{"id":"https://openalex.org/W2889417790","doi":"https://doi.org/10.1186/s12859-018-2287-y","title":"miRge 2.0 for comprehensive analysis of microRNA sequencing data","display_name":"miRge 2.0 for comprehensive analysis of microRNA sequencing data","publication_year":2018,"publication_date":"2018-07-23","ids":{"openalex":"https://openalex.org/W2889417790","doi":"https://doi.org/10.1186/s12859-018-2287-y","mag":"2889417790","pmid":"https://pubmed.ncbi.nlm.nih.gov/30153801"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2287-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2287-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2287-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2287-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101707918","display_name":"Yin Lu","orcid":"https://orcid.org/0000-0003-0633-7715"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yin Lu","raw_affiliation_strings":["Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062308537","display_name":"Alexander S. Baras","orcid":"https://orcid.org/0000-0003-2397-3342"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander S. Baras","raw_affiliation_strings":["Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010903919","display_name":"Marc K. Halushka","orcid":"https://orcid.org/0000-0002-7112-7389"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marc K. Halushka","raw_affiliation_strings":["Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA. mhalush1@jhmi.edu","Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA. mhalush1@jhmi.edu","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]},{"raw_affiliation_string":"Department of Pathology, Johns Hopkins University SOM, 720 Rutland Avenue/Ross Bldg. Rm 632B, Baltimore, MD, 21205, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101707918"],"corresponding_institution_ids":["https://openalex.org/I145311948"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.3403,"has_fulltext":true,"cited_by_count":82,"citation_normalized_percentile":{"value":0.93437226,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"19","issue":"1","first_page":"275","last_page":"275"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":1.0,"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":0.9998000264167786,"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":0.9994999766349792,"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/mirbase","display_name":"MiRBase","score":0.96195387840271},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.6646591424942017},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6382149457931519},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47433653473854065},{"id":"https://openalex.org/keywords/small-rna","display_name":"Small RNA","score":0.45781391859054565},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42841392755508423},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3030090630054474},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2040310502052307}],"concepts":[{"id":"https://openalex.org/C49305753","wikidata":"https://www.wikidata.org/wiki/Q6826947","display_name":"MiRBase","level":4,"score":0.96195387840271},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.6646591424942017},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6382149457931519},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47433653473854065},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.45781391859054565},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42841392755508423},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3030090630054474},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2040310502052307}],"mesh":[{"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":"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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"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":"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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"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":4,"locations":[{"id":"doi:10.1186/s12859-018-2287-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2287-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2287-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30153801","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30153801","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d0d41883240f490e812437654ccb782a","is_oa":true,"landing_page_url":"https://doaj.org/article/d0d41883240f490e812437654ccb782a","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-12 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5072980","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6112139","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2287-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2287-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2287-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.5699999928474426}],"awards":[{"id":"https://openalex.org/G2208326176","display_name":null,"funder_award_id":"1R01HL137811","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4525717195","display_name":null,"funder_award_id":"R01HL137811","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7727173809","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"},{"id":"https://openalex.org/G8156133396","display_name":null,"funder_award_id":"17GRNT33670405","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"},{"id":"https://openalex.org/G8898488596","display_name":null,"funder_award_id":"1R01HL137811","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320306230","display_name":"American Heart Association","ror":"https://ror.org/013kjyp64"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2889417790.pdf","grobid_xml":"https://content.openalex.org/works/W2889417790.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1486010693","https://openalex.org/W1493357981","https://openalex.org/W1968008181","https://openalex.org/W1976612131","https://openalex.org/W1984397688","https://openalex.org/W2009658305","https://openalex.org/W2015858554","https://openalex.org/W2022326327","https://openalex.org/W2026570544","https://openalex.org/W2032164130","https://openalex.org/W2036897871","https://openalex.org/W2077327925","https://openalex.org/W2086338797","https://openalex.org/W2086561953","https://openalex.org/W2089055162","https://openalex.org/W2090047954","https://openalex.org/W2099935683","https://openalex.org/W2108234281","https://openalex.org/W2109923675","https://openalex.org/W2112810020","https://openalex.org/W2115221577","https://openalex.org/W2119480083","https://openalex.org/W2124985265","https://openalex.org/W2130305733","https://openalex.org/W2130979840","https://openalex.org/W2142574304","https://openalex.org/W2146127418","https://openalex.org/W2149156028","https://openalex.org/W2150005295","https://openalex.org/W2162277004","https://openalex.org/W2164286670","https://openalex.org/W2170952313","https://openalex.org/W2180405650","https://openalex.org/W2185215643","https://openalex.org/W2523422689","https://openalex.org/W2558411436","https://openalex.org/W2588840062","https://openalex.org/W2606516787","https://openalex.org/W2783803296","https://openalex.org/W2794599452","https://openalex.org/W2951861059","https://openalex.org/W3105238694","https://openalex.org/W4237011200","https://openalex.org/W4239510810","https://openalex.org/W7075633510"],"related_works":["https://openalex.org/W2312637459","https://openalex.org/W2088415316","https://openalex.org/W2009658305","https://openalex.org/W2321938318","https://openalex.org/W2323693199","https://openalex.org/W2144674491","https://openalex.org/W3208144136","https://openalex.org/W2144704816","https://openalex.org/W2495804742","https://openalex.org/W2081819799"],"abstract_inverted_index":{"miRge":[0,15],"2.0":[1,16],"is":[2,17],"a":[3],"redesigned,":[4],"leading":[5],"miRNA":[6],"RNA-seq":[7],"aligner":[8],"with":[9],"several":[10],"improvements":[11],"and":[12],"novel":[13],"utilities.":[14],"freely":[18],"available":[19],"at:":[20],"https://github.com/mhalushka/miRge":[21],".":[22]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":23},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":2}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}