{"id":"https://openalex.org/W3138392738","doi":"https://doi.org/10.1093/bioinformatics/btab171","title":"<i>Ribo-ODDR</i> : oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq","display_name":"<i>Ribo-ODDR</i> : oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq","publication_year":2021,"publication_date":"2021-03-10","ids":{"openalex":"https://openalex.org/W3138392738","doi":"https://doi.org/10.1093/bioinformatics/btab171","mag":"3138392738","pmid":"https://pubmed.ncbi.nlm.nih.gov/33720291"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab171","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab171","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","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://doi.org/10.1093/bioinformatics/btab171","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009958002","display_name":"Ferhat Alkan","orcid":"https://orcid.org/0000-0001-6709-9605"},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Ferhat Alkan","raw_affiliation_strings":["Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006808917","display_name":"Joana Silva","orcid":"https://orcid.org/0000-0001-5301-1799"},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Joana Silva","raw_affiliation_strings":["Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057687538","display_name":"Eric Pint\u00f3 Barber\u00e0","orcid":null},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Eric Pint\u00f3 Barber\u00e0","raw_affiliation_strings":["Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025799089","display_name":"William J. Faller","orcid":"https://orcid.org/0000-0002-0738-2254"},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"William J. Faller","raw_affiliation_strings":["Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Division of Oncogenomics, Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5009958002","https://openalex.org/A5025799089"],"corresponding_institution_ids":["https://openalex.org/I2898336195"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6507,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.66272126,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"37","issue":"17","first_page":"2659","last_page":"2667"},"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":0.9995999932289124,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9966999888420105,"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/pipeline","display_name":"Pipeline (software)","score":0.8215721845626831},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5861353874206543},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41109079122543335},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28885799646377563},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21013134717941284}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8215721845626831},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5861353874206543},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41109079122543335},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28885799646377563},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21013134717941284}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btab171","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab171","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33720291","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33720291","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:research-information.bris.ac.uk:openaire_cris_publications/fb5c0132-4bef-41ea-8292-4094e9954767","is_oa":true,"landing_page_url":"https://research-information.bris.ac.uk/en/publications/fb5c0132-4bef-41ea-8292-4094e9954767","pdf_url":null,"source":{"id":"https://openalex.org/S4306400895","display_name":"Bristol Research (University of Bristol)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I36234482","host_organization_name":"University of Bristol","host_organization_lineage":["https://openalex.org/I36234482"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Alkan, F, Silva, J, Pint\u00f3 Barber\u00e0, E & Faller, W J 2021, 'Ribo-ODDR : oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq', Bioinformatics, vol. 37, no. 17, pp. 2659-2667. https://doi.org/10.1093/bioinformatics/btab171","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:europepmc.org:7322585","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8428583","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8428583","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8428583","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab171","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab171","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.44999998807907104,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1982603620","https://openalex.org/W2036897871","https://openalex.org/W2043880988","https://openalex.org/W2046634347","https://openalex.org/W2079517684","https://openalex.org/W2086561953","https://openalex.org/W2102496723","https://openalex.org/W2116528446","https://openalex.org/W2124799197","https://openalex.org/W2137903553","https://openalex.org/W2140729960","https://openalex.org/W2146152985","https://openalex.org/W2163672244","https://openalex.org/W2520675467","https://openalex.org/W2577903052","https://openalex.org/W2621126205","https://openalex.org/W2621281388","https://openalex.org/W2905967194","https://openalex.org/W2908902954","https://openalex.org/W2919017477","https://openalex.org/W2945902794","https://openalex.org/W2963893845","https://openalex.org/W2965875787","https://openalex.org/W2969963553","https://openalex.org/W3033554529","https://openalex.org/W3038870631","https://openalex.org/W3109403119","https://openalex.org/W6732537500"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"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":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2021-03-29T00:00:00"}
