{"id":"https://openalex.org/W2344352022","doi":"https://doi.org/10.1186/s13040-016-0095-3","title":"Visual programming for next-generation sequencing data analytics","display_name":"Visual programming for next-generation sequencing data analytics","publication_year":2016,"publication_date":"2016-04-27","ids":{"openalex":"https://openalex.org/W2344352022","doi":"https://doi.org/10.1186/s13040-016-0095-3","mag":"2344352022","pmid":"https://pubmed.ncbi.nlm.nih.gov/27127540"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-016-0095-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0095-3","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0095-3","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0095-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017152835","display_name":"Franco Milicchio","orcid":"https://orcid.org/0000-0002-4875-4894"},"institutions":[{"id":"https://openalex.org/I119003972","display_name":"Roma Tre University","ror":"https://ror.org/05vf0dg29","country_code":"IT","type":"education","lineage":["https://openalex.org/I119003972"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Franco Milicchio","raw_affiliation_strings":["Department of Engineering, Roma Tre University, Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Engineering, Roma Tre University, Rome, Italy","institution_ids":["https://openalex.org/I119003972"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002919205","display_name":"Rebecca Rose","orcid":"https://orcid.org/0000-0002-7711-2209"},"institutions":[{"id":"https://openalex.org/I47209331","display_name":"Nicholls State University","ror":"https://ror.org/04pq5x672","country_code":"US","type":"education","lineage":["https://openalex.org/I2799628689","https://openalex.org/I47209331"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rebecca Rose","raw_affiliation_strings":["Bioinfoexperts, LLC, Thibodaux, LA USA","Bioinfoexperts, LLC, Thibodaux, LA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinfoexperts, LLC, Thibodaux, LA USA","institution_ids":["https://openalex.org/I47209331"]},{"raw_affiliation_string":"Bioinfoexperts, LLC, Thibodaux, LA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030951014","display_name":"Jiang Bian","orcid":"https://orcid.org/0000-0002-2238-5429"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiang Bian","raw_affiliation_strings":["Department of Health Outcomes and Policy, University of Florida, Gainesville, FL USA","Department of Health Outcomes and Policy, University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Outcomes and Policy, University of Florida, Gainesville, FL USA","institution_ids":["https://openalex.org/I2800717037"]},{"raw_affiliation_string":"Department of Health Outcomes and Policy, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I2800717037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091887754","display_name":"Jae Min","orcid":"https://orcid.org/0000-0003-4112-9583"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jae Min","raw_affiliation_strings":["Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231 FL USA","Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231 FL USA","institution_ids":["https://openalex.org/I94062374"]},{"raw_affiliation_string":"Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039419132","display_name":"Mattia Prosperi","orcid":"https://orcid.org/0000-0002-9021-5595"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mattia Prosperi","raw_affiliation_strings":["Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231 FL USA","Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231 FL USA","institution_ids":["https://openalex.org/I94062374"]},{"raw_affiliation_string":"Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":3.0056,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.91061723,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"9","issue":"1","first_page":"16","last_page":"16"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.40849998593330383,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.40849998593330383,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.22190000116825104,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.07760000228881836,"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":0.7619647979736328},{"id":"https://openalex.org/keywords/visual-analytics","display_name":"Visual analytics","score":0.6406298875808716},{"id":"https://openalex.org/keywords/analytics","display_name":"Analytics","score":0.5606085658073425},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5312228798866272},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3572109639644623},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.32918575406074524},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3217388093471527}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7619647979736328},{"id":"https://openalex.org/C59732488","wikidata":"https://www.wikidata.org/wiki/Q2528440","display_name":"Visual analytics","level":3,"score":0.6406298875808716},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.5606085658073425},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5312228798866272},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3572109639644623},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.32918575406074524},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3217388093471527}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13040-016-0095-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0095-3","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0095-3","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:27127540","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27127540","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":"BioData mining","raw_type":null},{"id":"pmh:oai:UFDC:AA00040285_00001","is_oa":true,"landing_page_url":"http://ufdc.ufl.edu/AA00040285/00001","pdf_url":null,"source":{"id":"https://openalex.org/S4306400471","display_name":"University of Florida Digital Collections (University of Florida)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I33213144","host_organization_name":"University of Florida","host_organization_lineage":["https://openalex.org/I33213144"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"mixed material"},{"id":"pmh:oai:europepmc.org:3815022","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4848821","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"},{"id":"pmh:oai:iris.uniroma3.it:11590/299326","is_oa":false,"landing_page_url":"http://hdl.handle.net/11590/299326","pdf_url":null,"source":{"id":"https://openalex.org/S4377196120","display_name":"Iris (Roma Tre University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I119003972","host_organization_name":"Roma Tre University","host_organization_lineage":["https://openalex.org/I119003972"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s13040-016-0095-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0095-3","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0095-3","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6100000143051147}],"awards":[{"id":"https://openalex.org/G8778799187","display_name":"Virus discovery and epidemic tracing from high throughput metagenomic sequencing","funder_award_id":"634650","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2344352022.pdf","grobid_xml":"https://content.openalex.org/works/W2344352022.grobid-xml"},"referenced_works_count":81,"referenced_works":["https://openalex.org/W29297254","https://openalex.org/W37074620","https://openalex.org/W61372138","https://openalex.org/W149722931","https://openalex.org/W159192977","https://openalex.org/W1492324553","https://openalex.org/W1502767928","https://openalex.org/W1524344020","https://openalex.org/W1532103063","https://openalex.org/W1542893108","https://openalex.org/W1575965357","https://openalex.org/W1583897126","https://openalex.org/W1721251433","https://openalex.org/W1893885577","https://openalex.org/W1965572639","https://openalex.org/W1973094248","https://openalex.org/W1986700282","https://openalex.org/W1986708244","https://openalex.org/W1991975721","https://openalex.org/W1992326333","https://openalex.org/W1993817276","https://openalex.org/W1996423252","https://openalex.org/W2000528034","https://openalex.org/W2017344680","https://openalex.org/W2017952818","https://openalex.org/W2038637763","https://openalex.org/W2051380427","https://openalex.org/W2063514135","https://openalex.org/W2064189581","https://openalex.org/W2064632458","https://openalex.org/W2064676287","https://openalex.org/W2069899527","https://openalex.org/W2070342831","https://openalex.org/W2074490119","https://openalex.org/W2075996757","https://openalex.org/W2076151007","https://openalex.org/W2077902947","https://openalex.org/W2078370799","https://openalex.org/W2082447166","https://openalex.org/W2082801720","https://openalex.org/W2084821192","https://openalex.org/W2085411398","https://openalex.org/W2088386938","https://openalex.org/W2092784580","https://openalex.org/W2093516854","https://openalex.org/W2095836161","https://openalex.org/W2096977241","https://openalex.org/W2098466396","https://openalex.org/W2100827887","https://openalex.org/W2104301310","https://openalex.org/W2105821863","https://openalex.org/W2108234281","https://openalex.org/W2109453587","https://openalex.org/W2114850508","https://openalex.org/W2118377274","https://openalex.org/W2118526609","https://openalex.org/W2125753667","https://openalex.org/W2128567635","https://openalex.org/W2128880918","https://openalex.org/W2134148450","https://openalex.org/W2136482257","https://openalex.org/W2137974046","https://openalex.org/W2139168653","https://openalex.org/W2139244902","https://openalex.org/W2141200343","https://openalex.org/W2147841875","https://openalex.org/W2150934173","https://openalex.org/W2152060958","https://openalex.org/W2152381475","https://openalex.org/W2153657280","https://openalex.org/W2154652861","https://openalex.org/W2160697532","https://openalex.org/W2161645441","https://openalex.org/W2163338240","https://openalex.org/W2168602018","https://openalex.org/W2175425889","https://openalex.org/W2313195725","https://openalex.org/W4242673342","https://openalex.org/W6610112841","https://openalex.org/W6629601088","https://openalex.org/W6630166281"],"related_works":["https://openalex.org/W2362367986","https://openalex.org/W348707231","https://openalex.org/W2064719069","https://openalex.org/W3041760129","https://openalex.org/W4210310791","https://openalex.org/W2062940763","https://openalex.org/W2952667803","https://openalex.org/W202848325","https://openalex.org/W2171036274","https://openalex.org/W2350094487"],"abstract_inverted_index":{"BACKGROUND:":[0],"High-throughput":[1],"or":[2,186],"next-generation":[3],"sequencing":[4],"(NGS)":[5],"technologies":[6],"have":[7],"become":[8],"an":[9,160],"established":[10],"and":[11,17,23,27,39,67,78,122,157,176,203,235],"affordable":[12],"experimental":[13],"framework":[14,198,226],"in":[15,53,92,143,191,249],"biological":[16],"medical":[18],"sciences":[19],"for":[20,47,88,120,125,132],"all":[21,208],"basic":[22],"translational":[24],"research.":[25],"Processing":[26],"analyzing":[28],"NGS":[29,33,48,89,121,126,133,174],"data":[30,34,49,64,233],"is":[31,60,70],"challenging.":[32],"are":[35],"big,":[36],"heterogeneous,":[37],"sparse,":[38],"error":[40],"prone.":[41],"Although":[42],"a":[43,71,138,196,218],"plethora":[44],"of":[45,172,179,195,209,244],"tools":[46,124,247],"analysis":[50],"has":[51],"emerged":[52],"the":[54,75,79,95,108,113,170,177,193,210,215,229,242],"past":[55],"decade,":[56],"(i)":[57],"software":[58,83,116,155,225],"development":[59,178,243],"still":[61],"lagging":[62],"behind":[63],"generation":[65,234],"capabilities,":[66],"(ii)":[68],"there":[69],"'cultural'":[72],"gap":[73,231],"between":[74,232],"end":[76],"user":[77,163],"developer.":[80],"TEXT:":[81],"Generic":[82],"template":[84,100,201],"libraries":[85,101,117],"specifically":[86,119],"developed":[87],"can":[90],"help":[91,106],"dealing":[93],"with":[94,102,107],"former":[96],"problem,":[97],"whilst":[98],"coupling":[99],"visual":[103,204],"programming":[104,202,205],"may":[105],"latter.":[109],"Here":[110],"we":[111],"scrutinize":[112],"state-of-the-art":[114],"low-level":[115],"implemented":[118],"graphical":[123,162],"analytics.":[127],"An":[128],"ideal":[129],"developing":[130],"environment":[131],"should":[134,167],"be":[135],"modular":[136],"(with":[137,153],"native":[139],"library":[140],"interface),":[141,156],"scalable":[142],"computational":[144,197],"methods":[145],"(i.e.":[146],"serial,":[147],"multithread,":[148],"distributed),":[149],"transparent":[150],"(platform-independent),":[151],"interoperable":[152],"external":[154],"usable":[158],"(via":[159],"intuitive":[161],"interface).":[164],"These":[165],"characteristics":[166],"facilitate":[168,241],"both":[169],"run":[171],"standardized":[173],"pipelines":[175],"new":[180],"workflows":[181],"based":[182],"on":[183],"technological":[184],"advancements":[185],"users'":[187],"needs.":[188],"We":[189],"discuss":[190],"detail":[192],"potential":[194],"blending":[199],"generic":[200],"that":[206],"addresses":[207],"current":[211,230],"limitations.":[212],"CONCLUSION:":[213],"In":[214],"long":[216],"term,":[217],"proper,":[219],"well-developed":[220],"(although":[221],"not":[222],"necessarily":[223],"unique)":[224],"will":[227,239],"bridge":[228],"hypothesis":[236],"testing.":[237],"This":[238],"eventually":[240],"novel":[245],"diagnostic":[246],"embedded":[248],"routine":[250],"healthcare.":[251]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
