{"id":"https://openalex.org/W1500816652","doi":"https://doi.org/10.1186/1751-0473-2-1","title":"Genome display tool: visualizing features in complex data sets","display_name":"Genome display tool: visualizing features in complex data sets","publication_year":2007,"publication_date":"2007-02-14","ids":{"openalex":"https://openalex.org/W1500816652","doi":"https://doi.org/10.1186/1751-0473-2-1","mag":"1500816652","pmid":"https://pubmed.ncbi.nlm.nih.gov/17300731"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-2-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-2-1","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-1","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Lalitha Viswanath","orcid":null},"institutions":[{"id":"https://openalex.org/I1312106833","display_name":"Biotechnology Institute","ror":"https://ror.org/00s1jty20","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312106833"]},{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lalitha Viswanath","raw_affiliation_strings":["Department of Biology and Biochemistry, 3201 Cullen Boulevard, University of Houston, Houston, Texas 77204-5001, USA","University of Maryland Biotechnology Institute, 9600, Gudelsky Drive, Rockville, MD 20850, USA","University of Maryland Biotechnology Institute, Rockville, USA","Department of Biology and Biochemistry, University of Houston, Houston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology and Biochemistry, 3201 Cullen Boulevard, University of Houston, Houston, Texas 77204-5001, USA","institution_ids":["https://openalex.org/I44461941"]},{"raw_affiliation_string":"University of Maryland Biotechnology Institute, 9600, Gudelsky Drive, Rockville, MD 20850, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"University of Maryland Biotechnology Institute, Rockville, USA","institution_ids":["https://openalex.org/I1312106833"]},{"raw_affiliation_string":"Department of Biology and Biochemistry, University of Houston, Houston, USA","institution_ids":["https://openalex.org/I44461941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100334845","display_name":"Yue Lu","orcid":"https://orcid.org/0000-0002-5479-9095"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yue Lu","raw_affiliation_strings":["Department of Biology and Biochemistry, 3201 Cullen Boulevard, University of Houston, Houston, Texas 77204-5001, USA","Department of Epidemiology, 1515 Holcombe Blvd, M.D. Anderson Cancer Centre, Houston, TX 77030, USA","Department of Biology and Biochemistry, University of Houston, Houston, USA","Department of Epidemiology, M.D. Anderson Cancer Centre, Houston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology and Biochemistry, 3201 Cullen Boulevard, University of Houston, Houston, Texas 77204-5001, USA","institution_ids":["https://openalex.org/I44461941"]},{"raw_affiliation_string":"Department of Epidemiology, 1515 Holcombe Blvd, M.D. Anderson Cancer Centre, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Biology and Biochemistry, University of Houston, Houston, USA","institution_ids":["https://openalex.org/I44461941"]},{"raw_affiliation_string":"Department of Epidemiology, M.D. Anderson Cancer Centre, Houston, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058894543","display_name":"George E. Fox","orcid":"https://orcid.org/0000-0001-7767-8387"},"institutions":[{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"George E Fox","raw_affiliation_strings":["Department of Biology and Biochemistry, 3201 Cullen Boulevard, University of Houston, Houston, Texas 77204-5001, USA","[Univ. of Houston]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology and Biochemistry, 3201 Cullen Boulevard, University of Houston, Houston, Texas 77204-5001, USA","institution_ids":["https://openalex.org/I44461941"]},{"raw_affiliation_string":"[Univ. of Houston]","institution_ids":["https://openalex.org/I44461941"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I44461941","https://openalex.org/I66946132"],"apc_list":null,"apc_paid":null,"fwci":0.2691,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.57012189,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"2","issue":"1","first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2150000035762787,"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":0.2150000035762787,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.06830000132322311,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.06800000369548798,"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/computer-science","display_name":"Computer science","score":0.7661440372467041},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6626879572868347},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6011756658554077},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5771209001541138},{"id":"https://openalex.org/keywords/zoom","display_name":"Zoom","score":0.5512479543685913},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5426954627037048},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5091683268547058},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.49097636342048645},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.46876829862594604},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45675358176231384},{"id":"https://openalex.org/keywords/interactive-visualization","display_name":"Interactive visualization","score":0.4277965724468231},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.419085294008255},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.4109065532684326},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3317336440086365},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24840080738067627},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16671222448349},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14835646748542786},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09296661615371704}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7661440372467041},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6626879572868347},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6011756658554077},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5771209001541138},{"id":"https://openalex.org/C124913957","wikidata":"https://www.wikidata.org/wiki/Q1232548","display_name":"Zoom","level":3,"score":0.5512479543685913},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5426954627037048},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5091683268547058},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.49097636342048645},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.46876829862594604},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45675358176231384},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.4277965724468231},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.419085294008255},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.4109065532684326},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3317336440086365},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24840080738067627},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16671222448349},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14835646748542786},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09296661615371704},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C15336307","wikidata":"https://www.wikidata.org/wiki/Q1766051","display_name":"Lens (geology)","level":2,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1751-0473-2-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-2-1","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-1","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:17300731","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17300731","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:1805442","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1805442","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-2-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-2-1","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-1","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7575231745","display_name":"THE ORGINS OF TRANSLATION & EARLY EVOLUTION OF LIFE","funder_award_id":"NNG05GN75G","funder_id":"https://openalex.org/F4320306101","funder_display_name":"National Aeronautics and Space Administration"}],"funders":[{"id":"https://openalex.org/F4320306101","display_name":"National Aeronautics and Space Administration","ror":"https://ror.org/027ka1x80"},{"id":"https://openalex.org/F4320309549","display_name":"University of Houston","ror":"https://ror.org/040vwpm13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1500816652.pdf","grobid_xml":"https://content.openalex.org/works/W1500816652.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2123179625","https://openalex.org/W2128016314","https://openalex.org/W2138952930","https://openalex.org/W2145477956","https://openalex.org/W2155606054","https://openalex.org/W2163191830","https://openalex.org/W2164249947","https://openalex.org/W2170488656","https://openalex.org/W2915985519","https://openalex.org/W2993222596","https://openalex.org/W4295127969"],"related_works":["https://openalex.org/W2006240110","https://openalex.org/W2751110224","https://openalex.org/W4288663999","https://openalex.org/W3142151604","https://openalex.org/W2147036980","https://openalex.org/W2137394710","https://openalex.org/W1973315673","https://openalex.org/W1510524001","https://openalex.org/W2996372188","https://openalex.org/W2085846955"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,130,146,171,207,231,270],"enormity":[2],"of":[3,28,45,65,83,107,148,158,167,169,209,217,220,228,283,287,291,309],"the":[4,43,66,70,81,94,100,105,144,149,156,186,200,215,226,235,245,267,274,288,304,307,326],"information":[5,79],"contained":[6],"in":[7,59,80,116,143,185,225,253,258,266,293,323,336],"large":[8,295],"data":[9,40,296,305],"sets":[10],"makes":[11],"it":[12],"difficult":[13],"to":[14,22,76,102,111,199,237,303],"develop":[15],"intuitive":[16,285],"understanding.":[17],"It":[18,72],"would":[19],"be":[20,35,190,314,334],"useful":[21,335],"have":[23],"software":[24,91,272,332],"that":[25,33,68,138,188,280,312],"allows":[26,99,164,234,281],"visualization":[27,49],"possible":[29,310],"correlations":[30,311],"between":[31,244],"properties":[32,55],"can":[34,181,189,313],"associated":[36],"with":[37,140,175,276],"a":[38,117,127,161,176,277,294],"core":[39,85],"set.":[41,297],"In":[42],"case":[44],"bacterial":[46,119,324],"genomes,":[47],"existing":[48],"tools":[50],"focus":[51],"on":[52,126,155],"either":[53],"global":[54],"such":[56,339],"as":[57,93,340],"variations":[58],"composition":[60],"or":[61],"detailed":[62],"local":[63],"displays":[64],"features":[67,292,300],"comprise":[69],"annotation.":[71],"is":[73,151,173,196,211,328],"not":[74],"easy":[75],"visualize":[77,250],"other":[78,337],"context":[82],"this":[84],"information.":[86],"RESULTS:":[87],"A":[88],"Java":[89],"based":[90,154],"known":[92],"Genome":[95],"Display":[96],"Tool":[97],"(GDT),":[98],"user":[101,236,275],"simultaneously":[103],"view":[104],"distribution":[106,290],"multiple":[108],"attributes":[109],"pertaining":[110],"genes":[112,159,252],"and":[113,124,160,180,248,330],"intragenic":[114],"regions":[115,168],"single":[118,128],"genome":[120,227],"using":[121],"different":[122],"colours":[123],"shapes":[125],"screen.":[129],"display":[131,172,182,233],"represents":[132],"each":[133],"gene":[134],"by":[135,192,213],"small":[136],"boxes":[137,150],"correlate":[139],"physical":[141],"position":[142],"genome.":[145,268],"size":[147],"dynamically":[152],"allocated":[153],"number":[157,308],"zoom":[162],"feature":[163,184],"close-up":[165],"inspection":[166],"interest.":[170],"interfaced":[174],"MS-Access":[177],"relational":[178],"database":[179,187,201],"any":[183],"represented":[191],"discrete":[193],"values.":[194],"Data":[195],"readily":[197],"added":[198,302],"from":[202],"an":[203,284],"MS-Excel":[204],"spread":[205],"sheet.":[206],"functionality":[208],"GDT":[210,271],"demonstrated":[212],"comparing":[214],"results":[216],"two":[218,246],"predictions":[219],"recent":[221],"horizontal":[222],"transfer":[223],"events":[224],"Synechocystis":[229],"PCC-6803.":[230],"resulting":[232],"immediately":[238],"see":[239],"how":[240,251],"much":[241],"agreement":[242],"exists":[243],"methods":[247],"also":[249],"various":[254],"categories":[255],"(e.g.":[256],"predicted":[257],"both":[259],"methods,":[260],"one":[261],"method":[262],"etc)":[263],"are":[264,301],"distributed":[265],"CONCLUSION:":[269],"provides":[273],"powerful":[278],"tool":[279],"development":[282],"understanding":[286],"relative":[289],"As":[298],"additional":[299],"set,":[306],"visualized":[315],"grows":[316],"rapidly.":[317],"Although":[318],"described":[319],"here":[320],"for":[321],"use":[322],"genomics,":[325],"principle":[327],"general":[329],"similar":[331],"might":[333],"contexts":[338],"patient":[341],"studies.":[342]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2013,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
