{"id":"https://openalex.org/W3213217687","doi":"https://doi.org/10.1093/bioinformatics/btab765","title":"Scalable inference of transcriptional kinetic parameters from MS2 time series data","display_name":"Scalable inference of transcriptional kinetic parameters from MS2 time series data","publication_year":2021,"publication_date":"2021-11-05","ids":{"openalex":"https://openalex.org/W3213217687","doi":"https://doi.org/10.1093/bioinformatics/btab765","mag":"3213217687","pmid":"https://pubmed.ncbi.nlm.nih.gov/34788793"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab765","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab765","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btab765","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075090320","display_name":"Jonathan R. Bowles","orcid":"https://orcid.org/0000-0001-6042-8541"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Jonathan R Bowles","raw_affiliation_strings":["Faculty of Biology, Medicine and Health, The University of Manchester , Manchester M13 9PT, UK"],"affiliations":[{"raw_affiliation_string":"Faculty of Biology, Medicine and Health, The University of Manchester , Manchester M13 9PT, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024726624","display_name":"Caroline Hoppe","orcid":"https://orcid.org/0000-0001-5600-309X"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Caroline Hoppe","raw_affiliation_strings":["Department of Genetics, Yale University School of Medicine , New Haven, CT 06510, USA","Faculty of Biology, Medicine and Health, The University of Manchester , Manchester M13 9PT, UK"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Yale University School of Medicine , New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Faculty of Biology, Medicine and Health, The University of Manchester , Manchester M13 9PT, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001498675","display_name":"Hilary L. Ashe","orcid":"https://orcid.org/0000-0002-8379-7830"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Hilary L Ashe","raw_affiliation_strings":["Faculty of Biology, Medicine and Health, The University of Manchester , Manchester M13 9PT, UK"],"affiliations":[{"raw_affiliation_string":"Faculty of Biology, Medicine and Health, The University of Manchester , Manchester M13 9PT, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023995814","display_name":"Magnus Rattray","orcid":"https://orcid.org/0000-0001-8196-5565"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Magnus Rattray","raw_affiliation_strings":["Faculty of Biology, Medicine and Health, The University of Manchester , Manchester M13 9PT, UK"],"affiliations":[{"raw_affiliation_string":"Faculty of Biology, Medicine and Health, The University of Manchester , Manchester M13 9PT, UK","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5001498675","https://openalex.org/A5023995814","https://openalex.org/A5075090320"],"corresponding_institution_ids":["https://openalex.org/I28407311"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8115,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.71644735,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"4","first_page":"1030","last_page":"1036"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":1.0,"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/T11289","display_name":"Single-cell and spatial transcriptomics","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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9919999837875366,"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/inference","display_name":"Inference","score":0.6996968388557434},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.566166341304779},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46390292048454285},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.46084141731262207},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.45304325222969055},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4521803855895996},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4257010519504547},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32728415727615356},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1413465440273285}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6996968388557434},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.566166341304779},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46390292048454285},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.46084141731262207},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.45304325222969055},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4521803855895996},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4257010519504547},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32728415727615356},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1413465440273285},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab765","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab765","pdf_url":null,"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:34788793","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34788793","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:pure.atira.dk:openaire/3cdaa13e-61a6-4e6b-a6a3-8d5e1293ab33","is_oa":true,"landing_page_url":"https://research.manchester.ac.uk/en/publications/3cdaa13e-61a6-4e6b-a6a3-8d5e1293ab33","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bowles, J, Hoppe, C, Ashe, H & Rattray, M 2022, 'Scalable inference of transcriptional kinetic parameters from MS2 time series data', Bioinformatics (Oxford, England), vol. 38, no. 4, pp. 1030\u20131036. https://doi.org/10.1093/bioinformatics/btab765","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:8796374","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8796374","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab765","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab765","pdf_url":null,"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/G1705567162","display_name":null,"funder_award_id":"204832/Z/16/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G3044750163","display_name":null,"funder_award_id":"204832/B/16/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G3245262837","display_name":null,"funder_award_id":"215187/Z/19/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1435682058","https://openalex.org/W1976714996","https://openalex.org/W2005640477","https://openalex.org/W2019472515","https://openalex.org/W2021312680","https://openalex.org/W2066415979","https://openalex.org/W2077468928","https://openalex.org/W2080252570","https://openalex.org/W2103354991","https://openalex.org/W2113146724","https://openalex.org/W2114870653","https://openalex.org/W2122407134","https://openalex.org/W2127540003","https://openalex.org/W2128043711","https://openalex.org/W2141688036","https://openalex.org/W2142275632","https://openalex.org/W2149242848","https://openalex.org/W2167217694","https://openalex.org/W2167244112","https://openalex.org/W2300489152","https://openalex.org/W2345585090","https://openalex.org/W2411956266","https://openalex.org/W2461148724","https://openalex.org/W2469664870","https://openalex.org/W2491614679","https://openalex.org/W2787185499","https://openalex.org/W2886822966","https://openalex.org/W2896658465","https://openalex.org/W2952685709","https://openalex.org/W2998186233","https://openalex.org/W3047620487","https://openalex.org/W3112016512","https://openalex.org/W3121168794","https://openalex.org/W6682062739"],"related_works":["https://openalex.org/W2389214306","https://openalex.org/W4235240664","https://openalex.org/W2965083567","https://openalex.org/W1838576100","https://openalex.org/W2095886385","https://openalex.org/W2889616422","https://openalex.org/W2089704382","https://openalex.org/W1983399550","https://openalex.org/W97075385","https://openalex.org/W2357523926"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
