{"id":"https://openalex.org/W2167009288","doi":"https://doi.org/10.1093/bioinformatics/btq500","title":"Global modeling of transcriptional responses in interaction networks","display_name":"Global modeling of transcriptional responses in interaction networks","publication_year":2010,"publication_date":"2010-09-02","ids":{"openalex":"https://openalex.org/W2167009288","doi":"https://doi.org/10.1093/bioinformatics/btq500","mag":"2167009288","pmid":"https://pubmed.ncbi.nlm.nih.gov/20813878"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq500","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq500","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2713/48852313/bioinformatics_26_21_2713.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":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2713/48852313/bioinformatics_26_21_2713.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082648063","display_name":"Leo Lahti","orcid":"https://orcid.org/0000-0001-5537-637X"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Leo Lahti","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science and Technology, PO Box 15400, FI-00076 Aalto and 2Neuroscience Center, University of Helsinki, PO Box 54, FI-00014, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science and Technology, PO Box 15400, FI-00076 Aalto and 2Neuroscience Center, University of Helsinki, PO Box 54, FI-00014, Helsinki, Finland","institution_ids":["https://openalex.org/I32943570","https://openalex.org/I9927081","https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047952858","display_name":"Juha E. A. Knuuttila","orcid":"https://orcid.org/0000-0002-4409-9626"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Juha E. A. Knuuttila","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science and Technology, PO Box 15400, FI-00076 Aalto and 2Neuroscience Center, University of Helsinki, PO Box 54, FI-00014, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science and Technology, PO Box 15400, FI-00076 Aalto and 2Neuroscience Center, University of Helsinki, PO Box 54, FI-00014, Helsinki, Finland","institution_ids":["https://openalex.org/I32943570","https://openalex.org/I9927081","https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018305257","display_name":"Samuel Kaski","orcid":"https://orcid.org/0000-0003-1925-9154"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Samuel Kaski","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science and Technology, PO Box 15400, FI-00076 Aalto and 2Neuroscience Center, University of Helsinki, PO Box 54, FI-00014, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science and Technology, PO Box 15400, FI-00076 Aalto and 2Neuroscience Center, University of Helsinki, PO Box 54, FI-00014, Helsinki, Finland","institution_ids":["https://openalex.org/I32943570","https://openalex.org/I9927081","https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082648063"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6777,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.70164211,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"26","issue":"21","first_page":"2713","last_page":"2720"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9997000098228455,"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":0.9968000054359436,"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/context","display_name":"Context (archaeology)","score":0.678761899471283},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6454495191574097},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.6175432801246643},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5903221368789673},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5718321800231934},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5174623131752014},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4777223765850067},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41308334469795227},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34235164523124695},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17581135034561157},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1654435694217682}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.678761899471283},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6454495191574097},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.6175432801246643},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5903221368789673},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5718321800231934},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5174623131752014},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4777223765850067},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41308334469795227},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34235164523124695},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17581135034561157},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1654435694217682},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq500","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq500","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2713/48852313/bioinformatics_26_21_2713.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:20813878","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20813878","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:arXiv.org:1202.0501","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1202.0501","pdf_url":"https://arxiv.org/pdf/1202.0501","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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/btq500","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq500","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2713/48852313/bioinformatics_26_21_2713.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":[{"id":"https://metadata.un.org/sdg/17","score":0.46000000834465027,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167009288.pdf","grobid_xml":"https://content.openalex.org/works/W2167009288.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W1546709038","https://openalex.org/W1644749979","https://openalex.org/W1876024155","https://openalex.org/W1963600204","https://openalex.org/W1970357458","https://openalex.org/W1971166208","https://openalex.org/W1984273678","https://openalex.org/W1985231996","https://openalex.org/W1992045522","https://openalex.org/W1993817351","https://openalex.org/W2006477103","https://openalex.org/W2007402386","https://openalex.org/W2012116432","https://openalex.org/W2018843280","https://openalex.org/W2032065412","https://openalex.org/W2041329844","https://openalex.org/W2045656233","https://openalex.org/W2046831513","https://openalex.org/W2048368626","https://openalex.org/W2050195890","https://openalex.org/W2052977461","https://openalex.org/W2053427298","https://openalex.org/W2075963387","https://openalex.org/W2097698606","https://openalex.org/W2098212444","https://openalex.org/W2103017472","https://openalex.org/W2107580398","https://openalex.org/W2109972881","https://openalex.org/W2110687686","https://openalex.org/W2111823238","https://openalex.org/W2112811019","https://openalex.org/W2118069309","https://openalex.org/W2119062243","https://openalex.org/W2121604817","https://openalex.org/W2123060905","https://openalex.org/W2123712380","https://openalex.org/W2125964067","https://openalex.org/W2126449841","https://openalex.org/W2135827569","https://openalex.org/W2136107412","https://openalex.org/W2138133187","https://openalex.org/W2141703917","https://openalex.org/W2143707047","https://openalex.org/W2144317357","https://openalex.org/W2144544802","https://openalex.org/W2148974291","https://openalex.org/W2153794775","https://openalex.org/W2154452346","https://openalex.org/W2154972152","https://openalex.org/W2160697532","https://openalex.org/W2161732139","https://openalex.org/W2164665487","https://openalex.org/W2164683872","https://openalex.org/W2165151093","https://openalex.org/W2168319451","https://openalex.org/W2425246132","https://openalex.org/W2612972698","https://openalex.org/W3122709706","https://openalex.org/W4214823344","https://openalex.org/W4232383088","https://openalex.org/W4244055035","https://openalex.org/W4300075680","https://openalex.org/W4320800138","https://openalex.org/W6678274143","https://openalex.org/W6682691471"],"related_works":["https://openalex.org/W2130939068","https://openalex.org/W3163717165","https://openalex.org/W2114466827","https://openalex.org/W249159571","https://openalex.org/W2791736663","https://openalex.org/W2806770614","https://openalex.org/W2129949791","https://openalex.org/W2131550814","https://openalex.org/W1710460698","https://openalex.org/W3199739261"],"abstract_inverted_index":{"MOTIVATION:":[0],"Cell-biological":[1],"processes":[2],"are":[3,26,104],"regulated":[4],"through":[5],"a":[6,66,88,96,118],"complex":[7],"network":[8,32,89,121],"of":[9,31,74,98,134],"interactions":[10,101],"between":[11,40,102,128],"genes":[12,103],"and":[13,21,37,42,72,111,130,144],"their":[14,18],"products.":[15],"The":[16,48,80],"processes,":[17],"activating":[19],"conditions":[20,57],"the":[22,108,114,135],"associated":[23],"transcriptional":[24,75,93],"responses":[25,76],"often":[27],"unknown.":[28],"Organism-wide":[29],"modeling":[30],"activation":[33],"can":[34,51],"reveal":[35],"unique":[36],"shared":[38],"mechanisms":[39],"tissues,":[41],"potentially":[43],"as":[44],"yet":[45],"unknown":[46],"processes.":[47],"same":[49],"method":[50,81],"also":[52],"be":[53],"applied":[54],"to":[55,106,112],"cell-biological":[56],"in":[58,77,87,95,142],"one":[59],"or":[60],"more":[61],"tissues.":[62,99],"RESULTS:":[63],"We":[64],"introduce":[65],"novel":[67],"approach":[68],"for":[69,83],"organism-wide":[70],"discovery":[71],"analysis":[73],"interaction":[78],"networks.":[79],"searches":[82],"local,":[84],"connected":[85],"regions":[86],"that":[90],"exhibit":[91],"coordinated":[92],"response":[94],"subset":[97],"Known":[100],"used":[105],"limit":[107],"search":[109],"space":[110],"guide":[113],"analysis.":[115],"Validation":[116],"on":[117],"human":[119],"pathway":[120],"reveals":[122],"physiologically":[123],"coherent":[124],"responses,":[125],"functional":[126],"relatedness":[127],"tissues":[129],"coordinated,":[131],"context-specific":[132],"regulation":[133],"genes.":[136],"AVAILABILITY:":[137],"Implementation":[138],"is":[139],"freely":[140],"available":[141],"R":[143],"Matlab":[145],"at":[146],"http://www.cis.hut.fi/projects/mi/software/NetResponse":[147]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}
