{"id":"https://openalex.org/W2116899182","doi":"https://doi.org/10.1093/bioinformatics/btt534","title":"CruzDB: software for annotation of genomic intervals with UCSC genome-browser database","display_name":"CruzDB: software for annotation of genomic intervals with UCSC genome-browser database","publication_year":2013,"publication_date":"2013-09-12","ids":{"openalex":"https://openalex.org/W2116899182","doi":"https://doi.org/10.1093/bioinformatics/btt534","mag":"2116899182","pmid":"https://pubmed.ncbi.nlm.nih.gov/24037212"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt534","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt534","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/23/3003/48891228/bioinformatics_29_23_3003.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/29/23/3003/48891228/bioinformatics_29_23_3003.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005439778","display_name":"Brent S. Pedersen","orcid":"https://orcid.org/0000-0003-1786-2216"},"institutions":[{"id":"https://openalex.org/I4210134151","display_name":"University of Colorado Cancer Center","ror":"https://ror.org/04cqn7d42","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210134151"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brent S. Pedersen","raw_affiliation_strings":["1 Department of Medicine, University of Colorado Denver, School of Medicine, Denver, CO, USA and 2Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Medicine, University of Colorado Denver, School of Medicine, Denver, CO, USA and 2Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO, USA","institution_ids":["https://openalex.org/I4210134151","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042472677","display_name":"Ivana V. Yang","orcid":"https://orcid.org/0000-0002-1018-489X"},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]},{"id":"https://openalex.org/I4210134151","display_name":"University of Colorado Cancer Center","ror":"https://ror.org/04cqn7d42","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210134151"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ivana V. Yang","raw_affiliation_strings":["1 Department of Medicine, University of Colorado Denver, School of Medicine, Denver, CO, USA and 2Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Medicine, University of Colorado Denver, School of Medicine, Denver, CO, USA and 2Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO, USA","institution_ids":["https://openalex.org/I4210134151","https://openalex.org/I921990950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036093562","display_name":"Subhajyoti De","orcid":"https://orcid.org/0000-0002-2313-8593"},"institutions":[{"id":"https://openalex.org/I4210134151","display_name":"University of Colorado Cancer Center","ror":"https://ror.org/04cqn7d42","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210134151"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Subhajyoti De","raw_affiliation_strings":["1 Department of Medicine, University of Colorado Denver, School of Medicine, Denver, CO, USA and 2Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Medicine, University of Colorado Denver, School of Medicine, Denver, CO, USA and 2Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO, USA","institution_ids":["https://openalex.org/I4210134151","https://openalex.org/I921990950"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005439778"],"corresponding_institution_ids":["https://openalex.org/I4210134151","https://openalex.org/I921990950"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8165,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.74582653,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"29","issue":"23","first_page":"3003","last_page":"3006"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9998999834060669,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9998999834060669,"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":0.9998000264167786,"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":0.9997000098228455,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.8442851305007935},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.8240140080451965},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6545968055725098},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6214417219161987},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49830150604248047},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.44709697365760803},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35793763399124146},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.34477299451828003},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3295471966266632},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24405497312545776},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17198285460472107},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1674574613571167},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09075921773910522},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.05639207363128662}],"concepts":[{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.8442851305007935},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8240140080451965},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6545968055725098},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6214417219161987},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49830150604248047},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.44709697365760803},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35793763399124146},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.34477299451828003},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3295471966266632},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24405497312545776},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17198285460472107},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1674574613571167},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09075921773910522},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.05639207363128662}],"mesh":[{"descriptor_ui":"D004261","descriptor_name":"DNA Replication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004261","descriptor_name":"DNA Replication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004261","descriptor_name":"DNA Replication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D007438","descriptor_name":"Introns","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt534","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt534","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/23/3003/48891228/bioinformatics_29_23_3003.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:24037212","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24037212","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:CiteSeerX.psu:10.1.1.883.4683","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.883.4683","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2013/09/12/bioinformatics.btt534.full.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3834799","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3834799","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/btt534","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt534","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/23/3003/48891228/bioinformatics_29_23_3003.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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2116899182.pdf","grobid_xml":"https://content.openalex.org/works/W2116899182.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W2003250511","https://openalex.org/W2026186077","https://openalex.org/W2038774969","https://openalex.org/W2045974768","https://openalex.org/W2049656505","https://openalex.org/W2059073003","https://openalex.org/W2087616533","https://openalex.org/W2091567243","https://openalex.org/W2091798624","https://openalex.org/W2117446594","https://openalex.org/W2123421577","https://openalex.org/W2128016314","https://openalex.org/W2133465414","https://openalex.org/W2136145671","https://openalex.org/W2153087859","https://openalex.org/W2160333540","https://openalex.org/W2164354446","https://openalex.org/W2167827709","https://openalex.org/W2259938310","https://openalex.org/W2916083703","https://openalex.org/W4293196852","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W3138117676","https://openalex.org/W3111061871","https://openalex.org/W2581212852","https://openalex.org/W2099626126","https://openalex.org/W3092268165","https://openalex.org/W1999129612","https://openalex.org/W2175953840","https://openalex.org/W4213365651","https://openalex.org/W4229585093","https://openalex.org/W1759033142"],"abstract_inverted_index":{"We":[0,30],"present":[1],"CruzDB,":[2],"a":[3,106],"fast":[4],"and":[5,26,42,64],"intuitive":[6],"programmatic":[7],"interface":[8],"to":[9,61,79],"the":[10,32],"University":[11],"of":[12,23,34,82,88,108],"California,":[13],"Santa":[14],"Cruz":[15],"(UCSC)":[16],"genome":[17],"browser":[18],"that":[19],"facilitates":[20],"integrative":[21],"analyses":[22],"diverse":[24],"local":[25],"remotely":[27],"hosted":[28],"datasets.":[29],"showcase":[31],"syntax":[33],"CruzDB":[35],"using":[36],"microRNA":[37],"binding":[38],"sites":[39],"as":[40],"examples,":[41],"further":[43],"demonstrate":[44],"its":[45],"utility":[46],"with":[47,75],"three":[48],"biological":[49],"discoveries.":[50],"First,":[51],"DNA":[52],"replication":[53],"timing":[54],"is":[55],"stratified":[56],"in":[57,92,102,111],"gene":[58],"regions-exons":[59],"tend":[60],"replicate":[62],"early":[63],"introns":[65],"late":[66],"during":[67],"S":[68],"phase.":[69],"Second,":[70],"several":[71],"non-coding":[72],"variants":[73],"associated":[74],"cognitive":[76],"functions":[77],"map":[78],"lincRNA":[80],"transcripts":[81],"relevant":[83],"function,":[84],"suggesting":[85],"potential":[86],"function":[87],"these":[89],"regulatory":[90],"RNAs":[91],"neuronal":[93],"diseases.":[94],"Third,":[95],"lamina-associated":[96],"genomic":[97],"regions":[98],"are":[99],"highly":[100],"enriched":[101],"olfaction-related":[103],"genes,":[104],"indicating":[105],"role":[107],"nuclear":[109],"organization":[110],"their":[112],"regulation.":[113]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
