{"id":"https://openalex.org/W1963637535","doi":"https://doi.org/10.1093/bioinformatics/bti624","title":"SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles","display_name":"SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles","publication_year":2005,"publication_date":"2005-08-11","ids":{"openalex":"https://openalex.org/W1963637535","doi":"https://doi.org/10.1093/bioinformatics/bti624","mag":"1963637535","pmid":"https://pubmed.ncbi.nlm.nih.gov/16096347"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti624","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti624","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/20/3873/523130/bti624.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/20/3873/523130/bti624.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082376631","display_name":"Kavitha Bhasi","orcid":null},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"K. Bhasi","raw_affiliation_strings":["Department of Pharmaceutical Sciences, State University of New York at Buffalo, 14260-1200, USA","Department of Pharmaceutical Sciences, State University of New York at Buffalo Buffalo, NY 14260-1200, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, State University of New York at Buffalo, 14260-1200, USA","institution_ids":[]},{"raw_affiliation_string":"Department of Pharmaceutical Sciences, State University of New York at Buffalo Buffalo, NY 14260-1200, USA#TAB#","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027004349","display_name":"Alan Forrest","orcid":"https://orcid.org/0000-0003-2752-4819"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Forrest","raw_affiliation_strings":["Department of Pharmaceutical Sciences, State University of New York at Buffalo  Buffalo, NY 14260-1200, USA","Department of Pharmaceutical Sciences, State University of New York at Buffalo Buffalo, NY 14260-1200, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, State University of New York at Buffalo  Buffalo, NY 14260-1200, USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Pharmaceutical Sciences, State University of New York at Buffalo Buffalo, NY 14260-1200, USA#TAB#","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002609733","display_name":"Murali Ramanathan","orcid":"https://orcid.org/0000-0002-9943-150X"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Ramanathan","raw_affiliation_strings":["Department of Pharmaceutical Sciences, State University of New York at Buffalo  Buffalo, NY 14260-1200, USA","Department of Pharmaceutical Sciences, State University of New York at Buffalo Buffalo, NY 14260-1200, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, State University of New York at Buffalo  Buffalo, NY 14260-1200, USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Pharmaceutical Sciences, State University of New York at Buffalo Buffalo, NY 14260-1200, USA#TAB#","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082376631"],"corresponding_institution_ids":["https://openalex.org/I63190737"],"apc_list":null,"apc_paid":null,"fwci":0.7562,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.6776475,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"21","issue":"20","first_page":"3873","last_page":"3879"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973000288009644,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973000288009644,"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":0.9969000220298767,"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/T10604","display_name":"RNA Research and Splicing","score":0.9950000047683716,"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/transcription","display_name":"Transcription (linguistics)","score":0.6397151947021484},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.6155275702476501},{"id":"https://openalex.org/keywords/parametric-statistics","display_name":"Parametric statistics","score":0.6088027954101562},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5175780057907104},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44275039434432983},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.43997079133987427},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4004482328891754},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39989542961120605},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24482682347297668},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23118528723716736},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.22441160678863525}],"concepts":[{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.6397151947021484},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.6155275702476501},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.6088027954101562},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5175780057907104},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44275039434432983},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.43997079133987427},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4004482328891754},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39989542961120605},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24482682347297668},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23118528723716736},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.22441160678863525},{"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":"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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti624","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti624","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/20/3873/523130/bti624.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:16096347","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16096347","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:pubmedcentral.nih.gov:2607482","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2607482","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":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/bti624","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti624","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/20/3873/523130/bti624.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1963637535.pdf","grobid_xml":"https://content.openalex.org/works/W1963637535.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W122217472","https://openalex.org/W1571958186","https://openalex.org/W1965772857","https://openalex.org/W1969289662","https://openalex.org/W1971928443","https://openalex.org/W1983635800","https://openalex.org/W1985508225","https://openalex.org/W2006678310","https://openalex.org/W2016555030","https://openalex.org/W2045175150","https://openalex.org/W2047468407","https://openalex.org/W2060727155","https://openalex.org/W2073383382","https://openalex.org/W2090344516","https://openalex.org/W2091227064","https://openalex.org/W2102487458","https://openalex.org/W2142635246","https://openalex.org/W2152748491","https://openalex.org/W2159578516","https://openalex.org/W2162870748","https://openalex.org/W2404614501","https://openalex.org/W2418540904"],"related_works":["https://openalex.org/W2621258238","https://openalex.org/W2396122647","https://openalex.org/W2136161268","https://openalex.org/W3165943254","https://openalex.org/W2382781231","https://openalex.org/W1995675544","https://openalex.org/W3143668791","https://openalex.org/W4240199147","https://openalex.org/W2616002604","https://openalex.org/W2362348557"],"abstract_inverted_index":{"murali@acsu.buffalo.edu.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}