{"id":"https://openalex.org/W3209266852","doi":"https://doi.org/10.1093/bib/bbab448","title":"miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms","display_name":"miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms","publication_year":2021,"publication_date":"2021-09-30","ids":{"openalex":"https://openalex.org/W3209266852","doi":"https://doi.org/10.1093/bib/bbab448","mag":"3209266852","pmid":"https://pubmed.ncbi.nlm.nih.gov/34734232"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab448","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab448","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/A5031636481","display_name":"Hukam C. Rawal","orcid":"https://orcid.org/0000-0002-2727-9721"},"institutions":[{"id":"https://openalex.org/I19716509","display_name":"Jamia Hamdard","ror":"https://ror.org/03dwxvb85","country_code":"IN","type":"education","lineage":["https://openalex.org/I19716509"]},{"id":"https://openalex.org/I4210091233","display_name":"National Research Centre on Plant Biotechnology","ror":"https://ror.org/00cq3cz72","country_code":"IN","type":"facility","lineage":["https://openalex.org/I179420787","https://openalex.org/I4210091233"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Hukam Chand Rawal","raw_affiliation_strings":["ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India","School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India","institution_ids":["https://openalex.org/I4210091233"]},{"raw_affiliation_string":"School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India","institution_ids":["https://openalex.org/I19716509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071106092","display_name":"Shakir Ali","orcid":"https://orcid.org/0000-0002-4002-1231"},"institutions":[{"id":"https://openalex.org/I19716509","display_name":"Jamia Hamdard","ror":"https://ror.org/03dwxvb85","country_code":"IN","type":"education","lineage":["https://openalex.org/I19716509"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Shakir Ali","raw_affiliation_strings":["Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India","School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India","institution_ids":["https://openalex.org/I19716509"]},{"raw_affiliation_string":"School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India","institution_ids":["https://openalex.org/I19716509"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101897175","display_name":"Tapan Kumar Mondal","orcid":"https://orcid.org/0000-0001-6702-2990"},"institutions":[{"id":"https://openalex.org/I4210091233","display_name":"National Research Centre on Plant Biotechnology","ror":"https://ror.org/00cq3cz72","country_code":"IN","type":"facility","lineage":["https://openalex.org/I179420787","https://openalex.org/I4210091233"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Tapan Kumar Mondal","raw_affiliation_strings":["ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India"],"raw_orcid":"https://orcid.org/0000-0001-6702-2990","affiliations":[{"raw_affiliation_string":"ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India","institution_ids":["https://openalex.org/I4210091233"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101897175"],"corresponding_institution_ids":["https://openalex.org/I4210091233"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.2442,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.53790069,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"23","issue":"1","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":0.9975000023841858,"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":0.9975000023841858,"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":0.9973999857902527,"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"}},{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9966999888420105,"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/computational-biology","display_name":"Computational biology","score":0.6772687435150146},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.6651713848114014},{"id":"https://openalex.org/keywords/transfer-rna","display_name":"Transfer RNA","score":0.6151876449584961},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5943257212638855},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5454226136207581},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.5338422060012817},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.49113819003105164},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.48895394802093506},{"id":"https://openalex.org/keywords/small-rna","display_name":"Small RNA","score":0.4615708589553833},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.41724783182144165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4122348129749298},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2761526107788086},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24248036742210388},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.10241580009460449}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6772687435150146},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.6651713848114014},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.6151876449584961},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5943257212638855},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5454226136207581},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.5338422060012817},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.49113819003105164},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48895394802093506},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.4615708589553833},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.41724783182144165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4122348129749298},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2761526107788086},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24248036742210388},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.10241580009460449}],"mesh":[{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"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":2,"locations":[{"id":"doi:10.1093/bib/bbab448","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab448","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34734232","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34734232","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6200000047683716}],"awards":[{"id":"https://openalex.org/G2248577509","display_name":null,"funder_award_id":"BT/PR15619/AGIII/103/908/2015","funder_id":"https://openalex.org/F4320326656","funder_display_name":"Department of Biotechnology, Government of West Bengal"}],"funders":[{"id":"https://openalex.org/F4320326656","display_name":"Department of Biotechnology, Government of West Bengal","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1834932356","https://openalex.org/W1872030955","https://openalex.org/W1973408460","https://openalex.org/W1993165035","https://openalex.org/W2023529076","https://openalex.org/W2041453482","https://openalex.org/W2061513073","https://openalex.org/W2064557873","https://openalex.org/W2075716141","https://openalex.org/W2106039274","https://openalex.org/W2109525082","https://openalex.org/W2112192177","https://openalex.org/W2117147211","https://openalex.org/W2133613866","https://openalex.org/W2138098955","https://openalex.org/W2141384633","https://openalex.org/W2141707748","https://openalex.org/W2142214917","https://openalex.org/W2148224382","https://openalex.org/W2150722419","https://openalex.org/W2162391016","https://openalex.org/W2164256634","https://openalex.org/W2164419864","https://openalex.org/W2303912045","https://openalex.org/W2535820597","https://openalex.org/W2673248014","https://openalex.org/W2729766313","https://openalex.org/W2760037733","https://openalex.org/W2781763576","https://openalex.org/W2800206218","https://openalex.org/W2805169593","https://openalex.org/W2810144884","https://openalex.org/W2889417790","https://openalex.org/W2890298272","https://openalex.org/W2897185013","https://openalex.org/W2898440040","https://openalex.org/W2903837224","https://openalex.org/W2911703482","https://openalex.org/W2923758651","https://openalex.org/W2949470979","https://openalex.org/W2998924785","https://openalex.org/W3015986655","https://openalex.org/W3091970126","https://openalex.org/W3112059664","https://openalex.org/W3115442532","https://openalex.org/W3116325393","https://openalex.org/W3139106730"],"related_works":["https://openalex.org/W4223896405","https://openalex.org/W2059629050","https://openalex.org/W2074740504","https://openalex.org/W3013644380","https://openalex.org/W1996935079","https://openalex.org/W3210243923","https://openalex.org/W2145833061","https://openalex.org/W2258998699","https://openalex.org/W1998405066","https://openalex.org/W2171737904"],"abstract_inverted_index":{"In":[0],"recent":[1],"years,":[2],"microRNAs":[3],"(miRNAs)":[4],"and":[5,19,42,50,85,117,127,178,220,233,239],"tRNA-derived":[6],"RNA":[7,54,193],"fragments":[8],"(tRFs)":[9],"have":[10,162,182],"been":[11],"reported":[12],"extensively":[13],"following":[14],"different":[15,211],"approaches":[16,25,176],"of":[17,40,63,66,98,139,148,159,168,187,226],"identification":[18,39],"analysis.":[20],"Comprehensively":[21],"analyzing":[22,149],"the":[23,28,38,61,150,174,190,196,224],"present":[24],"to":[26,206,210,216],"overcome":[27],"existing":[29],"variations,":[30],"we":[31,161,181],"developed":[32],"a":[33,107,112,156,227],"benchmarking":[34],"methodology":[35,229],"each":[36],"for":[37,70,115,230,237],"miRNAs":[41,126,145,169],"tRFs,":[43],"termed":[44],"as":[45,111,171],"miRNA":[46,87,231],"Prediction":[47,55],"Methodology":[48,56],"(miRPreM)":[49],"tRNA-induced":[51],"small":[52,192],"non-coding":[53],"(tiRPreM),":[57],"respectively.":[58],"We":[59,133],"emphasized":[60],"use":[62],"respective":[64,153],"genome":[65,123],"organism":[67],"under":[68],"study":[69,114],"mapping":[71],"reads,":[72],"sample":[73],"data":[74,151],"with":[75,93,152,173,179],"at":[76],"least":[77],"two":[78,90],"biological":[79],"replicates,":[80],"normalized":[81],"read":[82],"count":[83],"support":[84,147],"novel":[86],"prediction":[88,232],"by":[89,103],"standard":[91,202],"tools":[92],"multiple":[94],"runs.":[95],"The":[96],"performance":[97],"these":[99,143],"methodologies":[100,197],"was":[101],"evaluated":[102],"using":[104],"Oryza":[105],"coarctata,":[106],"wild":[108],"rice":[109],"species":[110],"case":[113],"model":[116,238],"non-model":[118,240],"organisms.":[119,241],"With":[120],"organism-specific":[121],"reference":[122],"approach,":[124],"98":[125],"60":[128],"tRFs":[129,188],"were":[130],"exclusively":[131],"found.":[132],"observed":[134],"high":[135],"accuracy":[136],"(13":[137],"out":[138],"15)":[140],"when":[141],"tested":[142],"genome-specific":[144],"in":[146,201,204],"organism.":[154],"Such":[155],"strong":[157],"impact":[158],"miRPreM,":[160],"predicted":[163,183],"more":[164],"than":[165,214],"double":[166],"number":[167],"(186)":[170],"compared":[172],"traditional":[175],"(79)":[177],"tiRPreM,":[180],"all":[184],"known":[185],"classes":[186],"within":[189],"same":[191],"data.":[194],"Moreover,":[195],"presented":[198],"here":[199],"are":[200],"form":[203],"order":[205],"extend":[207],"its":[208],"applicability":[209],"organisms":[212],"rather":[213],"restricting":[215],"plants.":[217],"Hence,":[218],"miRPreM":[219],"tiRPreM":[221],"can":[222],"fulfill":[223],"need":[225],"comprehensive":[228],"tRF":[234],"identification,":[235],"respectively,":[236]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}