{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:01:15Z","timestamp":1787162475227,"version":"3.56.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2018,10,17]],"date-time":"2018-10-17T00:00:00Z","timestamp":1539734400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Toxicology Program"},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ZIA","award":["ES103318-01"],"award-info":[{"award-number":["ES103318-01"]}]},{"name":"National Institute of Environmental Health Sciences Bioinformatics"},{"name":"Sciome LLC","award":["HHSN273201700001C"],"award-info":[{"award-number":["HHSN273201700001C"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>A new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses the increasing use of transcriptomic dose-response data in toxicology, drug design, risk assessment and translational research. In this new version, we have implemented additional statistical filtering options (e.g. Williams\u2019 trend test), curve fitting models, Linux and Macintosh compatibility and support for additional transcriptomic platforms with up-to-date gene annotations. Furthermore, we have implemented extensive data visualizations, on-the-fly data filtering, and a batch-wise analysis workflow. We have also significantly re-engineered the code base to reflect contemporary software engineering practices and streamline future development. The first version of BMDExpress was developed in 2007 to meet an unmet demand for easy-to-use transcriptomic dose-response analysis software. Since its original release, however, transcriptomic platforms, technologies, pathway annotations and quantitative methods for data analysis have undergone a large change necessitating a significant re-development of BMDExpress. To that end, as of 2016, the National Toxicology Program assumed stewardship of BMDExpress. The result is a modernized and updated BMDExpress 2 that addresses the needs of the growing toxicogenomics user community.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>BMDExpress 2 is available at https:\/\/github.com\/auerbachs\/BMDExpress-2\/releases.<\/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\/bty878","type":"journal-article","created":{"date-parts":[[2018,10,15]],"date-time":"2018-10-15T15:13:08Z","timestamp":1539616388000},"page":"1780-1782","source":"Crossref","is-referenced-by-count":197,"title":["BMDExpress 2: enhanced transcriptomic dose-response analysis workflow"],"prefix":"10.1093","volume":"35","author":[{"given":"Jason R","family":"Phillips","sequence":"first","affiliation":[{"name":"Sciome LLC, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel L","family":"Svoboda","sequence":"additional","affiliation":[{"name":"Sciome LLC, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arpit","family":"Tandon","sequence":"additional","affiliation":[{"name":"Sciome LLC, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shyam","family":"Patel","sequence":"additional","affiliation":[{"name":"Sciome LLC, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Sedykh","sequence":"additional","affiliation":[{"name":"Sciome LLC, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deepak","family":"Mav","sequence":"additional","affiliation":[{"name":"Sciome LLC, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byron","family":"Kuo","sequence":"additional","affiliation":[{"name":"Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carole L","family":"Yauk","sequence":"additional","affiliation":[{"name":"Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longlong","family":"Yang","sequence":"additional","affiliation":[{"name":"D.S. Technologies, Inc, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Russell S","family":"Thomas","sequence":"additional","affiliation":[{"name":"National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeff S","family":"Gift","sequence":"additional","affiliation":[{"name":"National Center for Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J Allen","family":"Davis","sequence":"additional","affiliation":[{"name":"National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, OH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louis","family":"Olszyk","sequence":"additional","affiliation":[{"name":"CSRA Inc, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B Alex","family":"Merrick","sequence":"additional","affiliation":[{"name":"National Toxicology Program, NIEHS, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard S","family":"Paules","sequence":"additional","affiliation":[{"name":"National Toxicology Program, NIEHS, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fred","family":"Parham","sequence":"additional","affiliation":[{"name":"National Toxicology Program, NIEHS, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trey","family":"Saddler","sequence":"additional","affiliation":[{"name":"National Toxicology Program, NIEHS, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruchir R","family":"Shah","sequence":"additional","affiliation":[{"name":"Sciome LLC, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott S","family":"Auerbach","sequence":"additional","affiliation":[{"name":"National Toxicology Program, NIEHS, Research Triangle Park, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,10,17]]},"reference":[{"key":"2023013107485204300_bty878-B1","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1007\/s00204-016-1831-7","article-title":"Hepatic transcriptomic alterations for N, N-dimethyl-p-toluidine (DMPT) and p-toluidine after 5-day exposure in rats","volume":"91","author":"Dunnick","year":"2017","journal-title":"Arch. Toxicol."},{"key":"2023013107485204300_bty878-B2","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The Reactome Pathway Knowledgebase","volume":"46","author":"Fabregat","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2023013107485204300_bty878-B3","doi-asserted-by":"crossref","first-page":"D440","DOI":"10.1093\/nar\/gkm883","article-title":"The Gene Ontology project in 2008","volume":"36","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013107485204300_bty878-B4","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1002\/jat.3265","article-title":"BMDExpress Data Viewer - a visualization tool to analyze BMDExpress datasets","volume":"36","author":"Kuo","year":"2016","journal-title":"J. Appl. Toxicol."},{"key":"2023013107485204300_bty878-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3109\/10408444.2014.973934","article-title":"Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo a pyrene in drinking water","volume":"45","author":"Moffat","year":"2015","journal-title":"Crit. Rev. Toxicol."},{"key":"2023013107485204300_bty878-B6","article-title":"NTP Research Report on National Toxicology Program Approach to Genomic Dose-Response Modeling: Research Report 5","volume-title":"NTP Research Reports","year":"2018"},{"key":"2023013107485204300_bty878-B7","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/978-1-4939-6346-1_14","article-title":"CurveP method for rendering high-throughput screening dose-response data into digital fingerprints","volume":"1473","author":"Sedykh","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"2023013107485204300_bty878-B8","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1093\/toxsci\/kft178","article-title":"Incorporating new technologies into toxicity testing and risk assessment: moving from 21st century vision to a data-driven framework","volume":"136","author":"Thomas","year":"2013","journal-title":"Toxicol. Sci."},{"key":"2023013107485204300_bty878-B9","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1093\/toxsci\/kft094","article-title":"Temporal concordance between apical and transcriptional points of departure for chemical risk assessment","volume":"134","author":"Thomas","year":"2013","journal-title":"Toxicol. Sci."},{"key":"2023013107485204300_bty878-B10","article-title":"Benchmark dose technical guidance","volume-title":"Risk Assessment Forum","year":"2012"},{"key":"2023013107485204300_bty878-B11","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1186\/1471-2164-8-387","article-title":"BMDExpress: a software tool for the benchmark dose analyses of genomic data","volume":"8","author":"Yang","year":"2007","journal-title":"BMC Genomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/10\/1780\/48969989\/bioinformatics_35_10_1780.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/10\/1780\/48969989\/bioinformatics_35_10_1780.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T05:51:14Z","timestamp":1675144274000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/10\/1780\/5134066"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,10,17]]},"references-count":11,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2019,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty878","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,5,15]]},"published":{"date-parts":[[2018,10,17]]}}}