{"id":"https://openalex.org/W2951915650","doi":"https://doi.org/10.1093/bioinformatics/btz203","title":"Pinetree: a step-wise gene expression simulator with codon-specific translation rates","display_name":"Pinetree: a step-wise gene expression simulator with codon-specific translation rates","publication_year":2019,"publication_date":"2019-03-27","ids":{"openalex":"https://openalex.org/W2951915650","doi":"https://doi.org/10.1093/bioinformatics/btz203","mag":"2951915650","pmid":"https://pubmed.ncbi.nlm.nih.gov/30923831"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz203","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz203","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":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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6792109","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036944057","display_name":"Benjamin R. Jack","orcid":"https://orcid.org/0000-0001-7777-1653"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin R Jack","raw_affiliation_strings":["Department of Integrative Biology, The University of Texas at Austin , Austin, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Integrative Biology, The University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070411498","display_name":"Claus O. Wilke","orcid":"https://orcid.org/0000-0002-7470-9261"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Claus O Wilke","raw_affiliation_strings":["Department of Integrative Biology, The University of Texas at Austin , Austin, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Integrative Biology, The University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5036944057"],"corresponding_institution_ids":["https://openalex.org/I86519309"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.341,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.58597617,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"35","issue":"20","first_page":"4176","last_page":"4178"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987999796867371,"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":0.9987999796867371,"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":0.9986000061035156,"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":0.9965999722480774,"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/python","display_name":"Python (programming language)","score":0.8652330636978149},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.681637167930603},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4980950355529785},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4935694932937622},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.4669203758239746},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4474775195121765},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4169311225414276},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.396487295627594},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32102125883102417},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3006495237350464},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.2936265468597412}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8652330636978149},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.681637167930603},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4980950355529785},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4935694932937622},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.4669203758239746},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4474775195121765},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4169311225414276},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.396487295627594},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32102125883102417},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3006495237350464},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.2936265468597412},{"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":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz203","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz203","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30923831","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30923831","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:6792109","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6792109","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":"pmh:oai:pubmedcentral.nih.gov:6792109","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6792109","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5031208370","display_name":null,"funder_award_id":"W911NF-12-1-0390","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"},{"id":"https://openalex.org/G6118563721","display_name":null,"funder_award_id":"R01 GM088344","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7414076325","display_name":null,"funder_award_id":"DBI-0939454","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/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1976515682","https://openalex.org/W2005182269","https://openalex.org/W2011503994","https://openalex.org/W2017851065","https://openalex.org/W2023574837","https://openalex.org/W2084924279","https://openalex.org/W2106283620","https://openalex.org/W2155418451","https://openalex.org/W2171445530","https://openalex.org/W2294343283","https://openalex.org/W2493555073","https://openalex.org/W2612290321","https://openalex.org/W2613422241","https://openalex.org/W2762868004","https://openalex.org/W2795300196"],"related_works":["https://openalex.org/W2529681551","https://openalex.org/W2327204559","https://openalex.org/W3017187763","https://openalex.org/W2094069166","https://openalex.org/W4245752324","https://openalex.org/W4232504361","https://openalex.org/W1442603624","https://openalex.org/W2975451038","https://openalex.org/W2187207551","https://openalex.org/W4315640719"],"abstract_inverted_index":{"Pinetree":[0],"is":[1],"available":[2],"on":[3],"GitHub":[4],"(https://github.com/benjaminjack/pinetree)":[5],"and":[6],"the":[7],"Python":[8],"Package":[9],"Index":[10],"(https://pypi.org/project/pinetree/).":[11]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}
