{"id":"https://openalex.org/W4402422008","doi":"https://doi.org/10.3389/fbinf.2024.1395981","title":"Visual analysis of multi-omics data","display_name":"Visual analysis of multi-omics data","publication_year":2024,"publication_date":"2024-09-10","ids":{"openalex":"https://openalex.org/W4402422008","doi":"https://doi.org/10.3389/fbinf.2024.1395981","pmid":"https://pubmed.ncbi.nlm.nih.gov/39318761"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2024.1395981","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1395981","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1395981/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1395981/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102656371","display_name":"Austin Swart","orcid":null},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Austin Swart","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA, United States"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA, United States","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044919501","display_name":"Ron Caspi","orcid":"https://orcid.org/0000-0002-6113-3590"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ron Caspi","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA, United States"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA, United States","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015212276","display_name":"Suzanne Paley","orcid":"https://orcid.org/0000-0001-5763-8935"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suzanne Paley","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA, United States"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA, United States","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082071104","display_name":"Peter D. Karp","orcid":"https://orcid.org/0000-0002-5876-6418"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter D. Karp","raw_affiliation_strings":["Bioinformatics Research Group, SRI International, Menlo Park, CA, United States"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group, SRI International, Menlo Park, CA, United States","institution_ids":["https://openalex.org/I1298353152"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102656371"],"corresponding_institution_ids":["https://openalex.org/I1298353152"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13439792,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"4","issue":null,"first_page":"1395981","last_page":"1395981"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9878000020980835,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9864000082015991,"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/omics","display_name":"Omics","score":0.5496731996536255},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5265451073646545},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.445056289434433},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3915831446647644},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3318687081336975},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2317899465560913}],"concepts":[{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.5496731996536255},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5265451073646545},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.445056289434433},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3915831446647644},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3318687081336975},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2317899465560913}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2024.1395981","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1395981","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1395981/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39318761","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39318761","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11420163","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11420163","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11420163/pdf/fbinf-04-1395981.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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c8745e51f43e4950b5792b1454bd4ec0","is_oa":true,"landing_page_url":"https://doaj.org/article/c8745e51f43e4950b5792b1454bd4ec0","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 4 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2024.1395981","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1395981","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1395981/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1258912001","display_name":null,"funder_award_id":"NSF2109898","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5910240687","display_name":"CIBR: New Methods for Multi-Omics Data Analysis and Genome Analysis","funder_award_id":"2109898","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402422008.pdf","grobid_xml":"https://content.openalex.org/works/W4402422008.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1665355332","https://openalex.org/W1964136665","https://openalex.org/W1970344118","https://openalex.org/W1999758530","https://openalex.org/W2019240775","https://openalex.org/W2054127522","https://openalex.org/W2089691764","https://openalex.org/W2121411279","https://openalex.org/W2135435176","https://openalex.org/W2159675211","https://openalex.org/W2464114205","https://openalex.org/W2612989432","https://openalex.org/W2763472614","https://openalex.org/W2952143471","https://openalex.org/W2962889697","https://openalex.org/W2969443468","https://openalex.org/W3006743028","https://openalex.org/W3125335542","https://openalex.org/W4241630616","https://openalex.org/W4391026773","https://openalex.org/W6683974298"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,39,45,71,81,97,108],"tool":[3,153],"for":[4,49,159],"multi-omics":[5,62],"data":[6,19,157,176],"analysis":[7],"that":[8,50],"enables":[9],"simultaneous":[10],"visualization":[11,63],"of":[12,17,38,75],"up":[13],"to":[14,179,185],"four":[15],"types":[16],"omics":[18,68,125],"on":[20],"organism-scale":[21],"metabolic":[22,29,33,46,94],"network":[23,120],"diagrams.":[24,189],"The":[25,61,152,168],"tool's":[26],"interactive":[27],"web-based":[28],"charts":[30,53],"depict":[31],"the":[32,52,76,89,93,119,133,136,166,173,180],"reactions,":[34],"pathways,":[35],"and":[36,107,183],"metabolites":[37,163],"single":[40],"organism":[41],"as":[42,103,114,135],"described":[43],"in":[44,148],"pathway":[47],"database":[48],"organism;":[51],"are":[54,122],"constructed":[55],"using":[56],"automated":[57],"graphical":[58],"layout":[59],"algorithms.":[60],"facility":[64],"paints":[65],"each":[66],"individual":[67,160],"dataset":[69,83,100,111],"onto":[70],"different":[72],"\"visual":[73],"channel\"":[74],"metabolic-network":[77],"diagram.":[78],"For":[79],"example,":[80],"transcriptomics":[82],"might":[84],"be":[85,146],"displayed":[86,102,113,147,181],"by":[87,165],"coloring":[88],"reaction":[90,104],"arrows":[91],"within":[92,132],"chart,":[95],"while":[96],"companion":[98],"proteomics":[99],"is":[101,112],"arrow":[105],"thicknesses,":[106],"complementary":[109],"metabolomics":[110],"metabolite":[115],"node":[116],"colors.":[117],"Once":[118],"diagrams":[121],"painted":[123],"with":[124],"data,":[126],"semantic":[127],"zooming":[128],"provides":[129],"more":[130,187],"details":[131],"diagram":[134],"user":[137,169],"zooms":[138],"in.":[139],"Datasets":[140],"containing":[141],"multiple":[142],"time":[143],"points":[144],"can":[145,170],"an":[149],"animated":[150],"fashion.":[151],"will":[154],"also":[155],"graph":[156],"values":[158],"reactions":[161],"or":[162],"designated":[164],"user.":[167],"interactively":[171],"adjust":[172],"mapping":[174],"from":[175],"value":[177],"ranges":[178],"colors":[182],"thicknesses":[184],"provide":[186],"informative":[188]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
