{"id":"https://openalex.org/W2160828096","doi":"https://doi.org/10.1093/bioinformatics/btr016","title":"A <i>k</i>-mer scheme to predict piRNAs and characterize locust piRNAs","display_name":"A <i>k</i>-mer scheme to predict piRNAs and characterize locust piRNAs","publication_year":2011,"publication_date":"2011-01-11","ids":{"openalex":"https://openalex.org/W2160828096","doi":"https://doi.org/10.1093/bioinformatics/btr016","mag":"2160828096","pmid":"https://pubmed.ncbi.nlm.nih.gov/21224287"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr016","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/6/771/48867793/bioinformatics_27_6_771.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/6/771/48867793/bioinformatics_27_6_771.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047429064","display_name":"Yi Zhang","orcid":"https://orcid.org/0000-0002-4057-678X"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I34155123","display_name":"Hebei University of Science and Technology","ror":"https://ror.org/05h3pkk68","country_code":"CN","type":"education","lineage":["https://openalex.org/I34155123"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Zhang","raw_affiliation_strings":["1 State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 and 2Department of Mathematics, Hebei University of Science and Technology/Hebei Laboratory of Pharmaceutic Molecular Chemistry, Shijiazhuang, Hebei 050018, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 and 2Department of Mathematics, Hebei University of Science and Technology/Hebei Laboratory of Pharmaceutic Molecular Chemistry, Shijiazhuang, Hebei 050018, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I34155123"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100601692","display_name":"Xianhui Wang","orcid":"https://orcid.org/0000-0002-8732-829X"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I34155123","display_name":"Hebei University of Science and Technology","ror":"https://ror.org/05h3pkk68","country_code":"CN","type":"education","lineage":["https://openalex.org/I34155123"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xianhui Wang","raw_affiliation_strings":["1 State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 and 2Department of Mathematics, Hebei University of Science and Technology/Hebei Laboratory of Pharmaceutic Molecular Chemistry, Shijiazhuang, Hebei 050018, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 and 2Department of Mathematics, Hebei University of Science and Technology/Hebei Laboratory of Pharmaceutic Molecular Chemistry, Shijiazhuang, Hebei 050018, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I34155123"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049091907","display_name":"Le Kang","orcid":"https://orcid.org/0000-0003-4262-2329"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I34155123","display_name":"Hebei University of Science and Technology","ror":"https://ror.org/05h3pkk68","country_code":"CN","type":"education","lineage":["https://openalex.org/I34155123"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Le Kang","raw_affiliation_strings":["1 State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 and 2Department of Mathematics, Hebei University of Science and Technology/Hebei Laboratory of Pharmaceutic Molecular Chemistry, Shijiazhuang, Hebei 050018, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 and 2Department of Mathematics, Hebei University of Science and Technology/Hebei Laboratory of Pharmaceutic Molecular Chemistry, Shijiazhuang, Hebei 050018, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I34155123"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5049091907"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I34155123"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.1688,"has_fulltext":false,"cited_by_count":181,"citation_normalized_percentile":{"value":0.96788316,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"27","issue":"6","first_page":"771","last_page":"776"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9402999877929688,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9402999877929688,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.010700000450015068,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.00570000009611249,"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/piwi-interacting-rna","display_name":"Piwi-interacting RNA","score":0.933150053024292},{"id":"https://openalex.org/keywords/locust","display_name":"Locust","score":0.7652369737625122},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.6407052278518677},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5395327210426331},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5090193748474121},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46527621150016785},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38463515043258667},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3625975251197815},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1473374366760254},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.11384254693984985}],"concepts":[{"id":"https://openalex.org/C147724379","wikidata":"https://www.wikidata.org/wiki/Q2367421","display_name":"Piwi-interacting RNA","level":5,"score":0.933150053024292},{"id":"https://openalex.org/C2776041477","wikidata":"https://www.wikidata.org/wiki/Q83931","display_name":"Locust","level":2,"score":0.7652369737625122},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.6407052278518677},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5395327210426331},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5090193748474121},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46527621150016785},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38463515043258667},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3625975251197815},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1473374366760254},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.11384254693984985}],"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006110","descriptor_name":"Grasshoppers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006110","descriptor_name":"Grasshoppers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006110","descriptor_name":"Grasshoppers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D018626","descriptor_name":"Retroelements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":null,"qualifier_name":null,"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":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btr016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr016","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/6/771/48867793/bioinformatics_27_6_771.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21224287","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21224287","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:3051322","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3051322","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr016","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/6/771/48867793/bioinformatics_27_6_771.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6499999761581421,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160828096.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1970769181","https://openalex.org/W1976342457","https://openalex.org/W1976608804","https://openalex.org/W1977733607","https://openalex.org/W1993293753","https://openalex.org/W1999901063","https://openalex.org/W2001619934","https://openalex.org/W2009644747","https://openalex.org/W2011832929","https://openalex.org/W2012453729","https://openalex.org/W2020441317","https://openalex.org/W2029695210","https://openalex.org/W2035930185","https://openalex.org/W2047988520","https://openalex.org/W2048721314","https://openalex.org/W2054630546","https://openalex.org/W2087163851","https://openalex.org/W2101952636","https://openalex.org/W2103012554","https://openalex.org/W2111217101","https://openalex.org/W2120081922","https://openalex.org/W2121350246","https://openalex.org/W2122000580","https://openalex.org/W2127861583","https://openalex.org/W2132102978","https://openalex.org/W2138910750","https://openalex.org/W2141402301","https://openalex.org/W2169271641","https://openalex.org/W2171572477","https://openalex.org/W2172182636","https://openalex.org/W6657618476"],"related_works":["https://openalex.org/W2015402753","https://openalex.org/W2322107403","https://openalex.org/W2943992342","https://openalex.org/W4254016008","https://openalex.org/W1976342457","https://openalex.org/W3203020171","https://openalex.org/W1511345757","https://openalex.org/W2544598565","https://openalex.org/W2053969879","https://openalex.org/W3007386857"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identifying":[1],"piwi-interacting":[2],"RNAs":[3],"(piRNAs)":[4],"of":[5,50,84,90,115,131,138,162,171,184],"non-model":[6,185],"organisms":[7,186],"is":[8,34,96],"a":[9,31,82,88],"difficult":[10],"and":[11,21,47,60,87,93,136,150,164,199],"unsolved":[12],"problem":[13],"because":[14],"piRNAs":[15,114,130,163,183],"lack":[16],"conservative":[17],"secondary":[18],"structure":[19],"motifs":[20],"sequence":[22],"homology":[23],"in":[24,101,168],"different":[25],"species.":[26,103],"RESULTS:":[27],"In":[28],"this":[29],"article,":[30],"k-mer":[32],"scheme":[33,67],"proposed":[35],"to":[36,112,181,206],"identify":[37,113,182],"piRNA":[38,48],"sequences,":[39],"relying":[40],"on":[41,69,120],"the":[42,64,70,94,110,116,132,158,166,169,174,197,200,207],"training":[43],"sets":[44],"from":[45],"non-piRNA":[46],"sequences":[49],"five":[51],"model":[52],"species":[53],"sequenced:":[54],"rat,":[55],"mouse,":[56],"human,":[57],"fruit":[58],"fly":[59],"nematode.":[61],"Compared":[62],"with":[63,81,141],"existing":[65,142],"'static'":[66],"based":[68,119],"position-specific":[71,159],"base":[72,160],"usage,":[73],"our":[74],"novel":[75],"'dynamic'":[76],"algorithm":[77,111,198],"performs":[78],"much":[79],"better":[80],"precision":[83,95],"over":[85,91],"90%":[86],"sensitivity":[89],"60%,":[92],"verified":[97],"by":[98],"5-fold":[99],"cross-validation":[100],"these":[102],"To":[104],"test":[105],"its":[106],"validity,":[107],"we":[108,176],"use":[109],"migratory":[117],"locust":[118,133,143],"603":[121],"607":[122],"deep-sequenced":[123],"small":[124],"RNA":[125],"sequences.":[126,190],"Totally,":[127],"87":[128],"536":[129],"are":[134,203],"predicted,":[135],"4426":[137],"them":[139],"matched":[140],"transposons.":[144],"The":[145,192],"transcriptional":[146],"difference":[147],"between":[148],"solitary":[149],"gregarious":[151],"locusts":[152],"was":[153],"described.":[154],"We":[155],"also":[156],"revisit":[157],"usage":[161],"find":[165],"conservation":[167],"end":[170],"piRNAs.":[172],"Therefore,":[173],"method":[175],"developed":[177],"can":[178],"be":[179],"used":[180],"without":[187],"complete":[188],"genome":[189],"AVAILABILITY:":[191],"web":[193],"server":[194],"for":[195],"implementing":[196],"software":[201],"code":[202],"freely":[204],"available":[205],"academic":[208],"community":[209],"at":[210],"http://59.79.168.90/piRNA/index.php.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":58},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2016-06-24T00:00:00"}
