{"id":"https://openalex.org/W2141024654","doi":"https://doi.org/10.1093/bioinformatics/btn494","title":"tCal: transcriptional probability calculator using thermodynamic model","display_name":"tCal: transcriptional probability calculator using thermodynamic model","publication_year":2008,"publication_date":"2008-09-16","ids":{"openalex":"https://openalex.org/W2141024654","doi":"https://doi.org/10.1093/bioinformatics/btn494","mag":"2141024654","pmid":"https://pubmed.ncbi.nlm.nih.gov/18796477"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn494","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn494","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/22/2639/16885078/btn494.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/24/22/2639/16885078/btn494.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060877490","display_name":"Xin Zhou","orcid":"https://orcid.org/0000-0002-1407-7952"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Xin Zhou","raw_affiliation_strings":["College of Biological Sciences, China Agricultural University","College of Biological Sciences, China Agricultural University,"],"affiliations":[{"raw_affiliation_string":"College of Biological Sciences, China Agricultural University","institution_ids":["https://openalex.org/I52158045"]},{"raw_affiliation_string":"College of Biological Sciences, China Agricultural University,","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079263322","display_name":"Zhen Su","orcid":"https://orcid.org/0000-0001-6579-3847"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Zhen Su","raw_affiliation_strings":["College of Biological Sciences, China Agricultural University","College of Biological Sciences, China Agricultural University,"],"affiliations":[{"raw_affiliation_string":"College of Biological Sciences, China Agricultural University","institution_ids":["https://openalex.org/I52158045"]},{"raw_affiliation_string":"College of Biological Sciences, China Agricultural University,","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5060877490"],"corresponding_institution_ids":["https://openalex.org/I130238516","https://openalex.org/I52158045"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2693,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.60242336,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"24","issue":"22","first_page":"2639","last_page":"2640"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9977999925613403,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/sbml","display_name":"SBML","score":0.8527510166168213},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7531320452690125},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7173469066619873},{"id":"https://openalex.org/keywords/calculator","display_name":"Calculator","score":0.7020108103752136},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5498929619789124},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5344609022140503},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4657028317451477},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3604127764701843},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3400529623031616},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3299485445022583},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2454347312450409},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15939724445343018},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14932820200920105},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1159064769744873},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.11217251420021057}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.8527510166168213},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7531320452690125},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7173469066619873},{"id":"https://openalex.org/C2776836400","wikidata":"https://www.wikidata.org/wiki/Q31087","display_name":"Calculator","level":2,"score":0.7020108103752136},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5498929619789124},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5344609022140503},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4657028317451477},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3604127764701843},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3400529623031616},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3299485445022583},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2454347312450409},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15939724445343018},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14932820200920105},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1159064769744873},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.11217251420021057},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"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":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btn494","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn494","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/22/2639/16885078/btn494.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:18796477","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18796477","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn494","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn494","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/22/2639/16885078/btn494.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.41999998688697815}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2141024654.pdf","grobid_xml":"https://content.openalex.org/works/W2141024654.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W2001394772","https://openalex.org/W2022891974","https://openalex.org/W2046355391","https://openalex.org/W2134221731","https://openalex.org/W2144347639"],"related_works":["https://openalex.org/W1833372769","https://openalex.org/W2128782793","https://openalex.org/W1994518768","https://openalex.org/W104010570","https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2069162648","https://openalex.org/W3080133182","https://openalex.org/W2126025430","https://openalex.org/W1495449059"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}