{"id":"https://openalex.org/W2968168084","doi":"https://doi.org/10.1093/bioinformatics/btz643","title":"baerhunter: an <i>R</i> package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data","display_name":"baerhunter: an <i>R</i> package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data","publication_year":2019,"publication_date":"2019-08-13","ids":{"openalex":"https://openalex.org/W2968168084","doi":"https://doi.org/10.1093/bioinformatics/btz643","mag":"2968168084","pmid":"https://pubmed.ncbi.nlm.nih.gov/31418770"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz643","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz643","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113250927","display_name":"Aime Ozuna","orcid":null},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"A Ozuna","raw_affiliation_strings":["Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK","institution_ids":["https://openalex.org/I4210157240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026809098","display_name":"D. Liberto","orcid":null},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"D Liberto","raw_affiliation_strings":["Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK","institution_ids":["https://openalex.org/I4210157240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032924197","display_name":"Rosanna Joyce","orcid":null},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"R M Joyce","raw_affiliation_strings":["Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK","institution_ids":["https://openalex.org/I4210157240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050699940","display_name":"Kristine B. Arnvig","orcid":"https://orcid.org/0000-0002-6850-2547"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"K B Arnvig","raw_affiliation_strings":["Institute of Structural and Molecular Biology, Division of Biosciences, University College London , London, WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Structural and Molecular Biology, Division of Biosciences, University College London , London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032936205","display_name":"Irene Nobeli","orcid":"https://orcid.org/0000-0001-8616-170X"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"I Nobeli","raw_affiliation_strings":["Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK"],"raw_orcid":"https://orcid.org/0000-0001-8616-170X","affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Institute of Structural and Molecular Biology , London, WC1E 7HX, UK","institution_ids":["https://openalex.org/I4210157240"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5032936205"],"corresponding_institution_ids":["https://openalex.org/I4210157240"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3033,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.54764517,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"36","issue":"3","first_page":"966","last_page":"969"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5023999810218811,"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":0.5023999810218811,"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/T10066","display_name":"Gut microbiota and health","score":0.08959999680519104,"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":0.08720000088214874,"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/coding","display_name":"Coding (social sciences)","score":0.5788634419441223},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.576284646987915},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5529480576515198},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5491920113563538},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4782204329967499},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.45089083909988403},{"id":"https://openalex.org/keywords/untranslated-region","display_name":"Untranslated region","score":0.44294992089271545},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43757539987564087},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.43652093410491943},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4102490544319153},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.37999090552330017},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3148062527179718},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3078611493110657},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2139166295528412},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12736627459526062},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09573101997375488},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.06669872999191284}],"concepts":[{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.5788634419441223},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.576284646987915},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5529480576515198},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5491920113563538},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4782204329967499},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.45089083909988403},{"id":"https://openalex.org/C89604277","wikidata":"https://www.wikidata.org/wiki/Q424345","display_name":"Untranslated region","level":4,"score":0.44294992089271545},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43757539987564087},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.43652093410491943},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4102490544319153},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.37999090552330017},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3148062527179718},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3078611493110657},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2139166295528412},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12736627459526062},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09573101997375488},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.06669872999191284},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz643","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz643","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:31418770","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31418770","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:eprints.bbk.ac.uk.oai2:28596","is_oa":false,"landing_page_url":"https://eprints.bbk.ac.uk/id/eprint/28596/1/BIOINF-2019-0830_Ozuna_etal_accepted_version.pdf","pdf_url":"https://eprints.bbk.ac.uk/id/eprint/28596/1/BIOINF-2019-0830_Ozuna_etal_accepted_version.pdf","source":{"id":"https://openalex.org/S4306400465","display_name":"BIROn (Birkbeck, University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98259816","host_organization_name":"Birkbeck, University of London","host_organization_lineage":["https://openalex.org/I98259816"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10082522","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/10082522/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Bioinformatics , 36 (3) pp. 966-969. (2020)","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2449706252","display_name":null,"funder_award_id":"MR/L018519/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7012339150","display_name":null,"funder_award_id":"MR/S009647/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1591970889","https://openalex.org/W1990653290","https://openalex.org/W1991163952","https://openalex.org/W1996974387","https://openalex.org/W2010647598","https://openalex.org/W2060095084","https://openalex.org/W2067051926","https://openalex.org/W2087829872","https://openalex.org/W2112876600","https://openalex.org/W2119463761","https://openalex.org/W2150390148","https://openalex.org/W2150491437","https://openalex.org/W2155347381","https://openalex.org/W2179438025","https://openalex.org/W2592012729","https://openalex.org/W2766848373","https://openalex.org/W2889069059","https://openalex.org/W2917207851","https://openalex.org/W2947620157","https://openalex.org/W6763024190"],"related_works":["https://openalex.org/W2884291362","https://openalex.org/W1603543036","https://openalex.org/W2171277769","https://openalex.org/W1976142521","https://openalex.org/W4200520333","https://openalex.org/W4383032973","https://openalex.org/W2621804107","https://openalex.org/W2749991225","https://openalex.org/W1975704818","https://openalex.org/W2005416777"],"abstract_inverted_index":{"SUMMARY:":[0],"Standard":[1],"bioinformatics":[2],"pipelines":[3],"for":[4],"the":[5,36,55,110],"analysis":[6,82],"of":[7,27,32,38,57,76,83],"bacterial":[8],"transcriptomic":[9],"data":[10,129],"commonly":[11],"ignore":[12],"non-coding":[13,59,87],"but":[14],"functional":[15],"elements":[16],"e.g.":[17],"small":[18],"RNAs,":[19],"long":[20],"antisense":[21],"RNAs":[22,60],"or":[23],"untranslated":[24],"regions":[25],"(UTRs)":[26],"mRNA":[28],"transcripts.":[29],"The":[30,71,89,118],"root":[31],"this":[33],"problem":[34],"is":[35,74,91,122],"use":[37],"incomplete":[39],"genome":[40],"annotation":[41],"files.":[42],"Here,":[43],"we":[44],"present":[45],"baerhunter,":[46],"a":[47,68,77],"coverage-based":[48],"method":[49,90],"implemented":[50],"in":[51,99],"R,":[52],"that":[53,79],"automates":[54],"discovery":[56],"expressed":[58],"and":[61,86,96,104],"UTRs":[62],"from":[63],"RNA-seq":[64],"reads":[65],"mapped":[66],"to":[67,94],"reference":[69],"genome.":[70],"core":[72],"algorithm":[73],"part":[75],"pipeline":[78],"facilitates":[80],"downstream":[81],"both":[84],"coding":[85],"features.":[88],"simple,":[92],"easy":[93],"extend":[95],"customize":[97],"and,":[98],"limited":[100],"tests":[101],"with":[102],"simulated":[103],"real":[105],"data,":[106],"compares":[107],"favourably":[108],"against":[109],"currently":[111],"most":[112],"popular":[113],"alternative.":[114],"AVAILABILITY":[115],"AND":[116],"IMPLEMENTATION:":[117],"baerhunter":[119],"R":[120],"package":[121],"available":[123,131],"from:":[124],"https://github.com/irilenia/baerhunter.":[125],"SUPPLEMENTARY":[126],"INFORMATION:":[127],"Supplementary":[128],"are":[130],"at":[132],"Bioinformatics":[133],"online.":[134]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2019-08-22T00:00:00"}
