{"id":"https://openalex.org/W2143387738","doi":"https://doi.org/10.1093/bib/bbr078","title":"Visualizing next-generation sequencing data with JBrowse","display_name":"Visualizing next-generation sequencing data with JBrowse","publication_year":2012,"publication_date":"2012-03-12","ids":{"openalex":"https://openalex.org/W2143387738","doi":"https://doi.org/10.1093/bib/bbr078","mag":"2143387738","pmid":"https://pubmed.ncbi.nlm.nih.gov/22411711"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbr078","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr078","pdf_url":"https://academic.oup.com/bib/article-pdf/14/2/172/546080/bbr078.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/14/2/172/546080/bbr078.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051186755","display_name":"Oscar Westesson","orcid":null},"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":true,"raw_author_name":"O. Westesson","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, CA, USA","Department of Bioengineering, University of California, Berkeley , CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley , CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000226625","display_name":"Mitchell E. Skinner","orcid":null},"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":"M. Skinner","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054625887","display_name":"Ian Holmes","orcid":"https://orcid.org/0000-0001-7639-5369"},"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":"I. Holmes","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5051186755"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.7062,"has_fulltext":true,"cited_by_count":65,"citation_normalized_percentile":{"value":0.95908611,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"14","issue":"2","first_page":"172","last_page":"177"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9817000031471252,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9739999771118164,"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":0.7704712152481079},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.6345994472503662},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5902741551399231},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4808379113674164},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.43216472864151},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.4304999113082886},{"id":"https://openalex.org/keywords/web-browser","display_name":"Web browser","score":0.41684556007385254},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3803131580352783},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3362637758255005},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.32649433612823486},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.29389488697052},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2911054491996765},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2736320197582245},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.21995538473129272},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09389486908912659}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7704712152481079},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.6345994472503662},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5902741551399231},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4808379113674164},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.43216472864151},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.4304999113082886},{"id":"https://openalex.org/C2983909278","wikidata":"https://www.wikidata.org/wiki/Q6368","display_name":"Web browser","level":3,"score":0.41684556007385254},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3803131580352783},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3362637758255005},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.32649433612823486},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.29389488697052},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2911054491996765},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2736320197582245},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.21995538473129272},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09389486908912659},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003626","descriptor_name":"Data Display","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbr078","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr078","pdf_url":"https://academic.oup.com/bib/article-pdf/14/2/172/546080/bbr078.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22411711","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22411711","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2920663","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3603211","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3603211","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3603211","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbr078","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr078","pdf_url":"https://academic.oup.com/bib/article-pdf/14/2/172/546080/bbr078.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1078007678","display_name":null,"funder_award_id":"HG004483","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5338109553","display_name":null,"funder_award_id":"R01-HG004483","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/W2143387738.pdf","grobid_xml":"https://content.openalex.org/works/W2143387738.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1574182225","https://openalex.org/W2012884498","https://openalex.org/W2067151470","https://openalex.org/W2105114815","https://openalex.org/W2108234281","https://openalex.org/W2123056040","https://openalex.org/W2124262094","https://openalex.org/W2128016314","https://openalex.org/W2145477956","https://openalex.org/W2150934173","https://openalex.org/W2151397621","https://openalex.org/W2154519319","https://openalex.org/W2167155938"],"related_works":["https://openalex.org/W2161951664","https://openalex.org/W3174992442","https://openalex.org/W4298080220","https://openalex.org/W2949621373","https://openalex.org/W2791266083","https://openalex.org/W2590969672","https://openalex.org/W4302610923","https://openalex.org/W4310490448","https://openalex.org/W2105114815","https://openalex.org/W2143797649"],"abstract_inverted_index":{"JBrowse":[0,22],"is":[1],"a":[2,18,36],"web-based":[3],"genome":[4],"browser,":[5],"allowing":[6],"many":[7],"sources":[8],"of":[9,28,42],"data":[10,25],"to":[11,34],"be":[12],"visualized,":[13],"interpreted":[14],"and":[15,31],"navigated":[16],"in":[17],"coherent":[19],"visual":[20],"framework.":[21],"uses":[23],"efficient":[24],"structures,":[26],"pre-generation":[27],"image":[29],"tiles":[30],"client-side":[32],"rendering":[33],"provide":[35],"fast,":[37],"interactive":[38],"browsing":[39],"experience.":[40],"Many":[41],"JBrowse's":[43],"design":[44],"features":[45],"make":[46],"it":[47],"well":[48],"suited":[49],"for":[50],"visualizing":[51],"high-volume":[52],"data,":[53],"such":[54],"as":[55],"aligned":[56],"next-generation":[57],"sequencing":[58],"reads.":[59]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}