{"id":"https://openalex.org/W4409798146","doi":"https://doi.org/10.1093/bioinformatics/btaf250","title":"Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes","display_name":"Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes","publication_year":2025,"publication_date":"2025-04-25","ids":{"openalex":"https://openalex.org/W4409798146","doi":"https://doi.org/10.1093/bioinformatics/btaf250","pmid":"https://pubmed.ncbi.nlm.nih.gov/40279271"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf250","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf250","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf250/63011547/btaf250.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf250/63011547/btaf250.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5117310132","display_name":"Alison Kyrouz","orcid":null},"institutions":[{"id":"https://openalex.org/I189731429","display_name":"Wellesley College","ror":"https://ror.org/01srpnj69","country_code":"US","type":"education","lineage":["https://openalex.org/I189731429"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alison Kyrouz","raw_affiliation_strings":["Department of Computer Science, Wellesley College , Wellesley, MA 02481,","Wellesley College Department of Computer Science, , Wellesley, MA 02481,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wellesley College , Wellesley, MA 02481,","institution_ids":["https://openalex.org/I189731429"]},{"raw_affiliation_string":"Wellesley College Department of Computer Science, , Wellesley, MA 02481,","institution_ids":["https://openalex.org/I189731429"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110011018","display_name":"Lian Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I189731429","display_name":"Wellesley College","ror":"https://ror.org/01srpnj69","country_code":"US","type":"education","lineage":["https://openalex.org/I189731429"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lian Liu","raw_affiliation_strings":["Department of Computer Science, Wellesley College , Wellesley, MA 02481,","Wellesley College Department of Computer Science, , Wellesley, MA 02481,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wellesley College , Wellesley, MA 02481,","institution_ids":["https://openalex.org/I189731429"]},{"raw_affiliation_string":"Wellesley College Department of Computer Science, , Wellesley, MA 02481,","institution_ids":["https://openalex.org/I189731429"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102766360","display_name":"Lixin Qin","orcid":"https://orcid.org/0000-0003-0966-3006"},"institutions":[{"id":"https://openalex.org/I189731429","display_name":"Wellesley College","ror":"https://ror.org/01srpnj69","country_code":"US","type":"education","lineage":["https://openalex.org/I189731429"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lixin Qin","raw_affiliation_strings":["Department of Computer Science, Wellesley College , Wellesley, MA 02481,","Wellesley College Department of Computer Science, , Wellesley, MA 02481,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wellesley College , Wellesley, MA 02481,","institution_ids":["https://openalex.org/I189731429"]},{"raw_affiliation_string":"Wellesley College Department of Computer Science, , Wellesley, MA 02481,","institution_ids":["https://openalex.org/I189731429"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030823572","display_name":"Brian Tjaden","orcid":"https://orcid.org/0009-0002-8664-7296"},"institutions":[{"id":"https://openalex.org/I189731429","display_name":"Wellesley College","ror":"https://ror.org/01srpnj69","country_code":"US","type":"education","lineage":["https://openalex.org/I189731429"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Tjaden","raw_affiliation_strings":["Department of Computer Science, Wellesley College , Wellesley, MA 02481,","Wellesley College Department of Computer Science, , Wellesley, MA 02481,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wellesley College , Wellesley, MA 02481,","institution_ids":["https://openalex.org/I189731429"]},{"raw_affiliation_string":"Wellesley College Department of Computer Science, , Wellesley, MA 02481,","institution_ids":["https://openalex.org/I189731429"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5117310132"],"corresponding_institution_ids":["https://openalex.org/I189731429"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07983027,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9979000091552734,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9970999956130981,"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/orfs","display_name":"ORFS","score":0.6218445897102356},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.596463680267334},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5843622088432312},{"id":"https://openalex.org/keywords/long-non-coding-rna","display_name":"Long non-coding RNA","score":0.5797889232635498},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.5709470510482788},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5432890057563782},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5109238028526306},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47679829597473145},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.38430970907211304},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35261619091033936},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34644609689712524},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.295371413230896}],"concepts":[{"id":"https://openalex.org/C2780530800","wikidata":"https://www.wikidata.org/wiki/Q7072921","display_name":"ORFS","level":5,"score":0.6218445897102356},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.596463680267334},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5843622088432312},{"id":"https://openalex.org/C62203573","wikidata":"https://www.wikidata.org/wiki/Q15087973","display_name":"Long non-coding RNA","level":4,"score":0.5797889232635498},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.5709470510482788},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5432890057563782},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5109238028526306},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47679829597473145},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.38430970907211304},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35261619091033936},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34644609689712524},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.295371413230896},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":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":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf250","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf250","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf250/63011547/btaf250.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:40279271","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40279271","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:12054974","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12054974","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/btaf250","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf250","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf250/63011547/btaf250.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G5592155341","display_name":null,"funder_award_id":"GM102755","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409798146.pdf","grobid_xml":"https://content.openalex.org/works/W4409798146.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W2062640511","https://openalex.org/W2062896692","https://openalex.org/W2115534091","https://openalex.org/W2137390416","https://openalex.org/W2140874466","https://openalex.org/W2346160190","https://openalex.org/W2968334948","https://openalex.org/W2987349979","https://openalex.org/W3013495013","https://openalex.org/W3022137185","https://openalex.org/W3131134724","https://openalex.org/W3186298586","https://openalex.org/W3190998772","https://openalex.org/W3213835556","https://openalex.org/W4283277516","https://openalex.org/W4323044126","https://openalex.org/W4386083778","https://openalex.org/W4389167204","https://openalex.org/W4389272823","https://openalex.org/W4402098128","https://openalex.org/W6737947904"],"related_works":["https://openalex.org/W3199602943","https://openalex.org/W2547129954","https://openalex.org/W1924910987","https://openalex.org/W3146486132","https://openalex.org/W2276469649","https://openalex.org/W3031361789","https://openalex.org/W2205411991","https://openalex.org/W2357413449","https://openalex.org/W3094073736","https://openalex.org/W2390930459"],"abstract_inverted_index":{"Freely":[0],"available":[1,11],"for":[2],"use":[3],"on":[4],"the":[5],"web":[6],"at":[7,12],"https://cs.wellesley.edu/\u223cbtjaden/Popcorn.":[8],"Source":[9],"code":[10],"https://github.com/btjaden/Popcorn":[13],"and":[14],"https://doi.org/10.5281/zenodo.15120075.":[15]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
