{"id":"https://openalex.org/W2585531293","doi":"https://doi.org/10.1093/bioinformatics/btx047","title":"Riborex: fast and flexible identification of differential translation from Ribo-seq data","display_name":"Riborex: fast and flexible identification of differential translation from Ribo-seq data","publication_year":2017,"publication_date":"2017-01-30","ids":{"openalex":"https://openalex.org/W2585531293","doi":"https://doi.org/10.1093/bioinformatics/btx047","mag":"2585531293"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx047","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx047","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/11/1735/25153705/btx047.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"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/11/1735/25153705/btx047.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101412259","display_name":"Wenzheng Li","orcid":"https://orcid.org/0009-0008-4536-8948"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenzheng Li","raw_affiliation_strings":["Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100704016","display_name":"Weili Wang","orcid":"https://orcid.org/0000-0002-5009-2754"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weili Wang","raw_affiliation_strings":["Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045629825","display_name":"Philip J. Uren","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip J Uren","raw_affiliation_strings":["Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042340056","display_name":"Luiz O. F. Penalva","orcid":"https://orcid.org/0000-0003-4491-6769"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas Health Science Center at San Antonio","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Luiz O F Penalva","raw_affiliation_strings":["Children\u2019s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA","Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA"],"affiliations":[{"raw_affiliation_string":"Children\u2019s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065682481","display_name":"Andrew D. Smith","orcid":"https://orcid.org/0000-0002-3337-1970"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrew D Smith","raw_affiliation_strings":["Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5065682481"],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.9517,"has_fulltext":false,"cited_by_count":101,"citation_normalized_percentile":{"value":0.9711808,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"11","first_page":"1735","last_page":"1737"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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/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/T10604","display_name":"RNA Research and Splicing","score":0.9991000294685364,"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/computer-science","display_name":"Computer science","score":0.800207257270813},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.7128523588180542},{"id":"https://openalex.org/keywords/ribosome-profiling","display_name":"Ribosome profiling","score":0.5997456908226013},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5906401872634888},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5687381625175476},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.527969241142273},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.48988407850265503},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.44018206000328064},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.42627936601638794},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3373050093650818},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.334913969039917},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22598391771316528},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.17536094784736633},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15163898468017578},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12063443660736084},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08968278765678406},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08195233345031738}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.800207257270813},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.7128523588180542},{"id":"https://openalex.org/C182325514","wikidata":"https://www.wikidata.org/wiki/Q7322425","display_name":"Ribosome profiling","level":5,"score":0.5997456908226013},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5906401872634888},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5687381625175476},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.527969241142273},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.48988407850265503},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.44018206000328064},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.42627936601638794},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3373050093650818},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.334913969039917},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22598391771316528},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.17536094784736633},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15163898468017578},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12063443660736084},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08968278765678406},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08195233345031738},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx047","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx047","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/11/1735/25153705/btx047.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":"pmh:oai:europepmc.org:4930908","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860393","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx047","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx047","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/11/1735/25153705/btx047.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":[{"id":"https://openalex.org/G2246405235","display_name":null,"funder_award_id":"R01 HG006015","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2585531293.pdf","grobid_xml":"https://content.openalex.org/works/W2585531293.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W394412225","https://openalex.org/W1980396381","https://openalex.org/W2016450373","https://openalex.org/W2026570758","https://openalex.org/W2079517684","https://openalex.org/W2109101518","https://openalex.org/W2114104545","https://openalex.org/W2122796622","https://openalex.org/W2133594999","https://openalex.org/W2137526110","https://openalex.org/W2148342439","https://openalex.org/W2179438025","https://openalex.org/W2288312466","https://openalex.org/W2297940776","https://openalex.org/W2306137721","https://openalex.org/W2319914265","https://openalex.org/W2320443335","https://openalex.org/W2950101275","https://openalex.org/W6697398956","https://openalex.org/W6700404175"],"related_works":["https://openalex.org/W3190998772","https://openalex.org/W4317392263","https://openalex.org/W2161444195","https://openalex.org/W2589019771","https://openalex.org/W2129016585","https://openalex.org/W2985540061","https://openalex.org/W4200033037","https://openalex.org/W2185012154","https://openalex.org/W2764188251","https://openalex.org/W3105722198"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Global":[2],"analysis":[3,113],"of":[4,14,24,37],"translation":[5,38,63,92],"regulation":[6],"has":[7,104],"recently":[8],"been":[9],"enabled":[10],"by":[11],"the":[12],"development":[13],"Ribosome":[15],"Profiling,":[16],"or":[17],"Ribo-seq,":[18],"technology.":[19],"This":[20],"approach":[21],"provides":[22],"maps":[23],"ribosome":[25],"activity":[26],"for":[27,58,87,115,127],"each":[28],"expressed":[29],"gene":[30,52],"in":[31,47,91],"a":[32,84,96,105,122,133],"given":[33],"biological":[34],"sample.":[35],"Measurements":[36],"efficiency":[39],"are":[40,66,153],"generated":[41],"when":[42],"Ribo-seq":[43],"data":[44,152],"is":[45,132,136],"analyzed":[46],"combination":[48],"with":[49,61,100,121],"matched":[50],"RNA-seq":[51,112],"expression":[53],"profiles.":[54],"Existing":[55],"computational":[56,85],"methods":[57,141],"identifying":[59],"genes":[60],"differential":[62],"across":[64],"samples":[65],"based":[67],"on":[68],"sound":[69],"principles,":[70],"but":[71,103],"require":[72],"users":[73,120],"to":[74],"choose":[75],"between":[76],"accuracy":[77],"and":[78,146],"speed.":[79],"Results":[80],"We":[81],"present":[82],"Riborex,":[83],"tool":[86],"mapping":[88],"genome-wide":[89],"differences":[90],"efficiency.":[93],"Riborex":[94,108],"shares":[95],"similar":[97],"mathematical":[98],"structure":[99],"existing":[101],"methods,":[102],"simplified":[106],"implementation.":[107],"directly":[109],"leverages":[110],"established":[111],"frameworks":[114],"all":[116],"parameter":[117],"estimation,":[118],"providing":[119],"choice":[123],"among":[124],"robust":[125],"engines":[126],"these":[128],"computations.":[129],"The":[130],"result":[131],"method":[134],"that":[135],"dramatically":[137],"faster":[138],"than":[139],"available":[140,154],"without":[142],"sacrificing":[143],"accuracy.":[144],"Availability":[145],"Implementation":[147],"https://github.com/smithlabcode/riborex":[148],"Supplementary":[149,151],"information":[150],"at":[155],"Bioinformatics":[156],"online.":[157]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":20},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-04T08:04:53.788161","created_date":"2025-10-10T00:00:00"}