{"id":"https://openalex.org/W2101986518","doi":"https://doi.org/10.1093/bioinformatics/bts245","title":"Utilizing RNA-Seq data for de novo coexpression network inference","display_name":"Utilizing RNA-Seq data for de novo coexpression network inference","publication_year":2012,"publication_date":"2012-05-03","ids":{"openalex":"https://openalex.org/W2101986518","doi":"https://doi.org/10.1093/bioinformatics/bts245","mag":"2101986518","pmid":"https://pubmed.ncbi.nlm.nih.gov/22556371"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts245","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts245","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1592/48874282/bioinformatics_28_12_1592.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/28/12/1592/48874282/bioinformatics_28_12_1592.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024836197","display_name":"Ovidiu D. Iancu","orcid":null},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I4210107577","display_name":"Oregon Clinic","ror":"https://ror.org/01eadrh05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210107577"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ovidiu D. Iancu","raw_affiliation_strings":["1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA","institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210107577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000665006","display_name":"Sunita Kawane","orcid":null},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I4210107577","display_name":"Oregon Clinic","ror":"https://ror.org/01eadrh05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210107577"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sunita Kawane","raw_affiliation_strings":["1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA","institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210107577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061516412","display_name":"Daniel Bottomly","orcid":"https://orcid.org/0000-0001-7191-0990"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I4210107577","display_name":"Oregon Clinic","ror":"https://ror.org/01eadrh05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210107577"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Bottomly","raw_affiliation_strings":["1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA","institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210107577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007067790","display_name":"Robert P. Searles","orcid":"https://orcid.org/0000-0002-0378-2322"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I4210107577","display_name":"Oregon Clinic","ror":"https://ror.org/01eadrh05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210107577"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Searles","raw_affiliation_strings":["1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA","institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210107577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109190156","display_name":"Robert Hitzemann","orcid":null},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I4210107577","display_name":"Oregon Clinic","ror":"https://ror.org/01eadrh05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210107577"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Hitzemann","raw_affiliation_strings":["1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA","institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210107577"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066373576","display_name":"Shannon K. McWeeney","orcid":"https://orcid.org/0000-0001-8333-6607"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I4210107577","display_name":"Oregon Clinic","ror":"https://ror.org/01eadrh05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210107577"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shannon McWeeney","raw_affiliation_strings":["1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Behavioral Neuroscience, 2Oregon Clinical and Translational Research Institute and 3Massively Parallel Sequencing Shared Resource, Oregon Health & Science University, Portland, OR 97239-3098, USA, 4Research Service, Veterans Affairs Medical Center, Portland, OR 97239-3098, USA and 5Department of Biostatistics, Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA","institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210107577"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5024836197"],"corresponding_institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210107577"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":4.92,"has_fulltext":true,"cited_by_count":115,"citation_normalized_percentile":{"value":0.96365277,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"28","issue":"12","first_page":"1592","last_page":"1597"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9983999729156494,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9973999857902527,"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/rna-seq","display_name":"RNA-Seq","score":0.602074384689331},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5949546694755554},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5918745994567871},{"id":"https://openalex.org/keywords/centrality","display_name":"Centrality","score":0.565860390663147},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5425527691841125},{"id":"https://openalex.org/keywords/colocalization","display_name":"Colocalization","score":0.46775317192077637},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.4637497067451477},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4582561254501343},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4401392936706543},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3794046640396118},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33535194396972656},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21483004093170166},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21413370966911316},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18864503502845764},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1597164273262024},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.08485901355743408},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08428919315338135}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.602074384689331},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5949546694755554},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5918745994567871},{"id":"https://openalex.org/C53811970","wikidata":"https://www.wikidata.org/wiki/Q5062194","display_name":"Centrality","level":2,"score":0.565860390663147},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5425527691841125},{"id":"https://openalex.org/C40209533","wikidata":"https://www.wikidata.org/wiki/Q5147828","display_name":"Colocalization","level":2,"score":0.46775317192077637},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.4637497067451477},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4582561254501343},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4401392936706543},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3794046640396118},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33535194396972656},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21483004093170166},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21413370966911316},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18864503502845764},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1597164273262024},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.08485901355743408},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08428919315338135},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"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":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","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":"D008810","descriptor_name":"Mice, Inbred C57BL","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008811","descriptor_name":"Mice, Inbred DBA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008811","descriptor_name":"Mice, Inbred DBA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008811","descriptor_name":"Mice, Inbred DBA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts245","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts245","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1592/48874282/bioinformatics_28_12_1592.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:22556371","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22556371","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":"Comparative Study"},{"id":"pmh:oai:europepmc.org:2678375","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3493127","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3493127","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3493127","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts245","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts245","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1592/48874282/bioinformatics_28_12_1592.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":[],"awards":[{"id":"https://openalex.org/G1097632367","display_name":null,"funder_award_id":"U01 AA013484","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G1214337728","display_name":null,"funder_award_id":"R01 AA011114","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G1259923721","display_name":null,"funder_award_id":"P60 AA010760","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G1581679921","display_name":null,"funder_award_id":"P30 CA-069533","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1798011332","display_name":null,"funder_award_id":"R01 DA005228","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G1954115628","display_name":null,"funder_award_id":"5 P30 CA069533-13","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2446526039","display_name":null,"funder_award_id":"AA010760","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G288989767","display_name":null,"funder_award_id":"UL1TR000128","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G3668497772","display_name":null,"funder_award_id":"R29 AA011114","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G3958686631","display_name":null,"funder_award_id":"R01 MH051372","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G3991382852","display_name":null,"funder_award_id":"MH051372","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G4417789746","display_name":null,"funder_award_id":"5 UL1 RR 024140","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G4597726415","display_name":null,"funder_award_id":"P50 AA010760","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G5720351444","display_name":null,"funder_award_id":"DA005228","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G607985544","display_name":null,"funder_award_id":"AA011114","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G801436702","display_name":null,"funder_award_id":"UL 1RR024140","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G8638631755","display_name":null,"funder_award_id":"AA013484","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"}],"funders":[{"id":"https://openalex.org/F4320306127","display_name":"U.S. Department of Veterans Affairs","ror":"https://ror.org/05rsv9s98"},{"id":"https://openalex.org/F4320306203","display_name":"M.J. Murdock Charitable Trust","ror":"https://ror.org/02hxgd925"},{"id":"https://openalex.org/F4320337330","display_name":"National Institute on Alcohol Abuse and Alcoholism","ror":"https://ror.org/02jzrsm59"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2101986518.pdf","grobid_xml":"https://content.openalex.org/works/W2101986518.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1966327575","https://openalex.org/W1974033269","https://openalex.org/W1981509058","https://openalex.org/W1996984681","https://openalex.org/W2003572485","https://openalex.org/W2018045523","https://openalex.org/W2020541351","https://openalex.org/W2029835563","https://openalex.org/W2031662960","https://openalex.org/W2057498577","https://openalex.org/W2060705109","https://openalex.org/W2064294766","https://openalex.org/W2069733150","https://openalex.org/W2072602203","https://openalex.org/W2081837126","https://openalex.org/W2083129396","https://openalex.org/W2091901410","https://openalex.org/W2095998476","https://openalex.org/W2103017472","https://openalex.org/W2103814083","https://openalex.org/W2106608030","https://openalex.org/W2114104545","https://openalex.org/W2120024428","https://openalex.org/W2123491442","https://openalex.org/W2138255346","https://openalex.org/W2149159134","https://openalex.org/W2151820055","https://openalex.org/W2155804510","https://openalex.org/W2156247618","https://openalex.org/W2162543144","https://openalex.org/W2163480486","https://openalex.org/W2170989872"],"related_works":["https://openalex.org/W4362511917","https://openalex.org/W2904597490","https://openalex.org/W4362530199","https://openalex.org/W4362511560","https://openalex.org/W4377231761","https://openalex.org/W4285162488","https://openalex.org/W4362512073","https://openalex.org/W2769306272","https://openalex.org/W4362485908","https://openalex.org/W2268123450"],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA-Seq":[1,36,66,109,147],"experiments":[2],"have":[3],"shown":[4],"great":[5],"potential":[6],"for":[7,38],"transcriptome":[8],"profiling.":[9],"While":[10],"sequencing":[11],"increases":[12],"the":[13,27,33,90,145],"level":[14],"of":[15,29,35],"biological":[16],"detail,":[17],"integrative":[18],"data":[19,37,88,110,148],"analysis":[20],"is":[21,26],"also":[22],"important.":[23],"One":[24],"avenue":[25],"construction":[28,40],"coexpression":[30,49,67],"networks.":[31,63],"Because":[32],"capacity":[34],"network":[39,50,56,68,72,101,125,135,151],"has":[41],"not":[42],"been":[43],"previously":[44],"evaluated,":[45],"we":[46,143],"constructed":[47],"a":[48],"using":[51],"striatal":[52],"samples,":[53],"derived":[54],"its":[55],"properties":[57],"and":[58,117,128],"compared":[59,103],"it":[60],"with":[61,79,97,104],"microarray-based":[62],"RESULTS:":[64],"The":[65,100],"displayed":[69],"scale-free,":[70],"hierarchical":[71],"structure.":[73],"We":[74],"detected":[75],"transcripts":[76,131],"groups":[77],"(modules)":[78],"correlated":[80],"profiles;":[81],"modules":[82,96],"overlap":[83],"distinct":[84],"ontology":[85],"categories.":[86],"Neuroanatomical":[87],"from":[89,108],"Allen":[91],"Brain":[92],"Atlas":[93],"reveal":[94],"several":[95],"spatial":[98],"colocalization.":[99],"was":[102],"microarray-derived":[105],"networks;":[106],"correlations":[107,121],"were":[111],"higher,":[112],"likely":[113],"because":[114],"greater":[115],"sensitivity":[116],"dynamic":[118],"range.":[119],"Higher":[120],"result":[122],"in":[123],"higher":[124],"connectivity,":[126],"heterogeneity":[127],"centrality.":[129],"For":[130],"present":[132,144],"across":[133],"platforms,":[134],"structure":[136],"appeared":[137],"largely":[138],"preserved.":[139],"From":[140],"this":[141],"study,":[142],"first":[146],"de":[149],"novo":[150],"inference.":[152]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2016-06-24T00:00:00"}
