{"id":"https://openalex.org/W2168622188","doi":"https://doi.org/10.1093/bioinformatics/btp008","title":"BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network","display_name":"BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network","publication_year":2009,"publication_date":"2009-01-06","ids":{"openalex":"https://openalex.org/W2168622188","doi":"https://doi.org/10.1093/bioinformatics/btp008","mag":"2168622188","pmid":"https://pubmed.ncbi.nlm.nih.gov/19126577"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp008","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp008","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/4/543/48985593/bioinformatics_25_4_543.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/25/4/543/48985593/bioinformatics_25_4_543.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002237618","display_name":"Ryosuke Ishiwata","orcid":"https://orcid.org/0000-0001-5998-7901"},"institutions":[{"id":"https://openalex.org/I125602781","display_name":"Tokyo Medical and Dental University","ror":"https://ror.org/051k3eh31","country_code":"JP","type":"education","lineage":["https://openalex.org/I125602781"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryosuke R. Ishiwata","raw_affiliation_strings":["1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan"],"affiliations":[{"raw_affiliation_string":"1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan","institution_ids":["https://openalex.org/I125602781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047221773","display_name":"M. Morioka","orcid":"https://orcid.org/0000-0003-3511-7279"},"institutions":[{"id":"https://openalex.org/I125602781","display_name":"Tokyo Medical and Dental University","ror":"https://ror.org/051k3eh31","country_code":"JP","type":"education","lineage":["https://openalex.org/I125602781"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masaki S. Morioka","raw_affiliation_strings":["1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan"],"affiliations":[{"raw_affiliation_string":"1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan","institution_ids":["https://openalex.org/I125602781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049356235","display_name":"Soichi Ogishima","orcid":"https://orcid.org/0000-0001-8613-2562"},"institutions":[{"id":"https://openalex.org/I125602781","display_name":"Tokyo Medical and Dental University","ror":"https://ror.org/051k3eh31","country_code":"JP","type":"education","lineage":["https://openalex.org/I125602781"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Soichi Ogishima","raw_affiliation_strings":["1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan"],"affiliations":[{"raw_affiliation_string":"1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan","institution_ids":["https://openalex.org/I125602781"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101700469","display_name":"Hiroshi Tanaka","orcid":"https://orcid.org/0009-0001-3740-2236"},"institutions":[{"id":"https://openalex.org/I125602781","display_name":"Tokyo Medical and Dental University","ror":"https://ror.org/051k3eh31","country_code":"JP","type":"education","lineage":["https://openalex.org/I125602781"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroshi Tanaka","raw_affiliation_strings":["1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan"],"affiliations":[{"raw_affiliation_string":"1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan","institution_ids":["https://openalex.org/I125602781"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5049356235"],"corresponding_institution_ids":["https://openalex.org/I125602781"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9436,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.75034333,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"25","issue":"4","first_page":"543","last_page":"544"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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":0.9993000030517578,"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":0.998199999332428,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9926999807357788,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.7461189031600952},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6653538346290588},{"id":"https://openalex.org/keywords/course","display_name":"Course (navigation)","score":0.5892755389213562},{"id":"https://openalex.org/keywords/microarray-databases","display_name":"Microarray databases","score":0.4853319227695465},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4606293737888336},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.4543638825416565},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.45166754722595215},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43271923065185547},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2209460735321045},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08951258659362793},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07279700040817261},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07198554277420044},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06834807991981506}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7461189031600952},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6653538346290588},{"id":"https://openalex.org/C2777552389","wikidata":"https://www.wikidata.org/wiki/Q1962728","display_name":"Course (navigation)","level":2,"score":0.5892755389213562},{"id":"https://openalex.org/C548314002","wikidata":"https://www.wikidata.org/wiki/Q6839218","display_name":"Microarray databases","level":5,"score":0.4853319227695465},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4606293737888336},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.4543638825416565},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.45166754722595215},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43271923065185547},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2209460735321045},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08951258659362793},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07279700040817261},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07198554277420044},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06834807991981506},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0}],"mesh":[{"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp008","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp008","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/4/543/48985593/bioinformatics_25_4_543.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:19126577","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19126577","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp008","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp008","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/4/543/48985593/bioinformatics_25_4_543.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/G12401395","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G6267471473","display_name":null,"funder_award_id":"Grant-in-Aid","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7599130655","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7693551792","display_name":null,"funder_award_id":"(MEXT)","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G8044579487","display_name":null,"funder_award_id":"Japan","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2168622188.pdf","grobid_xml":"https://content.openalex.org/works/W2168622188.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W2021239799","https://openalex.org/W2039760291","https://openalex.org/W2167846577","https://openalex.org/W6660069806","https://openalex.org/W6684940156"],"related_works":["https://openalex.org/W2943416042","https://openalex.org/W1544923801","https://openalex.org/W4225274103","https://openalex.org/W2013728941","https://openalex.org/W3152114242","https://openalex.org/W2154046714","https://openalex.org/W2579659702","https://openalex.org/W2189613078","https://openalex.org/W1574055964","https://openalex.org/W2923661510"],"abstract_inverted_index":{"BioCichlid":[0],"is":[1],"freely":[2],"available":[3],"and":[4,16],"can":[5],"be":[6],"accessed":[7],"at":[8],"http://newton.tmd.ac.jp/.":[9],"Source":[10],"codes":[11],"for":[12],"both":[13],"biocichlid":[14],"server":[15],"client":[17],"are":[18],"also":[19],"available.":[20]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
