{"id":"https://openalex.org/W2111890322","doi":"https://doi.org/10.1093/bioinformatics/btu565","title":"PyBamView: a browser-based application for viewing short read alignments","display_name":"PyBamView: a browser-based application for viewing short read alignments","publication_year":2014,"publication_date":"2014-08-21","ids":{"openalex":"https://openalex.org/W2111890322","doi":"https://doi.org/10.1093/bioinformatics/btu565","mag":"2111890322","pmid":"https://pubmed.ncbi.nlm.nih.gov/25147359"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu565","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu565","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/23/3405/48931616/bioinformatics_30_23_3405.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/30/23/3405/48931616/bioinformatics_30_23_3405.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065055599","display_name":"Melissa Gymrek","orcid":"https://orcid.org/0000-0002-6086-3903"},"institutions":[{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]},{"id":"https://openalex.org/I4210157710","display_name":"Whitehead Institute for Biomedical Research","ror":"https://ror.org/04vqm6w82","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210157710","https://openalex.org/I63966007"]},{"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":true,"raw_author_name":"Melissa Gymrek","raw_affiliation_strings":["1 Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, 2Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and 3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"1 Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, 2Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and 3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I4210157710","https://openalex.org/I4210092658","https://openalex.org/I107606265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5065055599"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I4210092658","https://openalex.org/I4210157710"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.713,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.70700048,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"30","issue":"23","first_page":"3405","last_page":"3407"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9947999715805054,"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/T11879","display_name":"Protist diversity and phylogeny","score":0.9794999957084656,"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/mit-license","display_name":"MIT License","score":0.8896574378013611},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8581461906433105},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8545731902122498},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.796257495880127},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5928387641906738},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.503863513469696},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4845265746116638},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.45239323377609253},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4122498333454132},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3850864768028259},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33067381381988525},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2332679033279419},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12151145935058594}],"concepts":[{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.8896574378013611},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8581461906433105},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8545731902122498},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.796257495880127},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5928387641906738},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.503863513469696},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4845265746116638},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.45239323377609253},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4122498333454132},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3850864768028259},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33067381381988525},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2332679033279419},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12151145935058594},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu565","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu565","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/23/3405/48931616/bioinformatics_30_23_3405.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:25147359","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25147359","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:10.1.1.934.1502","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.934.1502","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/2014/08/21/bioinformatics.btu565.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu565","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu565","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/23/3405/48931616/bioinformatics_30_23_3405.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/G205123881","display_name":null,"funder_award_id":"32 CFR 168a","funder_id":"https://openalex.org/F4320333566","funder_display_name":"National Defense Science and Engineering Graduate"},{"id":"https://openalex.org/G7791925507","display_name":null,"funder_award_id":"CFR 168a","funder_id":"https://openalex.org/F4320333566","funder_display_name":"National Defense Science and Engineering Graduate"},{"id":"https://openalex.org/G8926491534","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320333566","funder_display_name":"National Defense Science and Engineering Graduate"}],"funders":[{"id":"https://openalex.org/F4320333566","display_name":"National Defense Science and Engineering Graduate","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2111890322.pdf","grobid_xml":"https://content.openalex.org/works/W2111890322.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2003398699","https://openalex.org/W2021341670","https://openalex.org/W2064815984","https://openalex.org/W2107318366","https://openalex.org/W2108234281","https://openalex.org/W2128016314","https://openalex.org/W2146663795","https://openalex.org/W2148875515","https://openalex.org/W2154397429","https://openalex.org/W2159075303"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4386463918","https://openalex.org/W3042795425","https://openalex.org/W4311683883","https://openalex.org/W4226330600","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W4385413248","https://openalex.org/W3097598351"],"abstract_inverted_index":{"PyBamView":[0],"is":[1,11],"available":[2,13],"as":[3],"a":[4],"standard":[5],"python":[6],"package.":[7],"The":[8],"source":[9],"code":[10],"freely":[12],"under":[14],"the":[15],"MIT":[16],"license":[17],"at":[18],"https://mgymrek.github.io/pybamview.":[19]},"counts_by_year":[{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}