{"id":"https://openalex.org/W2170276833","doi":"https://doi.org/10.1093/bioinformatics/btv187","title":"DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data","display_name":"DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data","publication_year":2015,"publication_date":"2015-04-02","ids":{"openalex":"https://openalex.org/W2170276833","doi":"https://doi.org/10.1093/bioinformatics/btv187","mag":"2170276833","pmid":"https://pubmed.ncbi.nlm.nih.gov/25840043"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv187","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv187","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/15/2568/50307039/bioinformatics_31_15_2568.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/31/15/2568/50307039/bioinformatics_31_15_2568.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103034989","display_name":"Shahar Alon","orcid":"https://orcid.org/0000-0002-7458-3478"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shahar Alon","raw_affiliation_strings":["1 Department of Neurobiology, George S. Wise Faculty of Life Sciences,","2 Sagol School of Neuroscience and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Neurobiology, George S. Wise Faculty of Life Sciences,","institution_ids":[]},{"raw_affiliation_string":"2 Sagol School of Neuroscience and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110275769","display_name":"Muhammad Erew","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Muhammad Erew","raw_affiliation_strings":["3 Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084507913","display_name":"Eli Eisenberg","orcid":"https://orcid.org/0000-0001-8681-3202"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Eli Eisenberg","raw_affiliation_strings":["2 Sagol School of Neuroscience and","3 Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Sagol School of Neuroscience and","institution_ids":[]},{"raw_affiliation_string":"3 Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5084507913"],"corresponding_institution_ids":["https://openalex.org/I16391192"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8069,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.85244169,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"31","issue":"15","first_page":"2568","last_page":"2570"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12610","display_name":"RNA regulation and disease","score":1.0,"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/T12610","display_name":"RNA regulation and disease","score":1.0,"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":0.9994000196456909,"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":0.9993000030517578,"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/deep-sequencing","display_name":"Deep sequencing","score":0.6240537166595459},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.585134744644165},{"id":"https://openalex.org/keywords/dream","display_name":"Dream","score":0.5315111875534058},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5255095958709717},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.520301878452301},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4887406826019287},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3966614305973053},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.32646286487579346},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2735135853290558},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14004841446876526},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.1302143633365631},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.08461984992027283}],"concepts":[{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.6240537166595459},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.585134744644165},{"id":"https://openalex.org/C2781095916","wikidata":"https://www.wikidata.org/wiki/Q36348","display_name":"Dream","level":2,"score":0.5315111875534058},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5255095958709717},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.520301878452301},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4887406826019287},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3966614305973053},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.32646286487579346},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2735135853290558},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14004841446876526},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.1302143633365631},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.08461984992027283},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","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":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv187","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv187","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/15/2568/50307039/bioinformatics_31_15_2568.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:25840043","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25840043","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:open-archive.highwire.org:bioinfo:31/15/2568","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/15/2568","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv187","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv187","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/15/2568/50307039/bioinformatics_31_15_2568.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":[],"funders":[{"id":"https://openalex.org/F4320306555","display_name":"Wisconsin Alumni Research Foundation","ror":"https://ror.org/00hwxbz16"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W146960052","https://openalex.org/W1968302884","https://openalex.org/W1970703807","https://openalex.org/W2017426710","https://openalex.org/W2022192230","https://openalex.org/W2056573404","https://openalex.org/W2092030071","https://openalex.org/W2114012664","https://openalex.org/W2115221577","https://openalex.org/W2119480083","https://openalex.org/W2124985265","https://openalex.org/W2138501360","https://openalex.org/W2154349943","https://openalex.org/W2156089250","https://openalex.org/W2158148192","https://openalex.org/W2162277004","https://openalex.org/W2413556790"],"related_works":["https://openalex.org/W1762480892","https://openalex.org/W597599663","https://openalex.org/W3194824274","https://openalex.org/W4205387075","https://openalex.org/W1537165133","https://openalex.org/W2390579330","https://openalex.org/W1578892932","https://openalex.org/W2387132837","https://openalex.org/W2316163406","https://openalex.org/W2369963050"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"DREAM:":[2],"detecting":[3],"RNA":[4],"editing":[5,18,49,76],"associated":[6],"with":[7,65],"microRNAs,":[8],"is":[9,61,83],"a":[10,62],"webserver":[11],"for":[12,47],"the":[13,33,38,44,53,57,66,69,74,87],"identification":[14],"of":[15,56,72],"mature":[16],"microRNA":[17,25],"events":[19],"using":[20],"deep":[21],"sequencing":[22,26],"data.":[23],"Raw":[24],"reads":[27,34],"can":[28],"be":[29],"provided":[30],"as":[31],"input,":[32],"are":[35],"aligned":[36],"against":[37],"genome":[39],"and":[40,51,68,80],"custom":[41],"scripts":[42],"process":[43],"data,":[45],"search":[46],"potential":[48],"sites":[50,77],"assess":[52],"statistical":[54,70],"significance":[55],"findings.":[58],"The":[59],"output":[60],"text":[63],"file":[64],"location":[67],"description":[71],"all":[73],"putative":[75],"detected.":[78],"Availability":[79],"implementation:":[81],"DREAM":[82],"freely":[84],"available":[85],"on":[86],"web":[88],"at":[89],"http://www.cs.tau.ac.il/\u223cmirnaed/.":[90],"Contact:":[91],"elieis@post.tau.ac.il":[92]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
