{"id":"https://openalex.org/W4400800674","doi":"https://doi.org/10.1093/bioinformatics/btae453","title":"Genome-wide analysis and visualization of copy number with CNVpytor in igv.js","display_name":"Genome-wide analysis and visualization of copy number with CNVpytor in igv.js","publication_year":2024,"publication_date":"2024-07-16","ids":{"openalex":"https://openalex.org/W4400800674","doi":"https://doi.org/10.1093/bioinformatics/btae453","pmid":"https://pubmed.ncbi.nlm.nih.gov/39018173"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae453","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae453","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/8/btae453/58749752/btae453.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/40/8/btae453/58749752/btae453.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052776638","display_name":"Arijit Panda","orcid":"https://orcid.org/0000-0001-5156-6459"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Arijit Panda","raw_affiliation_strings":["Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, United States"],"affiliations":[{"raw_affiliation_string":"Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, United States","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014452770","display_name":"Milovan \u0160uvakov","orcid":"https://orcid.org/0000-0002-5839-9611"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Milovan Suvakov","raw_affiliation_strings":["Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, United States"],"affiliations":[{"raw_affiliation_string":"Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, United States","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033125816","display_name":"Helga Thorvaldsd\u00f3ttir","orcid":null},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Helga Thorvaldsdottir","raw_affiliation_strings":["Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077622597","display_name":"Jill P. Mesirov","orcid":"https://orcid.org/0000-0002-9755-2818"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jill P Mesirov","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA 92093, United States","Moores Cancer Center, University of California San Diego , La Jolla, CA 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Moores Cancer Center, University of California San Diego , La Jolla, CA 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014218807","display_name":"James Robinson","orcid":"https://orcid.org/0000-0002-2187-5944"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James T Robinson","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA 92093, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078568342","display_name":"Alexej Abyzov","orcid":"https://orcid.org/0000-0001-5405-6729"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexej Abyzov","raw_affiliation_strings":["Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, United States"],"affiliations":[{"raw_affiliation_string":"Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, United States","institution_ids":["https://openalex.org/I1330342723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5052776638"],"corresponding_institution_ids":["https://openalex.org/I1330342723"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.576,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.73185184,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"40","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9986000061035156,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9980999827384949,"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":0.7432296872138977},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.626198947429657},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5482771992683411},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5284856557846069},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.45195406675338745},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.37486064434051514},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.34726211428642273},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.302196204662323},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.14341199398040771}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7432296872138977},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.626198947429657},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5482771992683411},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5284856557846069},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.45195406675338745},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.37486064434051514},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.34726211428642273},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.302196204662323},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.14341199398040771}],"mesh":[{"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":"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":"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae453","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae453","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/8/btae453/58749752/btae453.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:39018173","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39018173","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:pubmedcentral.nih.gov:11303504","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11303504","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11303504/pdf/btae453.pdf","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":"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/btae453","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae453","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/8/btae453/58749752/btae453.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[],"awards":[{"id":"https://openalex.org/G1434319672","display_name":null,"funder_award_id":"U24CA220242","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3480384865","display_name":null,"funder_award_id":"UG3NS132128","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G8415708874","display_name":null,"funder_award_id":"U24CA258406","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400800674.pdf"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2021341670","https://openalex.org/W2150506261","https://openalex.org/W2168133698","https://openalex.org/W2170490448","https://openalex.org/W2419528132","https://openalex.org/W2907009092","https://openalex.org/W3082136743","https://openalex.org/W3094167758","https://openalex.org/W3212059340","https://openalex.org/W4288422732","https://openalex.org/W4312114021","https://openalex.org/W4366224338"],"related_works":["https://openalex.org/W4309247532","https://openalex.org/W3096946169","https://openalex.org/W2113128227","https://openalex.org/W2144610372","https://openalex.org/W4312114021","https://openalex.org/W4311938462","https://openalex.org/W2121840477","https://openalex.org/W2515936044","https://openalex.org/W3123068371","https://openalex.org/W1518632238"],"abstract_inverted_index":{"The":[0,11],"CNVpytor":[1],"track":[2],"is":[3,13],"integrated":[4],"with":[5],"igv.js":[6],"and":[7,27],"available":[8,14],"at":[9,15,25],"https://github.com/igvteam/igv.js.":[10],"documentation":[12],"https://github.com/igvteam/igv.js/wiki/cnvpytor.":[16],"Usage":[17],"can":[18],"be":[19],"tested":[20],"in":[21],"the":[22],"IGV-Web":[23],"app":[24],"https://igv.org/app":[26],"also":[28],"on":[29],"https://github.com/abyzovlab/CNVpytor.":[30]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}