{"id":"https://openalex.org/W2166140491","doi":"https://doi.org/10.1093/bioinformatics/btv323","title":"pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge","display_name":"pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge","publication_year":2015,"publication_date":"2015-05-21","ids":{"openalex":"https://openalex.org/W2166140491","doi":"https://doi.org/10.1093/bioinformatics/btv323","mag":"2166140491","pmid":"https://pubmed.ncbi.nlm.nih.gov/26002883"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv323","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3072/49034665/bioinformatics_31_18_3072.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3072/49034665/bioinformatics_31_18_3072.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063649866","display_name":"Astrid Wachter","orcid":"https://orcid.org/0000-0002-4611-4260"},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Astrid Wachter","raw_affiliation_strings":["Department of Medical Statistics, Georg-August-University G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Statistics, Georg-August-University G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017944645","display_name":"Tim Bei\u00dfbarth","orcid":"https://orcid.org/0000-0001-6509-2143"},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tim Bei\u00dfbarth","raw_affiliation_strings":["Department of Medical Statistics, Georg-August-University G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Statistics, Georg-August-University G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5063649866"],"corresponding_institution_ids":["https://openalex.org/I74656192"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.8081,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.91103934,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"31","issue":"18","first_page":"3072","last_page":"3074"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9793999791145325,"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":0.9793999791145325,"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":0.0044999998062849045,"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/T13127","display_name":"Biotin and Related Studies","score":0.002199999988079071,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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":0.6065890192985535},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5635977387428284},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.5229183435440063},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4568231701850891},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.44883862137794495},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4434674382209778},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.39131349325180054},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3815363645553589},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32400059700012207},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17879775166511536},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07693853974342346}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6065890192985535},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5635977387428284},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.5229183435440063},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4568231701850891},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.44883862137794495},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4434674382209778},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.39131349325180054},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3815363645553589},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32400059700012207},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17879775166511536},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07693853974342346},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv323","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3072/49034665/bioinformatics_31_18_3072.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26002883","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26002883","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:open-archive.highwire.org:bioinfo:31/18/3072","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/18/3072","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv323","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3072/49034665/bioinformatics_31_18_3072.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G2606516721","display_name":null,"funder_award_id":"031A428B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7872701921","display_name":null,"funder_award_id":"0316173A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2166140491.pdf","grobid_xml":"https://content.openalex.org/works/W2166140491.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1989277387","https://openalex.org/W2023237744","https://openalex.org/W2050040190","https://openalex.org/W2053870136","https://openalex.org/W2096766502","https://openalex.org/W2098023402","https://openalex.org/W2105924489","https://openalex.org/W2128316695","https://openalex.org/W2130854041","https://openalex.org/W2131848047","https://openalex.org/W2133074013","https://openalex.org/W2136303131","https://openalex.org/W2142067151","https://openalex.org/W2144087930","https://openalex.org/W2155158051","https://openalex.org/W2159675211","https://openalex.org/W2171340202","https://openalex.org/W2171419763","https://openalex.org/W2199776355","https://openalex.org/W4237335579","https://openalex.org/W4242404314"],"related_works":["https://openalex.org/W4389426664","https://openalex.org/W2566205467","https://openalex.org/W3012616639","https://openalex.org/W3126000805","https://openalex.org/W3198565742","https://openalex.org/W2010064959","https://openalex.org/W2157390150","https://openalex.org/W2119742499","https://openalex.org/W1985266044","https://openalex.org/W4387011503"],"abstract_inverted_index":{"UNLABELLED:":[0],"Characterization":[1],"of":[2,12,29,50,73,94],"biological":[3],"processes":[4],"is":[5,129],"progressively":[6],"enabled":[7],"with":[8],"the":[9,26,70,82,91],"increased":[10],"generation":[11],"omics":[13],"data":[14,30,48],"on":[15,36,58,69,132],"different":[16,32],"signaling":[17],"levels.":[18],"Here":[19],"we":[20],"present":[21],"a":[22,88],"straightforward":[23],"approach":[24],"for":[25,90,117],"integrative":[27],"analysis":[28],"from":[31,41],"high-throughput":[33],"technologies":[34],"based":[35,57],"pathway":[37],"and":[38,54,65,77,102,120],"interaction":[39],"models":[40],"public":[42],"databases.":[43],"pwOmics":[44,128],"performs":[45],"pathway-based":[46],"level-specific":[47],"comparison":[49],"coupled":[51],"human":[52],"proteomic":[53],"genomic/transcriptomic":[55],"datasets":[56],"their":[59],"log":[60],"fold":[61],"changes.":[62],"Separate":[63],"downstream":[64],"upstream":[66],"analyses":[67,119],"results":[68],"functional":[71],"levels":[72],"pathways,":[74],"transcription":[75],"factors":[76],"genes/transcripts":[78],"are":[79],"performed":[80],"in":[81],"cross-platform":[83],"consensus":[84,111],"analysis.":[85],"These":[86],"provide":[87],"basis":[89],"combined":[92],"interpretation":[93],"regulatory":[95],"effects":[96],"over":[97],"time.":[98],"Via":[99],"network":[100,109],"reconstruction":[101],"inference":[103],"methods":[104],"(Steiner":[105],"tree,":[106],"dynamic":[107],"Bayesian":[108],"inference)":[110],"graphical":[112],"networks":[113],"can":[114],"be":[115],"generated":[116],"further":[118],"visualization.":[121],"AVAILABILITY":[122],"AND":[123],"IMPLEMENTATION:":[124],"The":[125],"R":[126],"package":[127],"freely":[130],"available":[131],"Bioconductor":[133],"(http://www.bioconductor.org/).":[134],"CONTACT:":[135],"astrid.wachter@med.uni-goettingen.de.":[136]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
