{"id":"https://openalex.org/W2087111048","doi":"https://doi.org/10.1016/s1672-0229(08)60043-1","title":"3D Genome Tuner: Compare Multiple Circular Genomes in a 3D Context","display_name":"3D Genome Tuner: Compare Multiple Circular Genomes in a 3D Context","publication_year":2009,"publication_date":"2009-09-01","ids":{"openalex":"https://openalex.org/W2087111048","doi":"https://doi.org/10.1016/s1672-0229(08)60043-1","mag":"2087111048","pmid":"https://pubmed.ncbi.nlm.nih.gov/19944387"},"language":"en","primary_location":{"id":"doi:10.1016/s1672-0229(08)60043-1","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(08)60043-1","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/s1672-0229(08)60043-1","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053486679","display_name":"Qi Wang","orcid":"https://orcid.org/0000-0002-7827-4808"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qi Wang","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China","Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China","institution_ids":["https://openalex.org/I2801577699","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070240569","display_name":"Qun Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qun Liang","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China","Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China","institution_ids":["https://openalex.org/I2801577699","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024767151","display_name":"Xiuqing Zhang","orcid":"https://orcid.org/0000-0002-3416-501X"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiuqing Zhang","raw_affiliation_strings":["Beijing Genomics Institute at Shenzhen , Shenzhen, 518083 , China","Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Genomics Institute at Shenzhen , Shenzhen, 518083 , China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China","institution_ids":["https://openalex.org/I2801577699","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053486679"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699","https://openalex.org/I4210165038"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.14889109,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"7","issue":"3","first_page":"143","last_page":"146"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9970999956130981,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8627690076828003},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6084529757499695},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.571736216545105},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5234284400939941},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49853992462158203},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4683838188648224},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4166107475757599},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.35231104493141174},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33315521478652954},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2740909457206726},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14732596278190613}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8627690076828003},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6084529757499695},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.571736216545105},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5234284400939941},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49853992462158203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4683838188648224},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4166107475757599},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.35231104493141174},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33315521478652954},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2740909457206726},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14732596278190613},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1016/s1672-0229(08)60043-1","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(08)60043-1","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19944387","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19944387","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:4016577","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054402","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1016/s1672-0229(08)60043-1","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(08)60043-1","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.5199999809265137,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G6463964146","display_name":null,"funder_award_id":"2006AA02A301","funder_id":"https://openalex.org/F4320335773","funder_display_name":"National High-tech Research and Development Program"}],"funders":[{"id":"https://openalex.org/F4320335773","display_name":"National High-tech Research and Development Program","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1520910643","https://openalex.org/W1990453950","https://openalex.org/W1991330646","https://openalex.org/W2024228623","https://openalex.org/W2055043387","https://openalex.org/W2068787541","https://openalex.org/W2077911023","https://openalex.org/W2090242275","https://openalex.org/W2103017472","https://openalex.org/W2107282968","https://openalex.org/W2115539957","https://openalex.org/W2121703775","https://openalex.org/W2122479165","https://openalex.org/W2123246614","https://openalex.org/W2123783735","https://openalex.org/W2124745504","https://openalex.org/W2130063668","https://openalex.org/W2138782170","https://openalex.org/W2142000458","https://openalex.org/W2151309250","https://openalex.org/W2152331922","https://openalex.org/W2156273926","https://openalex.org/W2156524568","https://openalex.org/W2157748357","https://openalex.org/W2160244495","https://openalex.org/W2162173039","https://openalex.org/W2163899891"],"related_works":["https://openalex.org/W2414506155","https://openalex.org/W2752117239","https://openalex.org/W1493660383","https://openalex.org/W2759519215","https://openalex.org/W2170130581","https://openalex.org/W2941201441","https://openalex.org/W4318240630","https://openalex.org/W2353729507","https://openalex.org/W2560359598","https://openalex.org/W3023271652"],"abstract_inverted_index":{"Circular":[0],"genomes,":[1,8],"being":[2],"the":[3,70],"largest":[4],"proportion":[5],"of":[6,27,46,55,72],"sequenced":[7],"play":[9],"an":[10,23,81],"important":[11],"role":[12],"in":[13,62],"genome":[14,28],"analysis.":[15],"However,":[16],"traditional":[17],"2D":[18],"circular":[19,47,60],"map":[20,48,51],"only":[21],"provides":[22],"overview":[24],"and":[25,49],"annotations":[26],"but":[29],"does":[30],"not":[31],"offer":[32],"feature-based":[33],"comparison.":[34],"For":[35],"remedying":[36],"these":[37],"shortcomings,":[38],"we":[39],"developed":[40],"3D":[41,64],"Genome":[42],"Tuner,":[43],"a":[44,63],"hybrid":[45],"comparative":[50,73],"tools.":[52],"Its":[53],"capability":[54],"viewing":[56],"comparisons":[57],"between":[58],"multiple":[59],"maps":[61],"space":[65],"offers":[66],"great":[67],"benefits":[68],"to":[69],"study":[71],"genomics.":[74],"The":[75],"program":[76],"is":[77],"freely":[78],"available":[79],"(under":[80],"LGPL":[82],"licence)":[83],"at":[84],"http://sourceforge.net/projects/dgenometuner.":[85]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
