810","descriptor_name":"Mice, Inbred C57BL","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008810","descriptor_name":"Mice, Inbred C57BL","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":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018384","descriptor_name":"Oxidative Stress","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-3016-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3016-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3016-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31481014","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31481014","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:92341a6164c74e43893e94b2fc182fd7","is_oa":true,"landing_page_url":"https://doaj.org/article/92341a6164c74e43893e94b2fc182fd7","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":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-9 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6724309","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6724309","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3016-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3016-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3016-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320315260","display_name":"Philip Morris International","ror":"https://ror.org/005rxfw29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2971908266.pdf","grobid_xml":"https://content.openalex.org/works/W2971908266.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W580095287","https://openalex.org/W1533243960","https://openalex.org/W1976029010","https://openalex.org/W1988111520","https://openalex.org/W1988964726","https://openalex.org/W1996421905","https://openalex.org/W1997707189","https://openalex.org/W2008375915","https://openalex.org/W2012530222","https://openalex.org/W2015780328","https://openalex.org/W2026759723","https://openalex.org/W2031249692","https://openalex.org/W2054801326","https://openalex.org/W2057411539","https://openalex.org/W2092168208","https://openalex.org/W2098817749","https://openalex.org/W2100980426","https://openalex.org/W2101490130","https://openalex.org/W2105603763","https://openalex.org/W2120890012","https://openalex.org/W2158328426","https://openalex.org/W2166164789","https://openalex.org/W2195611941","https://openalex.org/W2227752612","https://openalex.org/W2254323136","https://openalex.org/W2295176399","https://openalex.org/W2323768954","https://openalex.org/W2342439657","https://openalex.org/W2467488552","https://openalex.org/W2488876419","https://openalex.org/W2513762283","https://openalex.org/W2538323990","https://openalex.org/W2547431919","https://openalex.org/W2548808461","https://openalex.org/W2624468161","https://openalex.org/W2656695974","https://openalex.org/W2949333191","https://openalex.org/W4242182607"],"related_works":["https://openalex.org/W2155492529","https://openalex.org/W4252504573","https://openalex.org/W4385510321","https://openalex.org/W2101315668","https://openalex.org/W15348386","https://openalex.org/W3088642716","https://openalex.org/W2314128295","https://openalex.org/W4287026692","https://openalex.org/W2587303152","https://openalex.org/W2131550814"],"abstract_inverted_index":{"BACKGROUND:":[0],"High-throughput":[1],"gene":[2],"expression":[3,135],"technologies":[4],"provide":[5],"complex":[6],"datasets":[7],"reflecting":[8],"mechanisms":[9,76],"perturbed":[10],"in":[11,15,57,207],"an":[12,138,178],"experiment,":[13],"typically":[14],"a":[16,31,46,71,90,111,201],"treatment":[17,63],"versus":[18],"control":[19],"design.":[20],"Analysis":[21],"of":[22,37,45,74,114,160,203],"these":[23],"information-rich":[24],"data":[25,112,136],"can":[26],"be":[27,66],"guided":[28],"based":[29],"on":[30],"priori":[32],"knowledge,":[33],"such":[34,121],"as":[35,60,122],"networks":[36,83,117,205],"related":[38],"proteins":[39],"or":[40,62,126],"genes.":[41],"Assessing":[42],"the":[43,108,144,158,161,173,182,193,208],"response":[44],"specific":[47],"mechanism":[48],"and":[49,89,110,146,164,177,199],"investigating":[50],"its":[51,147],"biological":[52],"basis":[53],"is":[54,131,186],"extremely":[55],"important":[56],"systems":[58],"toxicology;":[59],"compounds":[61],"need":[64],"to":[65,70,80],"assessed":[67],"with":[68],"respect":[69],"predefined":[72],"set":[73,202],"key":[75,119],"that":[77],"could":[78],"lead":[79],"toxicity.":[81],"Two-layer":[82],"are":[84,141,152,170],"suitable":[85],"for":[86],"this":[87],"task,":[88],"robust":[91],"computational":[92],"methodology":[93,198],"specifically":[94],"addressing":[95],"those":[96],"needs":[97],"was":[98],"previously":[99],"published.":[100],"The":[101,150,166,189],"NPA":[102,190],"package":[103,113,145,162,191],"(":[104],"https://github.com/philipmorrisintl/NPA":[105],")":[106],"implements":[107,192],"algorithm,":[109],"eight":[115],"two-layer":[116,204],"representing":[118],"mechanisms,":[120],"xenobiotic":[123],"metabolism,":[124],"apoptosis,":[125],"epithelial":[127],"immune":[128],"innate":[129],"activation,":[130],"provided.":[132],"RESULTS:":[133],"Gene":[134],"from":[137],"animal":[139],"study":[140],"analyzed":[142,171],"using":[143,154,172],"network":[148,168,195],"models.":[149],"functionalities":[151],"implemented":[153],"R6":[155],"classes,":[156],"making":[157],"use":[159],"seamless":[163],"intuitive.":[165],"various":[167],"responses":[169],"leading":[174],"node":[175],"analysis,":[176],"overall":[179],"perturbation,":[180],"called":[181],"Biological":[183,209],"Impact":[184],"Factor,":[185],"computed.":[187],"CONCLUSIONS:":[188],"published":[194],"perturbation":[196],"amplitude":[197],"provides":[200],"encoded":[206],"Expression":[210],"Language.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5}],"updated_date":"2026-05-26T13:28:51.108037","created_date":"2025-10-10T00:00:00"}
