{"id":"https://openalex.org/W4407909305","doi":"https://doi.org/10.1093/bioinformatics/btaf091","title":"Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics","display_name":"Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics","publication_year":2025,"publication_date":"2025-02-25","ids":{"openalex":"https://openalex.org/W4407909305","doi":"https://doi.org/10.1093/bioinformatics/btaf091","pmid":"https://pubmed.ncbi.nlm.nih.gov/39999015"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf091","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf091","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf091/62168188/btaf091.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/advance-article-pdf/doi/10.1093/bioinformatics/btaf091/62168188/btaf091.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031949650","display_name":"Kari Lavikka","orcid":"https://orcid.org/0000-0002-4163-4945"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Kari Lavikka","raw_affiliation_strings":["Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","University of Helsinki Research Program in Systems Oncology, Faculty of Medicine, , Helsinki 00014,"],"affiliations":[{"raw_affiliation_string":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"University of Helsinki Research Program in Systems Oncology, Faculty of Medicine, , Helsinki 00014,","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091280428","display_name":"Altti Ilari Maarala","orcid":"https://orcid.org/0000-0001-8851-4265"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Altti Ilari Maarala","raw_affiliation_strings":["Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","University of Helsinki Research Program in Systems Oncology, Faculty of Medicine, , Helsinki 00014,"],"affiliations":[{"raw_affiliation_string":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"University of Helsinki Research Program in Systems Oncology, Faculty of Medicine, , Helsinki 00014,","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075672043","display_name":"Jaana Oikkonen","orcid":"https://orcid.org/0000-0002-1063-2736"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jaana Oikkonen","raw_affiliation_strings":["Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","University of Helsinki Research Program in Systems Oncology, Faculty of Medicine, , Helsinki 00014,"],"affiliations":[{"raw_affiliation_string":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"University of Helsinki Research Program in Systems Oncology, Faculty of Medicine, , Helsinki 00014,","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033102814","display_name":"Sampsa Hautaniemi","orcid":"https://orcid.org/0000-0002-7749-2694"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Sampsa Hautaniemi","raw_affiliation_strings":["Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","University of Helsinki Research Program in Systems Oncology, Faculty of Medicine, , Helsinki 00014,"],"affiliations":[{"raw_affiliation_string":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"University of Helsinki Research Program in Systems Oncology, Faculty of Medicine, , Helsinki 00014,","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5031949650"],"corresponding_institution_ids":["https://openalex.org/I133731052"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.3845,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.90191018,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"41","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9710999727249146,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9710999727249146,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9578999876976013,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.7410511374473572},{"id":"https://openalex.org/keywords/jellyfish","display_name":"Jellyfish","score":0.6882228851318359},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6549251079559326},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5931974053382874},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4837053418159485},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3446792960166931},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25229984521865845},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.19686073064804077},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.10859698057174683}],"concepts":[{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.7410511374473572},{"id":"https://openalex.org/C2779735984","wikidata":"https://www.wikidata.org/wiki/Q30178","display_name":"Jellyfish","level":2,"score":0.6882228851318359},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6549251079559326},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5931974053382874},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4837053418159485},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3446792960166931},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25229984521865845},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.19686073064804077},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.10859698057174683},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf091","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf091","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf091/62168188/btaf091.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:39999015","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39999015","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:europepmc.org:10713842","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11897425","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf091","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf091","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf091/62168188/btaf091.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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4407909305.pdf"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1550376883","https://openalex.org/W2155832181","https://openalex.org/W2410440539","https://openalex.org/W2551783467","https://openalex.org/W2619065478","https://openalex.org/W2756005140","https://openalex.org/W2767281692","https://openalex.org/W2996509803","https://openalex.org/W4364351665","https://openalex.org/W4377020147"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W1495501409","https://openalex.org/W4226377888","https://openalex.org/W2144833504","https://openalex.org/W4306893319","https://openalex.org/W4311965611","https://openalex.org/W4246426680","https://openalex.org/W973108520","https://openalex.org/W2340822924","https://openalex.org/W1494624369"],"abstract_inverted_index":{"Jellyfish":[0],"is":[1],"freely":[2],"available":[3],"with":[4],"MIT":[5],"license":[6],"at":[7],"https://github.com/HautaniemiLab/jellyfish":[8],"(JavaScript":[9],"library)":[10],"and":[11],"https://github.com/HautaniemiLab/jellyfisher":[12],"(R":[13],"package).":[14]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
