{"id":"https://openalex.org/W2936450312","doi":"https://doi.org/10.1093/bioinformatics/btz256","title":"Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights","display_name":"Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights","publication_year":2019,"publication_date":"2019-04-12","ids":{"openalex":"https://openalex.org/W2936450312","doi":"https://doi.org/10.1093/bioinformatics/btz256","mag":"2936450312","pmid":"https://pubmed.ncbi.nlm.nih.gov/30994899"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz256","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz256","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4671/30706668/btz256.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4671/30706668/btz256.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032998811","display_name":"Justin D. Finkle","orcid":"https://orcid.org/0000-0001-7296-9855"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin D Finkle","raw_affiliation_strings":["Interdisciplinary Biological Sciences, Northwestern University , Evanston, IL 60208, USA"],"affiliations":[{"raw_affiliation_string":"Interdisciplinary Biological Sciences, Northwestern University , Evanston, IL 60208, USA","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030550883","display_name":"Neda Bagheri","orcid":"https://orcid.org/0000-0003-0146-4627"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Neda Bagheri","raw_affiliation_strings":["Center for Synthetic Biology, Northwestern University , Evanston, IL 60208, USA","Chemistry of Life Processes, Northwestern University , Evanston, IL 60208, USA","Department of Chemical and Biological Engineering, Northwestern University , Evanston, IL 60208, USA","Interdisciplinary Biological Sciences, Northwestern University , Evanston, IL 60208, USA"],"affiliations":[{"raw_affiliation_string":"Center for Synthetic Biology, Northwestern University , Evanston, IL 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Chemistry of Life Processes, Northwestern University , Evanston, IL 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Northwestern University , Evanston, IL 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Interdisciplinary Biological Sciences, Northwestern University , Evanston, IL 60208, USA","institution_ids":["https://openalex.org/I111979921"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5030550883"],"corresponding_institution_ids":["https://openalex.org/I111979921"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0852,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.45194687,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"35","issue":"22","first_page":"4671","last_page":"4678"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.996399998664856,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.996399998664856,"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":0.9958000183105469,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9926000237464905,"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/in-silico","display_name":"In silico","score":0.662270188331604},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5984267592430115},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5627937316894531},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.555971622467041},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5426478981971741},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5139079093933105},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5104307532310486},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.49428296089172363},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.46638134121894836},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.46367570757865906},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4259897470474243},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4218358099460602},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3400033116340637},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.269561231136322},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.0905623733997345}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.662270188331604},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5984267592430115},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5627937316894531},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.555971622467041},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5426478981971741},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5139079093933105},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5104307532310486},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.49428296089172363},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.46638134121894836},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.46367570757865906},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4259897470474243},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4218358099460602},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3400033116340637},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.269561231136322},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0905623733997345},{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz256","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz256","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4671/30706668/btz256.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30994899","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30994899","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:europepmc.org:5823481","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6853664","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz256","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz256","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4671/30706668/btz256.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6347694119","display_name":null,"funder_award_id":"CBET-1653315","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320333924","display_name":"McCormick School of Engineering, Northwestern University","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2936450312.pdf","grobid_xml":"https://content.openalex.org/works/W2936450312.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1634376377","https://openalex.org/W1964865474","https://openalex.org/W1965853004","https://openalex.org/W1966327575","https://openalex.org/W2000507520","https://openalex.org/W2001536896","https://openalex.org/W2019998456","https://openalex.org/W2022159056","https://openalex.org/W2027287962","https://openalex.org/W2032551913","https://openalex.org/W2035018429","https://openalex.org/W2090808827","https://openalex.org/W2097643762","https://openalex.org/W2108421561","https://openalex.org/W2122342005","https://openalex.org/W2124241603","https://openalex.org/W2130410032","https://openalex.org/W2137526110","https://openalex.org/W2137857624","https://openalex.org/W2139997707","https://openalex.org/W2146329585","https://openalex.org/W2146512944","https://openalex.org/W2153485633","https://openalex.org/W2253524210","https://openalex.org/W2262923393","https://openalex.org/W2317505839","https://openalex.org/W2522895022","https://openalex.org/W2586394106","https://openalex.org/W2604808360","https://openalex.org/W2620721366","https://openalex.org/W2747878742","https://openalex.org/W2761392474","https://openalex.org/W2792581694","https://openalex.org/W2803928488","https://openalex.org/W2889722506","https://openalex.org/W2964145209","https://openalex.org/W6655871561","https://openalex.org/W6678481978","https://openalex.org/W6693547349","https://openalex.org/W6981678552"],"related_works":["https://openalex.org/W2156421048","https://openalex.org/W2135896045","https://openalex.org/W2010571965","https://openalex.org/W3128451840","https://openalex.org/W2884256268","https://openalex.org/W2002709996","https://openalex.org/W4387092964","https://openalex.org/W2171763327","https://openalex.org/W2103471012","https://openalex.org/W2966064480"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
