{"id":"https://openalex.org/W4388993297","doi":"https://doi.org/10.1093/bioinformatics/btad721","title":"Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods","display_name":"Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods","publication_year":2023,"publication_date":"2023-11-25","ids":{"openalex":"https://openalex.org/W4388993297","doi":"https://doi.org/10.1093/bioinformatics/btad721","pmid":"https://pubmed.ncbi.nlm.nih.gov/38006335"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad721","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad721","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad721/53811402/btad721.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/btad721/53811402/btad721.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066317582","display_name":"Daniel Stribling","orcid":"https://orcid.org/0000-0002-0649-9506"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel Stribling","raw_affiliation_strings":["Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, FL 32610, United States","UF Genetics Institute, University of Florida , Gainesville, FL 32610, United States","UF Health Cancer Center, University of Florida , Gainesville, FL 32610, United States"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"UF Genetics Institute, University of Florida , Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"UF Health Cancer Center, University of Florida , Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I2800717037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078909469","display_name":"Lauren A. Gay","orcid":"https://orcid.org/0000-0001-5715-6717"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lauren A Gay","raw_affiliation_strings":["Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, FL 32610, United States"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032322535","display_name":"Rolf Renne","orcid":"https://orcid.org/0000-0001-7391-8806"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rolf Renne","raw_affiliation_strings":["Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, FL 32610, United States","UF Genetics Institute, University of Florida , Gainesville, FL 32610, United States","UF Health Cancer Center, University of Florida , Gainesville, FL 32610, United States"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics and Microbiology, University of Florida , Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"UF Genetics Institute, University of Florida , Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"UF Health Cancer Center, University of Florida , Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I2800717037"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066317582"],"corresponding_institution_ids":["https://openalex.org/I2800717037","https://openalex.org/I33213144"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7613,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.73686352,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"39","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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":0.9994000196456909,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.8632326126098633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8087140917778015},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6314098834991455},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6077507138252258},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5914296507835388},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.574876606464386},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5406934022903442},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5385825037956238},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.4159679114818573},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.33402109146118164},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17365708947181702}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8632326126098633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8087140917778015},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6314098834991455},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6077507138252258},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5914296507835388},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.574876606464386},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5406934022903442},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5385825037956238},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.4159679114818573},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.33402109146118164},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17365708947181702},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad721","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad721","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad721/53811402/btad721.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:38006335","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38006335","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:10701094","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10701094","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10701094/pdf/btad721.pdf","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/btad721","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad721","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad721/53811402/btad721.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":[{"id":"https://metadata.un.org/sdg/9","score":0.5099999904632568,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2798581909","display_name":null,"funder_award_id":"T32CA257923","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3175519290","display_name":null,"funder_award_id":"P01-CA214091","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","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"},{"id":"https://openalex.org/F4320332659","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88"},{"id":"https://openalex.org/F5532646413","display_name":"Informatics Institute, University of Florida","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4388993297.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1551643567","https://openalex.org/W2011301426","https://openalex.org/W2019522436","https://openalex.org/W2022488654","https://openalex.org/W2086561953","https://openalex.org/W2104806799","https://openalex.org/W2114850508","https://openalex.org/W2117165052","https://openalex.org/W2121349393","https://openalex.org/W2150395782","https://openalex.org/W2162674813","https://openalex.org/W2180388440","https://openalex.org/W2400250419","https://openalex.org/W2604622795","https://openalex.org/W2765745983","https://openalex.org/W2794347818","https://openalex.org/W2807186452","https://openalex.org/W2900093945","https://openalex.org/W2968769578","https://openalex.org/W3128606201","https://openalex.org/W3134291187","https://openalex.org/W3150203197","https://openalex.org/W3159500317","https://openalex.org/W3215218082","https://openalex.org/W4200080473","https://openalex.org/W4365450858","https://openalex.org/W4383534884","https://openalex.org/W6655548692","https://openalex.org/W6755843697"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W3080200277","https://openalex.org/W2132241624","https://openalex.org/W4392173297","https://openalex.org/W4311683883","https://openalex.org/W4212902261","https://openalex.org/W2546377002","https://openalex.org/W4225687299","https://openalex.org/W3081674575","https://openalex.org/W4287673983"],"abstract_inverted_index":{"Hybkit":[0,19],"is":[1],"provided":[2,23],"free":[3],"and":[4,14,29],"open":[5],"source":[6],"under":[7],"the":[8],"GNU":[9],"GPL":[10],"license":[11],"at":[12],"github.com/RenneLab/hybkit":[13],"archived":[15],"on":[16],"Zenodo":[17],"(doi.org/10.5281/zenodo.7834299).":[18],"distributions":[20],"are":[21],"also":[22],"via":[24],"PyPI":[25],"(pypi.org/project/hybkit),":[26],"Conda":[27],"(bioconda.github.io/recipes/hybkit/README.html),":[28],"Docker":[30],"(quay.io/repository/biocontainers/hybkit).":[31]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
