{"id":"https://openalex.org/W2109525082","doi":"https://doi.org/10.1093/bioinformatics/btu380","title":"miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data","display_name":"miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data","publication_year":2014,"publication_date":"2014-06-14","ids":{"openalex":"https://openalex.org/W2109525082","doi":"https://doi.org/10.1093/bioinformatics/btu380","mag":"2109525082","pmid":"https://pubmed.ncbi.nlm.nih.gov/24930140"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu380","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/19/2837/49872374/bioinformatics_30_19_2837.pdf","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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/19/2837/49872374/bioinformatics_30_19_2837.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074646713","display_name":"Jikai Lei","orcid":"https://orcid.org/0000-0002-6081-2276"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jikai Lei","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA","Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824 USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824 USA#TAB#","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081855118","display_name":"Yanni Sun","orcid":"https://orcid.org/0000-0003-1373-8023"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanni Sun","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA","Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824 USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824 USA#TAB#","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074646713"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.4224,"has_fulltext":true,"cited_by_count":122,"citation_normalized_percentile":{"value":0.9324466,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"30","issue":"19","first_page":"2837","last_page":"2839"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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":0.9990000128746033,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9976999759674072,"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/T11482","display_name":"RNA modifications and cancer","score":0.9976999759674072,"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/microrna","display_name":"microRNA","score":0.7157989740371704},{"id":"https://openalex.org/keywords/small-rna","display_name":"Small RNA","score":0.6525746583938599},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5691930651664734},{"id":"https://openalex.org/keywords/memory-footprint","display_name":"Memory footprint","score":0.5544494986534119},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.537788450717926},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4969163239002228},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45877987146377563},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4584609270095825},{"id":"https://openalex.org/keywords/footprint","display_name":"Footprint","score":0.42740070819854736},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3850076496601105},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2805149555206299},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22115087509155273},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1331106424331665},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1147909164428711},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.10731571912765503},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09965837001800537}],"concepts":[{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.7157989740371704},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.6525746583938599},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5691930651664734},{"id":"https://openalex.org/C74912251","wikidata":"https://www.wikidata.org/wiki/Q6815727","display_name":"Memory footprint","level":2,"score":0.5544494986534119},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.537788450717926},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4969163239002228},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45877987146377563},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4584609270095825},{"id":"https://openalex.org/C132943942","wikidata":"https://www.wikidata.org/wiki/Q2562511","display_name":"Footprint","level":2,"score":0.42740070819854736},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3850076496601105},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2805149555206299},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22115087509155273},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1331106424331665},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1147909164428711},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.10731571912765503},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09965837001800537},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","qualifier_ui":null,"qualifier_name":null,"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":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu380","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/19/2837/49872374/bioinformatics_30_19_2837.pdf","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:24930140","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24930140","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:CiteSeerX.psu:10.1.1.975.105","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.975.105","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2014/06/14/bioinformatics.btu380.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu380","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/19/2837/49872374/bioinformatics_30_19_2837.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1171700966","display_name":null,"funder_award_id":"NSF CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G333296853","display_name":"CAREER:   New Technologies for Genome-Scale Comparative NcRNA Identification","funder_award_id":"0953738","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4624658857","display_name":"IPGA:  Developing an Effective, Portable Annotation Engine for Plant Genomes","funder_award_id":"1126998","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7826289663","display_name":null,"funder_award_id":"DBI-0953738","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/F4320337399","display_name":"Division of Integrative Organismal Systems","ror":"https://ror.org/01rvays47"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109525082.pdf","grobid_xml":"https://content.openalex.org/works/W2109525082.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2014208702","https://openalex.org/W2017426710","https://openalex.org/W2052785172","https://openalex.org/W2055894735","https://openalex.org/W2081747395","https://openalex.org/W2086561953","https://openalex.org/W2112810020","https://openalex.org/W2121673931","https://openalex.org/W2130305733","https://openalex.org/W2130386995","https://openalex.org/W2145251517","https://openalex.org/W2151883199","https://openalex.org/W2155340974"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W3137434606","https://openalex.org/W4372263373"],"abstract_inverted_index":{"https://github.com/hangelwen/miR-PREFeR":[0]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":14},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}