{"id":"https://openalex.org/W2998919570","doi":"https://doi.org/10.1093/bioinformatics/btaa030","title":"BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data","display_name":"BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data","publication_year":2020,"publication_date":"2020-01-14","ids":{"openalex":"https://openalex.org/W2998919570","doi":"https://doi.org/10.1093/bioinformatics/btaa030","mag":"2998919570","pmid":"https://pubmed.ncbi.nlm.nih.gov/31950985"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa030","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa030","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041632230","display_name":"Angela Serra","orcid":"https://orcid.org/0000-0002-3374-1492"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Angela Serra","raw_affiliation_strings":["BioMediTech Institute , Tampere University, Tampere 33100, Finland","Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003627670","display_name":"Laura Aliisa Saarim\u00e4ki","orcid":"https://orcid.org/0000-0003-1996-286X"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Laura Aliisa Saarim\u00e4ki","raw_affiliation_strings":["BioMediTech Institute , Tampere University, Tampere 33100, Finland","Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025810407","display_name":"Michele Fratello","orcid":"https://orcid.org/0000-0002-3997-2339"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Michele Fratello","raw_affiliation_strings":["BioMediTech Institute , Tampere University, Tampere 33100, Finland","Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038612379","display_name":"Veer Singh Marwah","orcid":"https://orcid.org/0000-0002-8272-0655"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Veer Singh Marwah","raw_affiliation_strings":["BioMediTech Institute , Tampere University, Tampere 33100, Finland","Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028682033","display_name":"Dario Greco","orcid":"https://orcid.org/0000-0001-9195-9003"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Dario Greco","raw_affiliation_strings":["BioMediTech Institute , Tampere University, Tampere 33100, Finland","Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland","Institute of Biotechnology , University of Helsinki, Helsinki 00014, Finland"],"raw_orcid":"https://orcid.org/0000-0001-9195-9003","affiliations":[{"raw_affiliation_string":"BioMediTech Institute , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Institute of Biotechnology , University of Helsinki, Helsinki 00014, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5028682033"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I166825849"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8638,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.85893635,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"36","issue":"9","first_page":"2932","last_page":"2933"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8865000009536743,"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/T10885","display_name":"Gene expression and cancer classification","score":0.8865000009536743,"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/T10433","display_name":"Carcinogens and Genotoxicity Assessment","score":0.02290000021457672,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.013799999840557575,"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/benchmark","display_name":"Benchmark (surveying)","score":0.8167880177497864},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7218770384788513},{"id":"https://openalex.org/keywords/akaike-information-criterion","display_name":"Akaike information criterion","score":0.7047728300094604},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6566821336746216},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.611923336982727},{"id":"https://openalex.org/keywords/table","display_name":"Table (database)","score":0.5976924896240234},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5849330425262451},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.505167543888092},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.48601800203323364},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2690029740333557},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09695613384246826},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08521634340286255}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.8167880177497864},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7218770384788513},{"id":"https://openalex.org/C126674687","wikidata":"https://www.wikidata.org/wiki/Q1662573","display_name":"Akaike information criterion","level":2,"score":0.7047728300094604},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6566821336746216},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.611923336982727},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.5976924896240234},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5849330425262451},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.505167543888092},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.48601800203323364},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2690029740333557},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09695613384246826},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08521634340286255},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"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":"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":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D043922","descriptor_name":"Toxicogenetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D043922","descriptor_name":"Toxicogenetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D043922","descriptor_name":"Toxicogenetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa030","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa030","pdf_url":null,"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:31950985","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31950985","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":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G541198402","display_name":null,"funder_award_id":"292307","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7626961633","display_name":null,"funder_award_id":"275151","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1518016665","https://openalex.org/W1993547444","https://openalex.org/W2091705039","https://openalex.org/W2118610649","https://openalex.org/W2163821484","https://openalex.org/W2212640525","https://openalex.org/W2790910980","https://openalex.org/W2800782238","https://openalex.org/W2918631818"],"related_works":["https://openalex.org/W1987464952","https://openalex.org/W1550358769","https://openalex.org/W2735932032","https://openalex.org/W2028169157","https://openalex.org/W2030252680","https://openalex.org/W2172884470","https://openalex.org/W2148077962","https://openalex.org/W2188061941","https://openalex.org/W4253044522","https://openalex.org/W1980950130"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,87],"analysis":[2,59],"of":[3,16,60,71,77,125,140,144],"dose-dependent":[4],"effects":[5,129],"on":[6,68,82],"the":[7,14,46,55,69,75,78,83,103,118,126,141,158],"gene":[8,95],"expression":[9,96],"is":[10,176,183],"gaining":[11],"attention":[12],"in":[13],"field":[15],"toxicogenomics.":[17],"Currently":[18],"available":[19,184,192],"computational":[20],"methods":[21],"are":[22,33,191],"usually":[23],"limited":[24],"to":[25,35,156,163,166],"specific":[26],"omics":[27],"platforms":[28],"or":[29],"biological":[30],"annotations":[31],"and":[32,74,98,108,115,130,137,152,165,182],"able":[34],"analyse":[36,164],"only":[37],"one":[38],"experiment":[39,147],"at":[40,148,170,185,193],"a":[41,50,94,99,135,145],"time.":[42],"RESULTS:":[43],"We":[44,63],"developed":[45],"software":[47,181],"BMDx":[48,88,133,161,175],"with":[49],"graphical":[51],"user":[52,119],"interface":[53],"for":[54,122],"Benchmark":[56],"Dose":[57],"(BMD)":[58],"transcriptomics":[61,146],"data.":[62],"implemented":[64,177],"an":[65,92,153,179],"approach":[66],"based":[67,81],"fitting":[70],"multiple":[72,168],"models":[73],"selection":[76],"optimal":[79],"model":[80],"Akaike":[84],"Information":[85],"Criterion.":[86],"tool":[89],"takes":[90],"as":[91,178],"input":[93],"matrix":[97],"phenotype":[100],"table,":[101],"computes":[102],"BMD,":[104],"its":[105],"related":[106],"values,":[107],"IC50/EC50":[109],"estimations.":[110],"It":[111],"reports":[112],"interactive":[113],"tables":[114],"plots":[116],"that":[117],"can":[120],"investigate":[121],"further":[123],"details":[124],"fitting,":[127],"dose":[128],"functional":[131],"enrichment.":[132],"allows":[134,162],"fast":[136],"convenient":[138],"comparison":[139],"BMD":[142],"values":[143],"different":[149],"time":[150],"points":[151],"effortless":[154],"way":[155],"interpret":[157],"results.":[159],"Furthermore,":[160],"compare":[167],"experiments":[169],"once.":[171],"AVAILABILITY":[172],"AND":[173],"IMPLEMENTATION:":[174],"R/Shiny":[180],"https://github.com/Greco-Lab/BMDx/.":[186],"SUPPLEMENTARY":[187],"INFORMATION:":[188],"Supplementary":[189],"data":[190],"Bioinformatics":[194],"online.":[195]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
