{"id":"https://openalex.org/W3011739213","doi":"https://doi.org/10.1093/bioinformatics/btaa192","title":"LogoJS: a Javascript package for creating sequence logos and embedding them in web applications","display_name":"LogoJS: a Javascript package for creating sequence logos and embedding them in web applications","publication_year":2020,"publication_date":"2020-03-14","ids":{"openalex":"https://openalex.org/W3011739213","doi":"https://doi.org/10.1093/bioinformatics/btaa192","mag":"3011739213","pmid":"https://pubmed.ncbi.nlm.nih.gov/32181813"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3573/33329305/btaa192.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3573/33329305/btaa192.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037976483","display_name":"Henry Pratt","orcid":"https://orcid.org/0000-0001-9413-834X"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Henry Pratt","raw_affiliation_strings":["Program in Bioinformatics and Integrative Biology , University of Massachusetts Medical School, Worcester, MA 01605, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Integrative Biology , University of Massachusetts Medical School, Worcester, MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084369008","display_name":"Zhiping Weng","orcid":"https://orcid.org/0000-0002-3032-7966"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhiping Weng","raw_affiliation_strings":["Program in Bioinformatics and Integrative Biology , University of Massachusetts Medical School, Worcester, MA 01605, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Integrative Biology , University of Massachusetts Medical School, Worcester, MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5084369008"],"corresponding_institution_ids":["https://openalex.org/I166722992"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5696,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.63609531,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"11","first_page":"3573","last_page":"3575"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.7369999885559082,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.7369999885559082,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.07000000029802322,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.039000000804662704,"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/javascript","display_name":"JavaScript","score":0.884557843208313},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7802752256393433},{"id":"https://openalex.org/keywords/logos-bible-software","display_name":"Logos Bible Software","score":0.7675575017929077},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6481354236602783},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5121907591819763},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.5063039064407349},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.47945132851600647},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4791569113731384},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.4204569160938263},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.31755995750427246},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29850077629089355},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2777491807937622},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08839812874794006}],"concepts":[{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.884557843208313},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7802752256393433},{"id":"https://openalex.org/C150506046","wikidata":"https://www.wikidata.org/wiki/Q6667822","display_name":"Logos Bible Software","level":2,"score":0.7675575017929077},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6481354236602783},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5121907591819763},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.5063039064407349},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.47945132851600647},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4791569113731384},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.4204569160938263},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.31755995750427246},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29850077629089355},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2777491807937622},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08839812874794006}],"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":"D009711","descriptor_name":"Nucleotides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","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":"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3573/33329305/btaa192.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32181813","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32181813","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.umassmed.edu:faculty_pubs-2688","is_oa":false,"landing_page_url":"https://escholarship.umassmed.edu/faculty_pubs/1677","pdf_url":null,"source":{"id":"https://openalex.org/S4306400883","display_name":"The Journal of the American Medical Association (JAMA) Network (American Medical Association)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173654999","host_organization_name":"American Medical Association","host_organization_lineage":["https://openalex.org/I173654999"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"University of Massachusetts Medical School Faculty Publications","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7267833","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7267833","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/btaa192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3573/33329305/btaa192.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7900000214576721,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G1613000916","display_name":null,"funder_award_id":"U24 HG009446","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4744320226","display_name":null,"funder_award_id":"HG009446","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"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3011739213.pdf","grobid_xml":"https://content.openalex.org/works/W3011739213.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1709815505","https://openalex.org/W1988393300","https://openalex.org/W2041877620","https://openalex.org/W2076455712","https://openalex.org/W2105114815","https://openalex.org/W2117131162","https://openalex.org/W2147946837","https://openalex.org/W2157009395","https://openalex.org/W2158266834","https://openalex.org/W2299876992","https://openalex.org/W2315002870","https://openalex.org/W2493763501","https://openalex.org/W2737196618","https://openalex.org/W2767749844","https://openalex.org/W2770178180","https://openalex.org/W2770182290","https://openalex.org/W2788408237","https://openalex.org/W2888425844","https://openalex.org/W2949171083","https://openalex.org/W2951212842","https://openalex.org/W2951894193","https://openalex.org/W4390668729","https://openalex.org/W6697496683"],"related_works":["https://openalex.org/W2795601048","https://openalex.org/W2403324299","https://openalex.org/W2621177934","https://openalex.org/W4286287737","https://openalex.org/W1844100222","https://openalex.org/W3009852816","https://openalex.org/W2513223212","https://openalex.org/W2169602156","https://openalex.org/W42576273","https://openalex.org/W4366451129"],"abstract_inverted_index":{"SUMMARY:":[0],"Sequence":[1],"logos":[2,30,41,102,118],"were":[3],"introduced":[4],"nearly":[5],"30":[6],"years":[7],"ago":[8],"as":[9],"a":[10,61,66,69,74,109,136,157],"human-readable":[11],"format":[12],"for":[13,65,80,100,112,140],"representing":[14],"consensus":[15],"sequences,":[16],"and":[17,25,53,119,132,142,155,171,178],"they":[18],"remain":[19],"widely":[20],"used.":[21],"As":[22],"new":[23],"experimental":[24],"computational":[26],"techniques":[27],"have":[28,31],"developed,":[29],"been":[32],"extended:":[33],"extra":[34],"symbols":[35,54],"represent":[36,60],"covalent":[37],"modifications":[38],"to":[39,91,96],"nucleotides,":[40],"with":[42,50,135],"multiple":[43],"letters":[44],"at":[45,166,185,195],"each":[46],"position":[47],"illustrate":[48],"models":[49],"multi-nucleotide":[51],"features":[52],"extending":[55],"below":[56],"the":[57,128],"x-axis":[58],"may":[59],"binding":[62],"energy":[63],"penalty":[64],"residue":[67],"or":[68],"negative":[70],"weight":[71],"output":[72],"from":[73],"neural":[75],"network.":[76],"Web-based":[77],"visualization":[78],"tools":[79],"genomic":[81],"data":[82,192],"are":[83,174,180,193],"increasingly":[84],"taking":[85],"advantage":[86],"of":[87],"modern":[88],"web":[89,123,138,162],"technology":[90],"offer":[92],"dynamic,":[93],"interactive":[94],"figures":[95],"users,":[97],"but":[98],"support":[99],"sequence":[101,117],"remains":[103],"limited.":[104],"Here,":[105],"we":[106],"present":[107],"LogoJS,":[108],"Javascript":[110,154],"package":[111,177],"rendering":[113],"customizable,":[114],"interactive,":[115],"vector-graphic":[116],"embedding":[120],"them":[121],"in":[122,152],"applications.":[124],"LogoJS":[125,148],"supports":[126],"all":[127],"aforementioned":[129],"logo":[130],"extensions":[131],"is":[133,149,164,183],"bundled":[134],"companion":[137],"application":[139,163,179],"creating":[141],"sharing":[143],"logos.":[144],"AVAILABILITY":[145],"AND":[146],"IMPLEMENTATION:":[147],"implemented":[150],"both":[151],"plain":[153],"ReactJS,":[156],"popular":[158],"user-interface":[159],"framework.":[160],"The":[161,176],"hosted":[165],"logojs.wenglab.org.":[167],"All":[168],"major":[169],"browsers":[170],"operating":[172],"systems":[173],"supported.":[175],"open-source;":[181],"code":[182],"available":[184,194],"GitHub.":[186],"CONTACT:":[187],"zhiping.weng@umassmed.edu.":[188],"SUPPLEMENTARY":[189],"INFORMATION:":[190],"Supplementary":[191],"Bioinformatics":[196],"online.":[197]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
