{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T20:33:17Z","timestamp":1784752397471,"version":"3.55.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,17]],"date-time":"2020-01-17T00:00:00Z","timestamp":1579219200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["275151"],"award-info":[{"award-number":["275151"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["292307"],"award-info":[{"award-number":["292307"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Unionur Horizon 2020 research and innovation programme","award":["814426"],"award-info":[{"award-number":["814426"]}]},{"name":"NanoinformaTIX"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The analysis of dose-dependent effects on the gene expression is gaining attention in the field of toxicogenomics. Currently available computational methods are usually limited to specific omics platforms or biological annotations and are able to analyse only one experiment at a time.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed the software BMDx with a graphical user interface for the Benchmark Dose (BMD) analysis of transcriptomics data. We implemented an approach based on the fitting of multiple models and the selection of the optimal model based on the Akaike Information Criterion. The BMDx tool takes as an input a gene expression matrix and a phenotype table, computes the BMD, its related values, and IC50\/EC50 estimations. It reports interactive tables and plots that the user can investigate for further details of the fitting, dose effects and functional enrichment. BMDx allows a fast and convenient comparison of the BMD values of a transcriptomics experiment at different time points and an effortless way to interpret the results. Furthermore, BMDx allows to analyse and to compare multiple experiments at once.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>BMDx is implemented as an R\/Shiny software and is available at https:\/\/github.com\/Greco-Lab\/BMDx\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa030","type":"journal-article","created":{"date-parts":[[2020,1,14]],"date-time":"2020-01-14T20:12:18Z","timestamp":1579032738000},"page":"2932-2933","source":"Crossref","is-referenced-by-count":43,"title":["BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data"],"prefix":"10.1093","volume":"36","author":[{"given":"Angela","family":"Serra","sequence":"first","affiliation":[{"name":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland"},{"name":"BioMediTech Institute , Tampere University, Tampere 33100, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura Aliisa","family":"Saarim\u00e4ki","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland"},{"name":"BioMediTech Institute , Tampere University, Tampere 33100, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michele","family":"Fratello","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland"},{"name":"BioMediTech Institute , Tampere University, Tampere 33100, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veer Singh","family":"Marwah","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland"},{"name":"BioMediTech Institute , Tampere University, Tampere 33100, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9195-9003","authenticated-orcid":false,"given":"Dario","family":"Greco","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Health Technology , Tampere University, Tampere 33100, Finland"},{"name":"BioMediTech Institute , Tampere University, Tampere 33100, Finland"},{"name":"Institute of Biotechnology , University of Helsinki, Helsinki 00014, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,1,17]]},"reference":[{"key":"2023013111484182500_btaa030-B1","author":"Chang","year":"2018"},{"key":"2023013111484182500_btaa030-B2","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.taap.2010.10.016","article-title":"Introduction to benchmark dose methods and us EPA\u2019s benchmark dose software (BMDS) version 2.1.1","volume":"254","author":"Davis","year":"2011","journal-title":"Toxicol. 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