{"id":"https://openalex.org/W1889881724","doi":"https://doi.org/10.1093/bioinformatics/btv385","title":"Hyperscape: visualization for complex biological networks","display_name":"Hyperscape: visualization for complex biological networks","publication_year":2015,"publication_date":"2015-06-24","ids":{"openalex":"https://openalex.org/W1889881724","doi":"https://doi.org/10.1093/bioinformatics/btv385","mag":"1889881724","pmid":"https://pubmed.ncbi.nlm.nih.gov/26108529"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv385","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv385","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3390/49035956/bioinformatics_31_20_3390.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/31/20/3390/49035956/bioinformatics_31_20_3390.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088664061","display_name":"Graham L. Cromar","orcid":null},"institutions":[{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Graham L. Cromar","raw_affiliation_strings":["1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029517941","display_name":"Anthony Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Anthony Zhao","raw_affiliation_strings":["1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108539576","display_name":"Alex Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Alex Yang","raw_affiliation_strings":["1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,","2 Department of Biochemistry and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,","institution_ids":["https://openalex.org/I2801317318"]},{"raw_affiliation_string":"2 Department of Biochemistry and","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085182984","display_name":"John Parkinson","orcid":"https://orcid.org/0000-0001-9815-1189"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"John Parkinson","raw_affiliation_strings":["1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,","2 Department of Biochemistry and","3 Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,","institution_ids":["https://openalex.org/I2801317318"]},{"raw_affiliation_string":"2 Department of Biochemistry and","institution_ids":[]},{"raw_affiliation_string":"3 Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5085182984","https://openalex.org/A5088664061"],"corresponding_institution_ids":["https://openalex.org/I185261750","https://openalex.org/I2801317318"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4518,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.65237127,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"31","issue":"20","first_page":"3390","last_page":"3391"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4162999987602234,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4162999987602234,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.07699999958276749,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0697999969124794,"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/visualization","display_name":"Visualization","score":0.7254606485366821},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6924750804901123},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4955023527145386},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3924252986907959},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30898118019104004},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2025010883808136}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7254606485366821},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6924750804901123},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4955023527145386},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3924252986907959},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30898118019104004},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2025010883808136}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004547","descriptor_name":"Elastic Tissue","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004547","descriptor_name":"Elastic Tissue","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004547","descriptor_name":"Elastic Tissue","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv385","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv385","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3390/49035956/bioinformatics_31_20_3390.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:26108529","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26108529","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:open-archive.highwire.org:bioinfo:31/20/3390","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/20/3390","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv385","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv385","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3390/49035956/bioinformatics_31_20_3390.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/G4268577139","display_name":null,"funder_award_id":"UMR 5086","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"}],"funders":[{"id":"https://openalex.org/F4320307845","display_name":"Heart and Stroke Foundation of Canada","ror":"https://ror.org/00qbpyp73"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1889881724.pdf","grobid_xml":"https://content.openalex.org/works/W1889881724.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2015684586","https://openalex.org/W2017248899","https://openalex.org/W2023208820","https://openalex.org/W2036410336","https://openalex.org/W2083786039","https://openalex.org/W2098383595","https://openalex.org/W2102225353","https://openalex.org/W2108496516","https://openalex.org/W2159675211","https://openalex.org/W4245562979"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2068608913","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W3124914020","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"MOTIVATION:":[0],"Network":[1],"biology":[2,77],"has":[3],"emerged":[4],"as":[5,69,106],"a":[6,52,107,116,122],"powerful":[7],"tool":[8],"to":[9,26,37,87],"uncover":[10,91],"the":[11,18,76,82,95],"organizational":[12],"properties":[13],"of":[14,20,63,75,78,85,97],"living":[15],"systems":[16],"through":[17],"application":[19,109],"graph":[21],"theoretic":[22],"approaches.":[23],"However,":[24],"due":[25],"limitations":[27],"in":[28],"underlying":[29],"data":[30,132],"models":[31],"and":[32,41,66,90,115],"visualization":[33],"software,":[34],"knowledge":[35],"relating":[36],"large":[38],"molecular":[39],"assemblies":[40],"biologically":[42],"active":[43],"fragments":[44],"is":[45,104],"poorly":[46],"represented.":[47],"RESULTS:":[48],"Here,":[49],"we":[50],"demonstrate":[51],"novel":[53],"hypergraph":[54],"implementation":[55],"that":[56],"better":[57],"captures":[58],"hierarchical":[59],"structures,":[60],"using":[61],"components":[62],"elastic":[64],"fibers":[65],"chromatin":[67],"modification":[68],"models.":[70],"These":[71],"reveal":[72],"unprecedented":[73],"views":[74],"these":[79],"systems,":[80],"demonstrating":[81],"unique":[83],"capacity":[84],"hypergraphs":[86],"resolve":[88],"overlaps":[89],"new":[92],"insights":[93],"into":[94],"subfunctionalization":[96],"variant":[98],"complexes.":[99],"AVAILABILITY":[100],"AND":[101],"IMPLEMENTATION:":[102],"Hyperscape":[103],"available":[105,120,134],"web":[108],"at":[110,135],"http://www.compsysbio.org/hyperscape.":[111],"Source":[112],"code,":[113],"examples":[114],"tutorial":[117],"are":[118,133],"freely":[119],"under":[121],"GNU":[123],"license.":[124],"CONTACTS:":[125],"john.parkinson@utoronto.ca":[126],"or":[127],"graham.cromar@gmail.com":[128],"SUPPLEMENTARY":[129],"INFORMATION:":[130],"Supplementary":[131],"Bioinformatics":[136],"online.":[137]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}