{"id":"https://openalex.org/W2480578423","doi":"https://doi.org/10.1093/bioinformatics/btw501","title":"Metrics for rapid quality control in RNA structure probing experiments","display_name":"Metrics for rapid quality control in RNA structure probing experiments","publication_year":2016,"publication_date":"2016-08-06","ids":{"openalex":"https://openalex.org/W2480578423","doi":"https://doi.org/10.1093/bioinformatics/btw501","mag":"2480578423","pmid":"https://pubmed.ncbi.nlm.nih.gov/27497441"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw501","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw501","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3575/16920410/btw501.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/32/23/3575/16920410/btw501.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073496871","display_name":"Krishna Choudhary","orcid":"https://orcid.org/0000-0002-7966-1527"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Krishna Choudhary","raw_affiliation_strings":["1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015855153","display_name":"Nathan P. Shih","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan P. Shih","raw_affiliation_strings":["1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101830334","display_name":"Fei Deng","orcid":"https://orcid.org/0000-0002-1997-4572"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fei Deng","raw_affiliation_strings":["1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067522520","display_name":"Mirko Ledda","orcid":"https://orcid.org/0000-0001-5089-7862"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mirko Ledda","raw_affiliation_strings":["1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100374493","display_name":"Bo Li","orcid":"https://orcid.org/0000-0003-0668-1620"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bo Li","raw_affiliation_strings":["2Center for RNA Systems Biology, University of California at Berkeley, Berkeley, CA, USA"],"affiliations":[{"raw_affiliation_string":"2Center for RNA Systems Biology, University of California at Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031144849","display_name":"Sharon Aviran","orcid":"https://orcid.org/0000-0003-1872-9820"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sharon Aviran","raw_affiliation_strings":["1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5031144849"],"corresponding_institution_ids":["https://openalex.org/I84218800"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.0917,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.87209516,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"23","first_page":"3575","last_page":"3583"},"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":0.9991999864578247,"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":0.612795352935791},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.5575006604194641},{"id":"https://openalex.org/keywords/control","display_name":"Control (management)","score":0.48211050033569336},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.414444237947464},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36003100872039795},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32999682426452637},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27645641565322876},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2220821976661682},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18505600094795227},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0984780490398407},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0730588436126709}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.612795352935791},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.5575006604194641},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.48211050033569336},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.414444237947464},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36003100872039795},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32999682426452637},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27645641565322876},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2220821976661682},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18505600094795227},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0984780490398407},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0730588436126709},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"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":"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":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000592","qualifier_name":"standards","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":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059629","descriptor_name":"Signal-To-Noise Ratio","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw501","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw501","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3575/16920410/btw501.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:27497441","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27497441","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:escholarship.org:ark:/13030/qt9r00c707","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/9r00c707","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 32, iss 23","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5181532","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5181532","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw501","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw501","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3575/16920410/btw501.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/G8798461885","display_name":null,"funder_award_id":"HG006860","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/W2480578423.pdf","grobid_xml":"https://content.openalex.org/works/W2480578423.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1584395599","https://openalex.org/W1640318440","https://openalex.org/W1747248992","https://openalex.org/W1877265446","https://openalex.org/W1964465701","https://openalex.org/W1974454061","https://openalex.org/W2003993220","https://openalex.org/W2026181790","https://openalex.org/W2026541379","https://openalex.org/W2035151243","https://openalex.org/W2036412199","https://openalex.org/W2037876032","https://openalex.org/W2038598202","https://openalex.org/W2041882488","https://openalex.org/W2046335009","https://openalex.org/W2046867713","https://openalex.org/W2050021156","https://openalex.org/W2070677411","https://openalex.org/W2071883352","https://openalex.org/W2076091642","https://openalex.org/W2097609482","https://openalex.org/W2098571862","https://openalex.org/W2100321825","https://openalex.org/W2100668965","https://openalex.org/W2108895594","https://openalex.org/W2120865735","https://openalex.org/W2122695112","https://openalex.org/W2129726167","https://openalex.org/W2131320639","https://openalex.org/W2134943543","https://openalex.org/W2139878468","https://openalex.org/W2141176452","https://openalex.org/W2146512944","https://openalex.org/W2155626763","https://openalex.org/W2158069307","https://openalex.org/W2168460913","https://openalex.org/W2212720078","https://openalex.org/W2335480701","https://openalex.org/W2400250419","https://openalex.org/W2412575231","https://openalex.org/W2416488948","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2384667405","https://openalex.org/W2389266787","https://openalex.org/W2363885542","https://openalex.org/W2387206255","https://openalex.org/W2355570285","https://openalex.org/W2364958354","https://openalex.org/W2352797113","https://openalex.org/W2372137583","https://openalex.org/W1548050717","https://openalex.org/W2374872591"],"abstract_inverted_index":{"The":[0],"data":[1,17],"and":[2],"methods":[3],"used":[4],"in":[5],"this":[6],"article":[7],"are":[8,18],"freely":[9],"available":[10,19],"at:":[11],"http://bme.ucdavis.edu/aviranlab/SPEQC_software":[12],"CONTACT:":[13],"saviran@ucdavis.eduSupplementary":[14],"information:":[15],"Supplementary":[16],"at":[20],"Bioinformatics":[21],"online.":[22]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
