{"id":"https://openalex.org/W2789640198","doi":"https://doi.org/10.1093/bioinformatics/bty161","title":"SCRAM: a pipeline for fast index-free small RNA read alignment and visualization","display_name":"SCRAM: a pipeline for fast index-free small RNA read alignment and visualization","publication_year":2018,"publication_date":"2018-03-15","ids":{"openalex":"https://openalex.org/W2789640198","doi":"https://doi.org/10.1093/bioinformatics/bty161","mag":"2789640198","pmid":"https://pubmed.ncbi.nlm.nih.gov/29554210"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty161","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty161","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2670/25230812/bty161.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/34/15/2670/25230812/bty161.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048607207","display_name":"Stephen J. Fletcher","orcid":"https://orcid.org/0000-0002-7905-9325"},"institutions":[{"id":"https://openalex.org/I4210138055","display_name":"Agriculture and Food","ror":"https://ror.org/03n17ds51","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I4210138055","https://openalex.org/I4387156119"]},{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I4210155873","display_name":"ARC Centre of Excellence for Plant Success in Nature and Agriculture","ror":"https://ror.org/058xdtn86","country_code":"AU","type":"facility","lineage":["https://openalex.org/I129801699","https://openalex.org/I1337719021","https://openalex.org/I160993911","https://openalex.org/I165143802","https://openalex.org/I2801453606","https://openalex.org/I4210132349","https://openalex.org/I4210155873","https://openalex.org/I56590836","https://openalex.org/I63525965"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Stephen J Fletcher","raw_affiliation_strings":["Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD, Australia","School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia"],"affiliations":[{"raw_affiliation_string":"Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD, Australia","institution_ids":["https://openalex.org/I4210155873","https://openalex.org/I4210138055"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045279138","display_name":"Mikael Bod\u00e9n","orcid":"https://orcid.org/0000-0003-3548-268X"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Mikael Boden","raw_affiliation_strings":["School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia"],"affiliations":[{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086257407","display_name":"Neena Mitter","orcid":"https://orcid.org/0000-0001-6146-6179"},"institutions":[{"id":"https://openalex.org/I4210155873","display_name":"ARC Centre of Excellence for Plant Success in Nature and Agriculture","ror":"https://ror.org/058xdtn86","country_code":"AU","type":"facility","lineage":["https://openalex.org/I129801699","https://openalex.org/I1337719021","https://openalex.org/I160993911","https://openalex.org/I165143802","https://openalex.org/I2801453606","https://openalex.org/I4210132349","https://openalex.org/I4210155873","https://openalex.org/I56590836","https://openalex.org/I63525965"]},{"id":"https://openalex.org/I4210138055","display_name":"Agriculture and Food","ror":"https://ror.org/03n17ds51","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I4210138055","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Neena Mitter","raw_affiliation_strings":["Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD, Australia"],"affiliations":[{"raw_affiliation_string":"Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD, Australia","institution_ids":["https://openalex.org/I4210155873","https://openalex.org/I4210138055"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012154899","display_name":"Bernard J. Carroll","orcid":"https://orcid.org/0000-0002-1976-8269"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Bernard J Carroll","raw_affiliation_strings":["School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia"],"affiliations":[{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5048607207"],"corresponding_institution_ids":["https://openalex.org/I165143802","https://openalex.org/I4210138055","https://openalex.org/I4210155873"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6515,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.67530911,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"15","first_page":"2670","last_page":"2672"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9984999895095825,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9979000091552734,"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/mit-license","display_name":"MIT License","score":0.927822470664978},{"id":"https://openalex.org/keywords/scram","display_name":"Scram","score":0.8622039556503296},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7258168458938599},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6863977313041687},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6596950888633728},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6158076524734497},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6081064343452454},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5497716069221497},{"id":"https://openalex.org/keywords/tracing","display_name":"Tracing","score":0.44558727741241455},{"id":"https://openalex.org/keywords/petroleum-seep","display_name":"Petroleum seep","score":0.42158716917037964},{"id":"https://openalex.org/keywords/small-rna","display_name":"Small RNA","score":0.41512250900268555},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3966849446296692},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32791393995285034},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.28653019666671753},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.27740511298179626},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.2589036226272583},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2127530872821808},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14614209532737732},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09529617428779602}],"concepts":[{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.927822470664978},{"id":"https://openalex.org/C124184767","wikidata":"https://www.wikidata.org/wiki/Q1591311","display_name":"Scram","level":2,"score":0.8622039556503296},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7258168458938599},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6863977313041687},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6596950888633728},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6158076524734497},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6081064343452454},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5497716069221497},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.44558727741241455},{"id":"https://openalex.org/C60554856","wikidata":"https://www.wikidata.org/wiki/Q17163370","display_name":"Petroleum seep","level":3,"score":0.42158716917037964},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.41512250900268555},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3966849446296692},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32791393995285034},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.28653019666671753},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.27740511298179626},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.2589036226272583},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2127530872821808},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14614209532737732},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09529617428779602},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C116915560","wikidata":"https://www.wikidata.org/wiki/Q83504","display_name":"Nuclear engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C516920438","wikidata":"https://www.wikidata.org/wiki/Q37129","display_name":"Methane","level":2,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty161","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty161","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2670/25230812/bty161.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:29554210","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29554210","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:espace.library.uq.edu.au:UQ:723929","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty161","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty161","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2670/25230812/bty161.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":[{"score":0.4300000071525574,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G271991197","display_name":null,"funder_award_id":"DP120103966","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G8127709009","display_name":null,"funder_award_id":"DP0988294","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G8188237028","display_name":null,"funder_award_id":"DP150104048","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2789640198.pdf","grobid_xml":"https://content.openalex.org/works/W2789640198.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2081747395","https://openalex.org/W2103441770","https://openalex.org/W2124985265","https://openalex.org/W2137988707","https://openalex.org/W2169456326","https://openalex.org/W2195136000","https://openalex.org/W2472783066","https://openalex.org/W2517997054","https://openalex.org/W2568602300","https://openalex.org/W2755021795"],"related_works":["https://openalex.org/W2789640198","https://openalex.org/W4309247532","https://openalex.org/W3096946169","https://openalex.org/W2113128227","https://openalex.org/W2144610372","https://openalex.org/W4312114021","https://openalex.org/W2121840477","https://openalex.org/W4311938462","https://openalex.org/W2515936044","https://openalex.org/W3123068371"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
